diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt index 26189ec4ca..5b03c4ce9f 100644 --- a/.cspell/custom-dictionary.txt +++ b/.cspell/custom-dictionary.txt @@ -2,18 +2,18 @@ ## NeXus related words AXISNAME -docstrings FIELDNAME GROUPNAME -groupname NAPI NIAC +UDUNITS +UDunits +UNKNOWNTYPE _NXcanSAS_minimum +docstrings +groupname nxdl nxdlformat -UNKNOWNTYPE -UDUNITS -UDunits somenxdl ## LateX, XML @@ -32,55 +32,184 @@ varphi # Words related to experimental techniques 360-gons +4DSTEM 532nmlaser AABB -aabb AABBs -abundancies ACOM +ARPES +ARXPS +ASTAR +Analzer +Angström +Ansatz +Backscatter +Backscattered +Beampath +Beamsplitter +Beamstops +Bfield +Bitdepth +CEOS +CGAL +CHANNELNAME +CMOS +CNRI +Coeff +Coprecipitation +DCOM +DFM +DXRD +Defocus +Delocalization, +EBSD +EBSP +ECCI +ECMOS +EDAX +EDAXH5 +EDXS +ESCA +E_LAPLACE_RITCHARDSON +Efield +Efield +Einzel +Ellipsometry +FFTW +FVNQHLCGSHLVEALYLVCGERGFFYTPKA +FWHM +Fullerenes +GEOREF +GISAS +GIVEQCCTSICSLYQLENYCN +GLOBULITIC +Gibbsian +Gini +Globar +HAGB +HAXPES +HDBSCAN +HEDM +HPDB +HRTEM +HWHM +Halfwidth +Hashvalue +Histo +ICAMS +ICAT +ICME +ICSD +IFES +IGSN +IGSNs +ISFET +ISNI +ISSN +IVAS +Idev +Inconel +Inplane +Iontype +Iontypes +Isocontour +Kfactor +LIMS +MPES +Microstructures +Monochromatized +NAPXPS +NFFT +NNNC +Ngrains +Nicol +Nuclides +PEEM +PRNG +PVDF +PYCCAPT +Parabolical +Piezo +Plottable +Prefactor +QUBE +Qdev +Qmean +RCSB +RDMS +RHIT +RRAW +RRNG +Raman +Ronchigram +SAS +SAXS +SERS +SNSnxtranslate +SPIE +SPLEED +SPPERS +STXM +SXES +Stereology +Stigmator +Superlattices +Supermirror +TCSPC +TERMS +TERS +Tdev +Titanates +Trac +Traj +Transfermatrix +Triplejunction +Unidata +VLEED +VOXELIZED +WAXS +WSAS +WWPDB +XDMF +XFEL +XPCS +Zincblende +Zirconate +aabb +abundancies aequatorial alphabetagamma alphaone alphatwo -Analzer -Angström -Ansatz -ARPES -ARXPS -ASTAR autophase backgr -Backscatter +backprojection backscatter -Backscattered backscattered backscattering backw beamline beamlines -Beampath beampath -Beamsplitter beamsplitter beamsplitters beamstop -Beamstops -Bfield bicrystal biprism -Bitdepth bitdepth bitfield bitfields bitmask bitmasked +bitshift blackbox blankers bromoiodide +bytesize calib calipher -cand canSAS +cand castaing_henry cbed cbfcat @@ -89,23 +218,17 @@ cbfsf cdeform cdeformed ceos -CEOS -CGAL -CHANNELNAME -CNRI cgal channeltron +childs clambed clust clusterer -CMOS coarsement -Coeff collectioncolumn combinatorially coorporation coprecipitates -Coprecipitation coprecipitation countrate cryo @@ -117,22 +240,18 @@ dataconverters dataspace datastructure datastructures -DCOM -dcom dbscan -Defocus +dcom deconvolution decorrelation defocus defocusing deloc -Delocalization, delocalization delocalized derr detectorn deuterated -DFM diagionalized diffractogram disclination @@ -144,124 +263,77 @@ downsample downsampled downsampling dspacing -DXRD -E_LAPLACE_RITCHARDSON -equispaced ebeam -EBSD ebsd -EBSP -ECCI -Efield -ECMOS -EDAX -EDAXH5 -EDXS -Efield -Einzel einzel electronanalyzer electronvolt ellipsometer ellipsometers ellipsometry -Ellipsometry emittance -energydispersion endstation endstations +energydispersion equisized -ESCA +equispaced eucentric eulerian fastaxisname -FFTW +feedthrough flatfield fluence focallength folksonomies -fscan +forw fractography frustrum -FVNQHLCGSHLVEALYLVCGERGFFYTPKA -FWHM -forw -Fullerenes +fscan gault geiser -Globar globar globulitic -GIVEQCCTSICSLYQLENYCN -GEOREF -GISAS -GLOBULITIC -Gibbsian -Gini golay +granularization granularize granularized -HAGB hagb -Halfwidth halfwidth -Hashvalue hashvalues -HAXPES -HDBSCAN hdbscan -HEDM -hexapole +heterophase hexahedrally -hkil -Histo +hexapole histo histogrammed +hkil homochoric -HPDB -HRTEM -HWHM +homophase hydroxonium hyperslab hyperspectral ibeam -ICAMS -ICAT -ICME -ICSD -Idev -IFES -IGSN -IGSNs illuminatable -Inconel infty -Inplane inplane +interconvert +interp intersector ionlabels -Iontype -Iontypes iontype iontypes -ISFET -ISNI -Isocontour isocontour isocontouring isosurface isosurfacing isovalue ityp -ISSN -IVAS ivec ivecmax kbeta -Kfactor lagb laserline -LIMS +linearities lockin magn max_sothree_bandwidth @@ -269,15 +341,12 @@ max_stwo_bandwidth measurand microcope microscopists -Microstructures microstructures microtip microtips misorientations mmcif -MPES monochromating -Monochromatized monochromator monochromators monoclinic @@ -290,24 +359,21 @@ multidetector multipole multipoles multiscale +n-gons +n_speci nabla -ncal nanoparticle -NAPXPS +ncal ndim -NFFT -Ngrains -Nicol -NNNC -npts nonlinearities +npts nshapepar nstd nsurf nsym -Nuclides nuclid nuclides +nuclids numevents numobj numpulses @@ -318,25 +384,20 @@ numvalue numx numy nvalue -n-gons -n_speci objs octupole -openloop oned +openloop orcid +orientable outcoming overvoltage -Parabolical pdbx -PEEM phaseplate photodiode -Piezo piezo piezoelectrics piezos -Plottable plottable pmatrix polariton @@ -352,21 +413,9 @@ polytope polytopes polyvinylidene potentiostat -Prefactor -PRNG proxigram pseudosymmetry ptychography -PVDF -PYCCAPT -QUBE -Qdev -Qmean -RCSB -RDMS -RHIT -RRNG -Raman raman raylight rdeform @@ -384,8 +433,6 @@ retrieveable reusage ripleyk rois -Ronchigram -SAS sasdata sasdetector sasentry @@ -397,11 +444,10 @@ sassample sassource sastransmission saveframe -SAXS scanbox scanfield scanpoints -SERS +semiaxes setpoint setpoints sextett @@ -409,89 +455,60 @@ shapepar shipswing shring slowaxisname -SNSnxtranslate soller_angle sonoluminescence spatstat spectr. spectralfilter sphx -SPLEED -SPIE -SPPERS spwidth stepsize -Stereology -Stigmator stigmators +stxm subgrain subgrains subprocessing superconcepts supercontinuum -Superlattices -Supermirror supermirror supermirrors -STXM -stxm -SXES tautomeric -TCSPC -TERMS -TERS -Tdev tensorial tessellator tetrahedralization tetrahedralize +thermalized thermomechanical -Titanates -Trac -Traj traj transferfunction transfermatrices -Transfermatrix transfermatrix triglycine -Triplejunction turbomolecular twotheta twotime underconstrained underload undulator -Unidata unvalidated vibropolishing -VLEED voxelated voxelization -VOXELIZED watertightness wavelen wavelenghts wavenumber waveplate -WAXS wilhelmy -WSAS -WWPDB xdim -XDMF xdmf -XFEL -XPCS ydim zener -Zincblende -Zirconate zoneplate # Names used for publications, places, companies, etc. -Acta.Crysta Acta +Acta.Crysta Adrien Adv. Opt. Techn. Aimo @@ -500,11 +517,13 @@ Ankerest Appl Aspnes Azzam +Baluffi Bashara Bergmann Berkels -bluesky +Bollmann Bonse +Borkowski Bravais Breen Britton @@ -512,7 +531,6 @@ Bruker Brückner Bünger Cameca -cameca Cameca's Cardona DESY @@ -521,15 +539,15 @@ Dierksen Dillamore Dimiduk Dimkou -Dresselhaus Doniach-Sunjic +Dresselhaus +Dunin EIKOS Erlangen Ewald Felfer Fleischmann Fluerasu -fRecoVolume Freysoldt Friedel Frigo @@ -545,27 +563,22 @@ Glan Glan-Focault Gottstein Graeff -gatan_imaging Groeber Götz Güntherodt Haase Hartmeier Hawkes -Hoshen-Kopelman Heusler Hielscher -icatproject.org -inchi -Inspico -invizo +Hoshen-Kopelman IUPAC +Inspico J. Appl. Cryst. J. Phys. D: Appl. Phys. -Jägle JEOL Jorio -kanapy +Jägle Katnagallu Keerthi Kikuchi @@ -573,14 +586,12 @@ Kitrick Kocks Konijnenberg Kopelman -kuehbach -Kühbach Krakauer Krakauer/Seidman Kushnir -Laidlaw -laplace_ritchardson +Kühbach LAWATAP +Laidlaw Leoben Leuning Levenberg-Marquardt @@ -591,126 +602,134 @@ Lorensen Lumma Malac Manz -MatWerk Markus +MatWerk Mater Charac -Megas McInnes McStas +Megas Mersenne -mkuehbach Miessen Mießen Monajem Morawiec +NCNR +NFDI +NION Nanonis Nellist Neumann -NCNR -NFDI Niessen -NION Nion -nion Nolze Normarski OINA -Ophus ORCID -orientation_rodrigues ORNL +Ophus PANalytical Patala Pauly Pedersen Peltier Pennycock -piola Popko Poschenrieder -Protochips Preiß Primig +Protochips Rainer Reichmann Reimer Remmele Rielli -ripleyk Rochon -Romaner Rollett -rollett_holm -rotation_rodrigues +Romaner Rowenhorst Saxena +Schmitz's Schoenflies -schottky Schröder Sebald -sebald_gottstein Seblock -seblock Seidman Seitz Senarmont -shermann Shermann Soller Stender TAPHR +Tait Tanaka Techn -Thilo -Teutrie -Tait Tera +Teutrie +Thilo Tougaard Tsai Turnbull Typke Uchic VIBSO -Volterra -Voigt -von Neumann VORONOI VORONOY +Voigt +Volterra Voronoi -voronoi Wellenreuther +Weppelman Windl Winkelmann Zaver Zener Zollner +bluesky +cameca +fRecoVolume +gatan_imaging +icatproject.org +inchi +invizo +kanapy +kuehbach +laplace_ritchardson +mkuehbach +nion +orientation_rodrigues +piola +ripleyk +rollett_holm +rotation_rodrigues +schottky +sebald_gottstein +seblock +shermann +von Neumann +voronoi # Software -ifes_apt_tc_data_modeling Nanobeam +OMERO +Paraview +ifes_apt_tc_data_modeling nanochem nanoprobe paraprobe paraprobe-parmsetup-nanochem -Paraview pynxtools pyxem # other languages Institut -Kristallzüchtung -Krystallstructur -Krystallsysteme -Metallkunde -Metallphysik # en-UK which requires to many changes +Neighbour analyse analyser analysers behaviour defracted -Neighbour neighbour normalisation normalise @@ -727,13 +746,13 @@ visualisation # misc Azimuthally +Granularizing azimuthally bookkeep bookkeeps bookkept -extremal characterizable -Granularizing +extremal hehe inbetween misorienting diff --git a/applications/NXapm.nxdl.xml b/applications/NXapm.nxdl.xml new file mode 100644 index 0000000000..86c0e50130 --- /dev/null +++ b/applications/NXapm.nxdl.xml @@ -0,0 +1,1597 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of hit qualities, the so-called hit types, distinguished. + + + + + Number of delay-line-detector (DLD) wires of the detector. + + + + + Number of bins used in the mass-to-charge-state-ratio spectrum. + + + + + Number of pulses collected in between start_time and end_time resolved by an + instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of + ions included in the reconstructed volume if the application definition is used + to store results of an already reconstructed dataset. + + + + + Number of pulses returned by the hit_finding algorithm. + Neither necessarily equal to p nor to n. + + + + + Number of ions spatially filtered from results of the hit_finding algorithm + from which an instance of a reconstructed volume has been generated. + These ions get new identifier assigned in the process, the so-called + evaporation_id. This identifier must not be confused with the pulse_id. + This value is typically smaller than both p and p_out. + + + + + Number of mass resolution values. + + + + + Application definition for real or simulated atom probe and field-ion microscopy experiments. + + Atom probe tomography and field-ion microscopy are methods for characterizing materials + through induced controlled extraction of individual atoms as ions and molecular ions from + a sharp needle-shaped specimen. + + Offering isotopic and nanometer-scale resolution, atom probe data enable quantification of + local chemical composition and computing of volumetric reconstructions which are models for + the atomic architecture of the small specimen volume analyzed. These reconstructions provide + input for characterization of atomic segregation at crystal defects. The term microstructural features + is considered as a narrow synonym for crystal defects. + + The aim of the NXapm application definition is to provide a general yet specific enough + solution to serialize artifacts for virtually all atom probe and field-ion microcopy experiments. + + Before summarizing the design of the base classes and the parts of the NXapm application definition, + it is worthwhile to recall and distinguish concepts that are related to atom extraction + events and the molecular ions that are frequently generated by the sequence of events: + + * An atom probe instrument uses laser or voltage pulsing events to trigger ion extraction events. + * These ions are accelerated in an electric field towards a position-sensitive detector system. + Physical events and corresponding signal on this detector is triggered by an ion hitting the detector. + Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. + * Note that only a part the specimen volume can be measured and finite detection efficiency means that + not all atoms in the measured volume will be detected. Neutral atoms can escape detection. Some ions + escape detection because they hit into walls of the analysis_chamber. + + Raw data are typically processed as follows: + + * Detector pulses and their timing are processed and discriminated into signal events of different quality levels. + High quality events might be considered in further processing to identify the corresponding molecular ion + and its original position in the reconstructed volume. + * Signal calibration and filtering steps are applied to convert raw time-of-flight data to calibrated + mass-to-charge state ratio values and obtain calibrated impact positions on the detector. + * Ranging and identifying an ion that corresponds to each detector event. + Isotopic abundance and theoretical models inform these ranging algorithms. + * Finally, such selected ion impact positions and iontypes are used to compute a reconstructed volume of + the specimen using backprojection algorithms. In effect, an atom probe measurement is a combination of + a data acquisition and a data analysis workflow. + + Not only in AMETEK/Cameca's APSuite/IVAS software, which the majority of atom probers use, these concepts + are well distinguished. However, the algorithms used to transform correlations between pulses and physical + events into actual events, the so-called detector hits of ions, is a proprietary one. This algorithm is also + referred to as the hit finding algorithm. + + Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting + schema where the course of the specimen evaporation is documented such that quantities are a function of + evaporation_id i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. + That is the evaporation_id values take the role of an implicit time and course of the experiment given that + ion extraction physically is a sequential process. + + This application definition includes fields that the atom probe community has decided to represent best practices + for reporting atom probe measurements. Exemplar mapping tables are provided for documents that reported these + best practices to translate technical term into concepts of the NXapm application definition. + + *The NeXus application definition NXapm defines a hierarchical data model with ten building blocks:* + + The data model represents a tree of concepts. The tree is constructed from groups of concepts representing + the branches, together with fields and attributes representing leaves. NXapm is defined by composing and + specializing base classes into the following ten categories: + + - The field ``definition`` specifies that the data schema is NXapm. In combination with + administrative metadata such as the attribute ``NeXus_version`` provided by :ref:`NXroot` this + specifies which version of NXapm the instance data in a NeXus/HDF5 file are compliant with. + - The fields ``run_number``, ``experiment_alias``, ``experiment_description`` and + the group ``userID`` provide concepts for storing organizational metadata that + contextualize the work within the research workflow and humans involved in this. + - The fields ``start_time``, ``end_time`` provide concepts for framing a temporal context for the research. + - The groups ``citeID``, ``noteID`` provide concepts for adding contextual details such as citations or notes + that are associated with the data, i.e. other artifacts that are deemed relevant when reporting about + a measurement or simulation. These groups are useful when NXapm is used as a serialization format for + technology-partner-agnostic archival of data and metadata that have been collected during a session with + an atom probe instrument. The terms run and session are understood as exact synonyms that refer to an + uninterrupted period of measurement. Resuming measurement on a specimen after an interruption is viewed + as a new run and the new data should not be appended to the previous run, but written to either a new NXentry, + or a new file. Removing the specimen from the instrument is an interruption. Changing evaporation conditions + while the specimen is remains in the analysis_chamber and resuming thereafter the measurement + is not considered as an interruption. It is a common strategy to probe the evaporation process for different + instrument parameters. Each individual collection should then though be stored in an own NXevent_data_apm + group. Parking the specimen to the buffer_chamber and resuming the measurement at a later stage is an interruption. + During a run, the microscope is used for a certain amount of time to characterize a single specimen. + - The groups ``sample`` and ``specimen`` provide concepts for storing metadata about the sample and the specimen, + i.e. the smaller part that was removed from the sample to be measured in the atom probe session. + The term "tip" in the context of atom probe research is considered jargon. + Specimen is an exact synonym for tip. + - The field ``operation_mode`` and group ``measurement`` provides concepts that + are useful for describing a measurement during a session with an atom probe or field-ion microscope. + This includes the chain of events of data and metadata that were collected during such a session. + - The group ``simulation`` provides concepts that are useful for describing a simulation of an + atom extraction, ionization, and ion trajectory simulation. Combined with ``measurement`` + this provides a data schema for defining a digital twin of the instrument and its setup. + - The groups ``consistent_rotations``, and ``NAMED_reference_frame`` provide concepts for + reporting coordinate systems (frames of reference) and rotation conventions that clarify how data + should be interpreted specifying the rotation of orientable objects in the microscope, its components, + or of crystals and crystal defects in the material analyzed. + - The group ``atom_probeID`` provides concepts for the computational workflows that were + used to convert raw detector data into reconstructed ion positions and documentation of + ranging definitions made. + - The group ``profiling`` provides concepts for reporting computational details such as + programs and libraries used, for documenting the libraries of virtual environments such as those used + by conda or python virtual environment, including details about the computing hardware used, and + documenting capabilities for performance analyses and benchmarking of the software or its parts. + + *Design choices:* + + Given that most atom probe instruments across the globe were built by AMETEK/Cameca and are delivered + with the AP Suite/IVAS software there is some homogeneity in how a measurement is performed and which data + artifacts and algorithms used for data processing. Complementary use of open-source software specifically for + the reconstruction, ranging, and later data processing stages contributes to a landscape of multiple tools in use. + Therefore, communication of atom probe research differs between user groups. This holds even more so true + for the sub community in atom probe which study physical mechanisms involved during ionization to the point that + here that almost each research work defines different simulation tools with different types of data artifacts. + + NXapm defines constraints on the existence and cardinality of concepts and its concept branches but seeks to + offer a compromise. The key design pattern followed is that most branches are made optional or at most recommended + but their child concepts are conditionally required. Thereby, NXapm can cover a variety of simple but also complex + use cases. An example of this parent-optional-but-childs-stronger-restricted design is the combination of the + optional group ``measurement`` with its required child ``measurement/instrument``: + Users which report simulations are not forced to document the instrument but users which have characterized + a specimen are motivated to report about the instrument. They are though not necessarily required to report all + the details of the instruments' components because the design pattern is applied recursively. + + *NXapm distinguishes and stores instance data based on how long they remain unchanged:* + + ``measurement`` provides two groups ``measurement/instrument`` and ``measurement/eventID``. + The first group is designed for storing metadata about the instrument that do not change over the course of the session. + Examples are the name of the technology partner who built the microscope or whether a laser or voltage pulser + and reflectron exists or not. The second group is designed for metadata and data that are collected during + the session with the instrument. These, are stored as instances of ``measurement/eventID``, + events that can be time-stamped individually. + Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose is to + store those specific state and settings of the instrument that was present during the collection of the event. + Thereby, changing conditions such as campaigns with different target detection rate can be stored. + + Noteworthy, such an approach of the atom probe detecting groups of events and storing these as groups has also + been in use in the proprietary software via CamecaRoot, a set of customized data structures and file formats that use + the CernRoot library. By virtue of design this reduces unnecessary repetition of metadata stored in the first group. + + ``atom_probeID`` offer classes for the each task relevant task in the data processing pipeline that converts raw detector + event data to calibrated mass-to-charge-state-ratio values and hit_position on the detector. These include + ``initial_specimen``, and ``final_specimen`` locations for storing images of the specimen prior/after the measurement as + considered best practice by AMETEK/Cameca, ``raw_data`` for delay-line timing data, ``hit_finding`` for details of the + hit finding algorithm, ``hit_spatial_filtering`` a process that filters hits of too low quality and those laying outside the about + to be computed reconstruction volume. Furthermore, group ``voltage_and_bowl`` offers a place for documenting calibrations + and processing non-linearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the + conversion from time-of-flight to mass-to-charge-state-ratio values. + + Finally, the groups ``reconstruction`` and ``ranging`` were designed to match and document the classical approaches how + from all the previous sources of input one can compute a reconstructed volume, and apply peak fitting routines on the + mass-to-charge-state-ratio histogram to label ions, i.e. range them for their isotopic identity. + Group ``atom_probeID/reconstruction/naive_discretization`` offers a standardized way to report simple + three-dimensional histograms. Group ``atom_probeID/ranging/peak_identification/ionID`` and its + complementing group ``atom_probeID/ranging/peak_identification/ionID/charge_state_analysis`` + solves the issue that the ranging definitions in classical file formats are not reported for always for their isotopic identity + and charge state. The field ``atom_probeID/ranging/peak_identification/iontypes`` provides a place for + storing a compact representation of the results of each ranging definition made at the level of each ion. + + *The compatibility of NXapm and NXem:** + + The design of NXapm mirrors that of :ref:`NXem`. This was an intentional choice to support the increasingly stronger connection between + these two materials characterization methods, especially in light of recent advances in the direct coupling of atom probe and + transmission electron microscopes and scanning transmission electron microscopes. + + + + + + + + + + + The configuration of the software that was used to generate this NeXus file. + + + + A collection of all programs and libraries which are considered relevant + to understand with which software tools this NeXus file instance was + generated. Ideally, to enable a binary recreation from the input data. + + Examples include the name and version of the libraries used to write the + instance. Ideally, the software which writes these NXprogram instances + also includes the version of the set of NeXus classes i.e. the specific + set of base classes, application definitions, and contributed definitions + with which the here described concepts can be resolved. + + For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ + which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ + research data management system, it makes sense to store e.g. the GitHub + repository commit and respective submodule references used. + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + + The identifier whereby the experiment is referred to in the control software. + + It is common practice in atom probe research to refer to a measurement on a single + specimen as a run. When working with AMETEK/Cameca instruments it is a common + practice also to store all data associated with such a run in files whose name + is composed from a prefix that details the type of instrument (e.g. R5076) followed + by the run_number. These filenames are often used as the specimen_name or + experiment_identifier. The terms run and session are understood as exact synonyms. + + For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, + or the instruments at GPM in Rouen, use the identifier which matches + best conceptually to the LEAP run number. + + The field does not have to be required, if the information is recoverable + in the dataset which for LEAP instruments is the case; provided these + RHIT or HITS files respectively are stored alongside a data artifact. + With NXapm the RHIT or HITS can be stored via NXnote in the + hit_finding algorithm section. + + As a destructive microscopy technique, a run can be performed only once. + It is possible, however, to interrupt a run and restart data acquisition + while still using the same specimen. In this case, each evaporation run + needs to be distinguished with different run numbers. + We follow this habit of most atom probe groups. Such interrupted runs + should be stored as individual :ref:`NXentry` instances in one NeXus file. + + + + + Alias or short name which scientists can use to refer to this experiment. + + + + + Free-text description about the experiment. + + Users are strongly advised to parameterize the description of their experiment + by using respective groups and fields and base classes instead of writing prose + into the field. + + + + + ISO 8601 time code with local time zone offset to UTC information + included when the atom probe session started. If the exact duration of + the measurement is not relevant, start_time only should be used. + + The start_time is required in order to ensure that at least one point in time + is provided for full temporal context to a measurement and simulation + when writing instance data using NXapm. Otherwise, the instance data + can not be sorted in order or even placed in a logical sequence to other + steps of the research workflow, which would disallow using functionalities + in research data management systems that rely on temporal context. + + Specifying start_time and end_time is useful for capturing more detailed + bookkeeping of the experiment. The user should be aware that even with + having both dates specified, it may not be possible to infer how long + the experiment took or for how long data were collected. + + More detailed timing data over the course of the experiment have to be + collected to compute this event chain during the experiment. For this + purpose the :ref:`NXevent_data_apm` instance should be used. + + + + + ISO 8601 time code with local time zone offset to UTC included + when the atom probe session ended. + + Writing the end_time can be a tricky in practice. If written at the start + of the experiment, it can only be an estimate. If written at the end, there + is the risk for having the computer crash or lose power. The absence of + end_time should not be interpreted as that the experiment was aborted. + Only, the field ``status`` should be used for communicating such abortion. + + + + + How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime + + + + + + + + + + + + + + What type of atom probe experiment is performed to inform research data management + systems and allow filtering: + + * apt are experiments where the analysis_chamber has no imaging gas. + Experiments with LEAP instruments are typically with this operation_mode. + * fim are experiments where the analysis_chamber has an imaging gas, + which should be specified with the atmosphere in the analysis_chamber group. + * apt_fim should be used for combinations of the two imaging modes. + Few experiments of this type have been performed, as it can be detrimental + to LEAP systems (see `S. Katnagallu et al. <https://doi.org/10.1017/S1431927621012381>`_). + + + + + + + + + + + + + + + + Description of the sample from which the specimen was prepared or + site-specifically cut out using e.g. a focused-ion beam instrument. + + In NXapm, a measurement is performed on a specimen. Since APM specimens + are very small, they are typically cut from a larger object with some + scientific significance, which NXapm refers to as a sample. + + + + + False, if the sample is a real one. + True, if the sample is a virtual one. + + + + + Given name/alias for the sample. + + + + + Qualitative information about the grain size, here specifically + described as the equivalent spherical diameter of an assumed + average grain size for the crystal ensemble. + + If the specimen does not contain many crystals average values + might be an unreliable descriptor. + + Reporting a grain size may be useful though as it allows + judging if specific features are expected to be found in the + detector hit map. + + + + + Magnitude of the standard deviation of the grain_diameter. + + + + + An array of elapsed time, the independent axis, of a time-temperature curve. + + This field can be used in combination with heat_treatment_temperature and + heat_treatment_temperature_errors as well as heat_treatment_quenching_rate + and heat_treatment_quenching_rate_errors respectively. In this case, these fields + should also be stored as an array with the same dimensions as heat_treatment_time + to store the dependant axes of a time-temperature curve as well as its first derivative. + + + + + If heat_treatment_time is absent, the temperature of the last heat treatment step + before quenching. + + Knowledge about this value can give an idea how the sample + was heat treated. However, if a documentation of the annealing + treatment as a function of time is available one should better + rely on this information and have it stored alongside the NeXus file. + + If heat_treatment_time is provided, the temperature. + Consult the docstring of heat_treatment_time. + + + + + Magnitude of the standard deviation of the heat_treatment_temperature. + + If heat_treatment_time is provided, the magnitude of the standard derivation of the + temperature. Consult the docstring of heat_treatment_time. + + + + + If heat_treatment_time is absent, the rate of the last quenching step. + + Knowledge about this value can give an idea how the sample was heat treated. + However, there are many situations where one can imagine that the scalar value + for just the quenching rate is insufficient. + + If heat_treatment_time is provided, the first derivative of the time-temperature curve. + Consult the docstring of heat_treatment_time for further details. + + + + + Magnitude of the standard deviation of the heat_treatment_quenching_rate. + + If heat_treatment_time is provided, the magnitude of the standard deviation of + the first derivative of the time-temperature curve. + Consult the docstring of heat_treatment_time for further details. + + + + + + The chemical composition of the sample. + + Typically, it is assumed that this more macroscopic composition is representative + for the material so that the composition of the typically substantially less + voluminous specimen probes from the more voluminous sample. + + + + + + + + + + + + Description of the specimen that was cut off from the sample. + + In atom probe jargon this is typically referred to as the tip. + + + + + False, if the specimen is a real one. + True, if the specimen is a virtual one. + + + + + Given name or an alias. Better use identifierNAME and identifier_parent instead. + + A single NXentry should be used only for the characterization of a single specimen. + + + + + Identifier of the sample from which the specimen was cut or the string "n/a". + + The purpose of this field is to support functionalities for tracking sample + provenance via a research data management system. + + + + + ISO 8601 time code with local time zone offset to UTC information + when the specimen was prepared. + + Ideally, report the end of the preparation, i.e. the last known time + the measured specimen surface was actively prepared. Ideally, this + matches the last timestamp that is mentioned in the digital resource + pointed to by identifier_parent. + + Knowing when the specimen was exposed to e.g. specific atmosphere is + especially required for environmentally sensitive material such as + hydrogen charged specimens or experiments including tracers with a + short half time. + + + + + List of comma-separated elements from the IUPAC periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by identifier_parent or walk through + eventually deeply nested groups in data instances. + + + + + Discouraged free-text field. + + + + + True, if the specimen contains a grain or phase boundary. + False, if the specimen is a single crystal. + + + + + True, if the specimen is amorphous. + False, if the specimen is not. + + + + + Ideally measured otherwise best elaborated guess of the initial radius of the + specimen. + + + + + Ideally measured, otherwise best estimate, of the initial shank angle. + + This is a measure of the specimen taper. + Define it in such a way that the base of the specimen is modelled + as a conical frustrum so that the shank angle is the smallest angle + between the specimen space z-axis and a vector on the lateral surface + of the cone. + + + + + + The conventions used when reporting crystal orientations. + We follow the best practices of the Material Science community + that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + Convention how a positive rotation angle is defined when viewing + from the end of the rotation unit vector towards its origin. + This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + Counter_clockwise is equivalent to a right-handed choice. + Clockwise is equivalent to a left-handed choice. + + + + + + + + + How are rotations interpreted into an orientation according to convention 3 + of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + + How are Euler angles interpreted given that there are several choices e.g. zxz, xyz + according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + The most frequently used convention in Materials Science is zxz, which is based on the work + of H.-J. Bunge but using other conventions is possible. Proper Euler angles are distinguished + from Tait-Bryan angles. + + + + + + + + + + + + + + + + + + + To which angular range is the rotation angle argument of an + axis-angle pair parameterization constrained according to + convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + Which sign convention is followed when converting orientations + between different parametrizations/representations according + to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + + + A coordinate system. Multiple instances require unique names. + + Several Euclidean coordinate systems (CS) are used in the field of atom probe: + + * World space; + a CS specifying a local coordinate system of the planet earth which + identifies into which direction gravity is pointing such that + the laboratory space CS can be rotated into this world CS. + * The laboratory space; + a CS specifying the room where the instrument is located in or + a physical landmark on the instrument, e.g. the direction of the + transfer rod where positive is the direction how the rod + has to be pushed during loading a specimen into the instrument. + In summary, this CS is defined by the chassis of the instrument. + Suggested name of the group ``laboratory_reference_frame``. + * The specimen space; + a CS affixed to either the base or the initial apex of the specimen, + whose z axis points towards the detector. + Suggested name of the group ``specimen_reference_frame``. + * The detector space; + a CS affixed to the detector plane whose xy plane is usually in the + detector and whose z axis points towards the specimen. + This is a distorted space with respect to the reconstructed ion + positions. + Suggested name of the group ``detector_reference_frame``. + * The reconstruction space; + a CS in which the reconstructed ion positions are defined. + The orientation depends on the analysis software used. + * Eventually further coordinate systems attached to the + flight path of individual ions might be defined. + Suggested name of the group ``reconstruction_reference_frame``. + + To achieve unique names, the prefix "NAMED" should be replaced to + with something derived from an alias for the coordinate system, + or the value of the "alias" field. + + Use the suffix _reference_frame when creating specific instances + of NXcoordinate_system e.g. laboratory_reference_frame, + reconstruction_reference_frame and so on and so forth. + + In atom probe microscopy a frequently used choice for the detector + space (CS) is discussed with the so-called detector space image + stack. This is a stack of two-dimensional histograms of detected ions + within a predefined evaporation identifier interval. Typically, the set of + ion evaporation sequence identifiers is grouped into chunks. + + For each chunk a histogram of the ion hit positions on the detector + is computed. This leaves the possibility for inconsistency between + the so-called detector space and the e.g. specimen space. + + To avoid these ambiguities, instances of :ref:`NXtransformations` should be used. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A region-of-interest analyzed either during or after the session for which + specific processed data of the measured or simulated data are available. + + If a single instance is required the group should be named atom_probe. + If multiple groups are required these should be named atom_probe1, atom_probe2, + and so on and so forth. + + + + SEM or TEM image of the initial specimen taken before the measurement. + + + + + + + + + + + + + + + + + + + + + + + SEM or TEM image of the final specimen taken after completion of the + measurement. + + + + + + + + + + + + + + + + + + + + + + + Document the control software that was used on the instrument with which raw data + were collected. + + For almost all atom probe instruments, the recorded raw data and metadata follow + proprietary semantics. Therefore, this group can currently often not be filled with + more than the control software and some pointing to digital artifacts (e.g. proprietary files) + that have been collected during the measurement in an effort to document as best as + possible all steps of an analysis workflow. + + The physical quantities measured in an atom probe experiment are time-of-flight and + tuples of arrival_time_pairs as a function of the event chain on the pulser. + From these tuples, hits are computed in a process called hit_finding. + + + + + The control software that was used for running the measurement. + + At least the main software should be reported. If this is the only program + to report name the group "program" and use its below fields program and + version to detail the version used. E.g. program AP Suite, version 6.3 + + It is recommended to report multiple programs though, i.e. also the libraries + and dependencies of the software. In the case of AP Suite/IVAS this can be used + to document the AP Suite GUI, LAS, CamecaRoot, and CernRoot versions. + In this case always name the program groups program1, program2, ... + with program one being AP Suite/IVAS. + + In the case of an open-source instrument, like P. Felfer's Oxcart or G. Schmitz's + M-TAP instruments, also use program1, program2, ... with program1 representing + the control software e.g. `M. Monajem and P. Felfer pyCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_. + Further instances (program2, ...) can be used to list the dependencies, the + python virtual environment. + + + + + + + + Possibility to point to files that contain raw data. + + Exemplar files that could be pointed to here when working with + AMETEK/Cameca instruments are the proprietary STR, RRAW, or HITS + files that AP Suite/IVAS generates. + + + + + + + + + The number of delay-line-detector (DLD) wires present. + + + + + + + + + + Alias tuple, typical for the begin and the end of each DLD wire + of the detector. Order follows arrival_time_pairs. + + The order of the first dimension should match that of the + second dimension of the arrival_time_pairs field. + + + + + + + + + Raw readings from the analog-to-digital-converter + timing circuits of the detector wires. + + + + + + + + + + + The configuration of a hit finding algorithm and its output. + + Hit finding is the process of deciding which detector signals are significant + and assigning specific ions colliding with the detector + to each observed event. + + + + + + + + + + + + + + + + Evaluated ion impact coordinates on the detector. + Use the depends_on field to specify which reference + frame the positions are defined in. + + + + + + + + Contains the path to an instance of NX_coordinate_system + in which the positions are defined. + + + + + + Number of events of type "golden" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventGolden + field of a CamecaRoot RHIT/HITS file. + + + + + Number of events of type "incomplete" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventIncomplete + field of a CamecaRoot RHIT/HITS file. + + + + + Number of events of type "multiple" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventMultiple + field of a CamecaRoot RHIT/HITS file. + + + + + Number of events of type "partials" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventPartials + field of a CamecaRoot RHIT/HITS file. + + + + + Number of events when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventRecords + field of a CamecaRoot RHIT/HITS file. + + + + + Hit quality is an integer that specifies which category/type a hit was assigned to. + This field lists the human-readable, possibly though proprietary types distinguished. + The indices of this array are used in hit_quality to encode hit_quality for each + pulse in a more efficient way than by repeating the string that is used for each + type as it is provided in this field. + + As an example, assume two types, "golden" and "partial", are distinguished. + If hit_quality_type stores the array "golden", "partial", the index 0 + in hit_quality identifies all those pulses of category "golden", + while the index 1 in hit_quality identifies all of category "partial". + + + + + + + + Hit quality identifier for each pulse. + Identifier has to be within hit_quality_type. + + + + + + + + The number of ions determined to have been collected on the same pulse. + These ions may hit different pixels, or even the same detector pixel. + The hit_multiplicity is not related to the makeup of the ions and should not be + confused with the number of atoms or elements that constitute a molecular ion. + + + + + + + + + + + + + + + + + + + + + + Integer which defines the first evaporation_id. + Typically, this is either zero or one. + + + + + There are two possibilities to report evaporation_id values: + + If evaporation_id_offset is provided, the evaporation_id values are defined + by the sequence :math:`[evaporation\_id\_offset, evaporation\_id\_offset + n]` + with :math:`n` the number of ions in the reconstructed volume. + + Alternatively, evaporation_id_offset is not provided but instead a + a sequence of :math:`n` values is defined, these integer values + do not need to be sorted. + + + + + + + + + + + + + + + Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. + + The voltage-and-bowl correction is a data post-processing step to correct ion impact + positions for flight path differences, detector bias, and nonlinearities. + + + + + + + + + + + + + + + + + Reference mass-to-charge state ratio value + + For example 16 Da as mentioned by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). + + + + + + Raw time-of-flight data without corrections. + + + + + + + + The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate + + + + + Calibrated time-of-flight. + + + + + + + + + + + + + + + + + + + + + + + Mass calibration with unit peaks/interp. as mentioned by `T. Blum et al. + <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). + + + + + Inverse of the mass resolution :math:`\frac{M}{\Delta M}` as mentioned by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). + + Multiple values can be reported but reporting each is only useful when stating also: + + * The full width at which :math:`{\Delta M}_{fw}` fraction of maximum this value was defined. + Examples are at tenth :math:`{\Delta M}_{10}` or at half maximum (FWHM). + Consequently, mass_resolution_fw should needs to be a vector of the same length + and using the same order like used for mass_resolution, i.e. the first mass resolution was + defined at the maximum as defined by the first value from mass_resolution_fw. + * The reference molecular ion e.g. :math:`^{16}{O_{2}}^{+}` + As many instances of mass_resolutionION should be used with instances + numbered starting from 1 up to the length of the mass_resolution vector. + + + + + + + + The full width at which :math:`{\Delta M}_{fw}` fraction of maximum this value was defined. + Examples are at tenth :math:`{\Delta M}_{10}` or at half maximum (FWHM). + Consequently, mass_resolution_fw should needs to be a vector of the same length + and using the same order like used for mass_resolution, i.e. the first mass resolution was + defined at the maximum as defined by the first value from mass_resolution_fw. + + + + + + + + The reference molecular ion e.g. :math:`^{16}{O_{2}}^{+}` + As many instances of mass_resolutionION should be used with instances + numbered starting from 1 up to the length of the mass_resolution vector. + + + + + + + + + + + + + + + + + + + + + For LEAP and APSuite/IVAS-based analyses the root file which stores + the settings whereby an RHIT/HITS file can be used to regenerate the + reconstructed volume that is here referred to. + + The respective RHIT/HITS file should ideally be specified in the serialized + group of the hit_finding section of this application definition. + + + + + + + + + For LEAP and APSuite/IVAS-based analyses the resulting typically + file with the reconstructed positions and calibrated mass-to-charge- + state ratio values. + + For other data collection/analysis software the data artifact which comes + closest conceptually to AMETEK/Cameca's typical file formats. + + These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, + which should be stored alongside this record in the research data + management system. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The respective ranging definitions file RNG/RRNG/ENV/HDF5. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (Out-of-sync, time-independent) background levels in ppm/ns + reported by e.g. APSuite/IVAS for LEAP systems. + + + + + The mass-resolving power (MRP) value + + `D. Larson et al. <https://doi.org/10.1007/978-1-4614-8721-0>`_ report Eq. D.8 in page 282: + + :math:`MRP = \frac{1}{2\delta t} \cdot \sqrt{\frac{m}{n}\frac{1}{2eV}L}`, + + with :math:`\delta t` representing the timing imprecision, :math:`\frac{m}{n}` the mass-to-charge state ratio, + :math:`e` the elementary charge, :math:`V` the potential difference, and :math:`L` the flight path length. + + Timing imprecision is caused by variations of flight path length and voltage, + the fact that the precision of electronics is finite and a spread of the + time-of-departure of individual ions is observed. + + + + + Mass-to-charge state ratio :math:`\frac{m}{n}` at which mrp_value was specified. + + + + + Potential difference :math:`V` at which mrp_value was specified. + + + + + Flight path length :math:`L` at which mrp_value was specified. + + + + + + + + + + + + + + + + Category for the peak offering a qualitative statement of the location of the peak + in light of limited mass-resolving power that is relevant for + composition quantification. See `D. Larson et al. (p172) <https://doi.org/10.1007/978-1-4614-8721-0>`_ + for examples of each category: + + * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` + * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` + * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states + * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` + * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` + * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` + + + + + + + + + + + + + + + + + + + + + + + + + + Ions that were ranged. + + The value zero is reserved for documenting that an ion was unranged. + Identifier for ranged ions need to start at 1 up to number_of_ion_types. + + + + + + + + + + + + + + + + + + + + + + + + The iontype identifier for each ion that was best matching; + stored in the order of the evaporation_id. + + The value zero is reserved for documenting that an ion was unranged. + Identifier for ranged ions need to start at 1 up to number_of_ion_types. + + + + + + + + + + diff --git a/applications/NXem.nxdl.xml b/applications/NXem.nxdl.xml new file mode 100644 index 0000000000..ad9fe43f47 --- /dev/null +++ b/applications/NXem.nxdl.xml @@ -0,0 +1,1805 @@ + + + + + + Application definition for normalized representation of electron microscopy research. + + This application definition is a comprehensive, general description for the + standardization of data and metadata collected using electron microscopy. + + NXem is designed to be used for documenting experiments or computer simulations in which + controlled electron beams are used to study electron-beam matter interactions, to simulate this, + to explore physical mechanisms and phenomena, or to characterize materials. + + *The NeXus application definition NXem defines a hierarchical data model with ten building blocks:* + + The data model represents a tree of concepts. The tree is constructed from groups of concepts + representing the branches surplus fields and attributes representing leafs. + + *NXem an introduction for typical use cases in material characterization and simulation:* + + Transmission electron microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) + Scanning Electron Microscopy (SEM) + Scanning Electron Microscopy combined a Focused-Ion Beam (SEM/FIB) + + *A deeper dive into the branches of NXem:* + + NXem is constructed from composing and specializing base classes into the following ten categories: + + - The field ``definition`` specifies that the data schema is NXem. In combination with + administrative metadata such as the ``NeXus_version`` provided by :ref:`NXroot` this + specifies which version of NXem the instance data in a NeXus/HDF5 file are compliant with. + - The fields ``identifier_experiment``, ``experiment_alias``, ``experiment_description`` and + the group ``userID`` provide concepts for storing organizational metadata that + contextualize the work within the research workflow and humans involved in this. + - The fields ``start_time``, ``end_time`` provide concepts for framing a temporal context for the research. + - The groups ``citeID``, ``noteID`` provide concepts for adding contextual details such as citations + that are associated with or notes, i.e. other artifacts that are deemed relevant when reporting about a measurement + or simulation. These groups are useful when NXem is used as a serialization format for technology-partner-agnostic + archival of data and metadata that have been collected during a session with an electron microscope or when a + simulation was performed. + - The group ``sampleID`` provides concepts for storing metadata about the sample that was + characterized or simulated during the session. + - The group ``measurement`` provides concepts that are useful for describing a measurement + during a session with an electron microscope. This includes the chain of events of data and metadata that + were collected during such a session. + - The group``simulation`` provides concepts that are useful for describing a simulation of an + electron beam that interacts with matter. Combined with ``measurement`` this provides a data schema + for defining a digital twin of the microscope and its optical setup. + - The groups ``consistent_rotations``, ``NAMED_reference_frame`` provide concepts for + reporting coordinate systems (frames of reference) and rotation conventions that clarify how data + should be interpreted specifying the rotation of orientable objects in the microscope, its components, + or of crystals and crystal defects in the material analyzed. These metadata support interpretation for + downstream or on-the-fly data analyses which electron microscopes typically nowadays perform + during a session. Examples are the indexing of diffraction patterns, image analysis in general, or + analyses of the chemical composition. + - The group ``roiID`` provides concepts for reporting several domain- and technique-specific + configuration parameter and results of data processing steps that were applied. + - The group ``profiling`` provides concepts for reporting computational details such as + programs and libraries used, for documenting the libraries of virtual environments such as those used + by conda or python virtual environment, including details about the computing hardware used, and + documenting capabilities for performance analyses and benchmarking of the software or its parts. + + *Design choices:* + + Specific details about how an electron microscope was used and eventually its configuration modified differ + between user groups. This holds also true for computer simulations of electron-beam matter interaction. + Different peer groups in different sub-domains in electron microscopy consider different data and metadata + relevant. NXem defines constraints on the existence and cardinality of concepts and its concept branches + but seeks to offer a compromise. The key design pattern followed is that most branches are made optional + or at most recommended but their child concepts conditional required. Thereby, NXem can cover a variety + of simple but also complex use cases. An example of this parent-optional-but-childs-stronger-restricted design + is the combination of the optional group ``measurement`` with its required child + ``measurement/instrument``: Users which report simulations are not forced to document the instrument + but users which have characterized a sample are motivated to report about the instrument. They are though not + necessarily required to report all the details of the instruments' components because the design pattern is-used + applied recursively. + + *Inclusive design, one schema for scanning, focused-ion beam, and transmission electron microscopes:* + + Contrary to many other proposals of a data schema for electron microscopy, NXem seeks to highlight the similarity + of the three fundamental types of electron microscopes that are nowadays used most routinely in academia and + industry: An electron microscope is a beamline that provides a controlled beam of electrons combined with eventually + beams of other particles (ions) to investigate electron/ion(-beam) matter interaction. + This design of per-particle-type concept branches is realized in the base classes ``NXebeam_column`` and ``NXibeam_column``. + These provide concepts for reporting the technical components that are typically used for generating a controllable + (and typically scanning) beam of particles such as electrons or ions. + + Focused-ion beam capabilities are modelled by adding an optional group ``measurement/instrument/ibeam_column``. + We foresee that this design is beneficial also in the future when research should be documented where photon-electron + interactions via an electron microscope are combined. The current proposal though does not include such a + ``NXpbeam_column`` base class that could be used for photon-/light-beam, i.e. laser plus optical + beam path descriptions and components. + + We acknowledge that scanning and transmission electron microscopes are different types of instruments that have distinct differences + in the electron-optical setup and the components used. What remains the same from the perspective of an observer who monitors the + experiment inside the electron-matter interaction volume, i.e. in, on, or close to the surface of the specimen is the imaginary split + into an upper and a lower half-space. In the upper half-space a specific but eventually differently shaped electron beam illuminates + the specimen when comparing a scanning with a transmission electron microscope. In the lower half-space the beam or particles exit + the specimen or end up thermalized in thick specimens. + + *NXem distinguishes and stores instance data based on how long they remain unchanged:* + + ``measurement`` provides two groups ``measurement/instrument`` and ``measurement/eventID``. + The first group is designed for storing metadata about the instrument which do not change over the course of the session. Examples are + the name of the technology partner who built the microscope, the microscope's serial number, or the type of lenses mounted, etc. + The second group is designed for metadata and data that are collected during the microscope session. For these, specializations of + ``NXdata`` specifically ``NXimage`` and ``NXspectrum`` are provided. Each ``measurement/eventID`` event can be time-stamped + individually. Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose + is to store those specific state and settings of the microscope that was present during the collection of the event. + This includes lens settings, apertures used, aberrations, and other components, etc. + By virtue of design this reduces unnecessary repetition of metadata stored in the first group like is often observed + in image-based archival formats like TIFF, PNG, etc. + + *NXem offers domain-specific classes for standardized reporting of method-specific configurations, data processing, and results:* + + These include ``NXem_img`` for generic and specific imaging including diffraction, ``NXem_eds`` for energy-dispersive X-ray spectroscopy, + ``NXem_ebsd`` for electron backscatter diffraction, as well as ``NXem_eels`` for electron energy loss spectroscopy. These branches provide + examples that proof how NeXus can be used for combining session-centric data storage with data processing. These examples are naturally + incomplete but show at different levels of technical depth and breath how standardization can be useful even to report specifically formatted + data representations like multi-dimensional plotting. Thereby, downstream processing using software for data analyses or research data + management can take advantage of a standardized reporting rather than demanding for a zoo of parsers that interconvert + between many representations. + + *NXem within the ecosystem of data schemata for electron microscopy:** + + We support the statement that substantially fewer standardized rather than many ad hoc schemata are required to facilitate the + documentation and exchange of knowledge within electron microscopy. We tailored NXem to serve the materials science and + materials engineering usage of electron microscopy to provide a complementary coverage to what OMERO has established for + the bio- and life science usage of electron microscopy. + + + + + + + + + + The configuration of the software that was used to generate this NeXus file. + + + + A collection of all programs and libraries used to generate this NeXus file. + Ideally, this would enable a binary recreation from the input data. + + Examples include the name and version of the libraries used to write the + instance. Ideally, the software which writes these NXprogram instances + also includes the version of the set of NeXus classes i.e. the specific set + of base classes, application definitions, and contributed definitions + with which the here described concepts can be resolved. + + For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ + which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ + research data management system, it makes sense to store e.g. the GitHub + repository commit and respective submodule references used. + + Instances can also be used to document the modules and libraries that + are offered by the computational environment such as those parsed + from conda or python virtualenv environments. + + + + + + + + + A (globally) unique persistent identifier for referring to this experiment. + + + + + Alias (short name) which scientists can use to refer to this experiment. + + + + + Free-text description about the experiment. + + Users are strongly advised to parameterize the description of their experiment + by using respective groups and fields and base classes instead of writing prose + into the field. + + + + + ISO 8601 time code with local time zone offset to UTC information included + when the microscope session started. If the application demands that time + codes in this section of the application definition should only be used + for specifying when the experiment was performed - and the exact + duration is not relevant - use this start_time field. + + Often though it is useful to specify a time interval via setting both a start_time + and an end_time because this enables software tools and users to collect a + more detailed bookkeeping of the experiment. + + Users should be aware though that even using only start_time and end_time + may not be sufficient to infer how long the experiment took or for how long + data were acquired. To bookkeep more fine-grained timestamps over the + course of the experiment is possible with start_time and end_time fields + of respective :ref:`NXevent_data_em` instances. + + + + + ISO 8601 time code with local time zone offset to UTC included when + the microscope session ended. + + See docstring of the start_time field to see how to use the + start_time and end_time together. + + + + + + Collection of serialized resources associated with the experiment. + Examples of such resources are files which are formatted using proprietary + data models of technology partners as those generated by the control software + of the microscope during the instrument session. + + + + + + + + + Information about persons who performed or were involved in the microscope + session or simulation run. + + + + + + + Given (first) name and surname. + + + + + Name of the affiliation at the point in time when the experiment was performed. + + + + + Postal address of the affiliation. + + + + + Email address at the point in time when the experiment was performed. + + Writing the most permanently used email is recommended. + + + + + Telephone number at the point in time when the experiment was performed. + + + + + User role at the point in time when the experiment was performed. + + Examples are technician operating the microscope, student, postdoc, + principle investigator, or guest. + + + + + + A physical entity which contains material intended to be investigated. + Sample and specimen are treated as de facto synonyms. + Samples can be real or virtual ones as annotated via is_simulation. + + The suggested best practice is to call this group sample. In those cases when + multiple samples need to be grouped inside one entry, these SAMPLE groups + should be named using the prefix sample followed an index starting from 1, i.e. + (sample1, sample2). + + There are at least two strategies how to store (meta)data when one analyzes multiple + samples - not different ROIs on a single sample though - in one session. + + One strategy is to store each sample and its results under an own NXem/ENTRY. + This is one of the most frequent use cases as during most sessions typically only a + single sample is investigated. In this case the name of this group should be sample. + + If multiple samples are investigated storing each of them in their own ENTRY group eventually will + demand unnecessary duplication of instrument details. + + This can be avoided by using another strategy for storing samples and their results. + Namely, by using only one instance of NXem/ENTRY. That NXem/ENTRY should then be named, + like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., + i.e. instances should use sample as a name prefix. + + In this case the collection of events should use identifier_sample to state clearly for which + of the samples loaded the (characterization) event was detected. + + This concept is related to term `Specimen`_ of the EMglossary standard. + + .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 + + + + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). + + + + + + + + + + + + + Ideally, (globally) unique persistent identifier which distinguishes this sample from all others + and especially the predecessor/origin from where that sample was cut off. An example of cutting off + is a steel sheet that is the parent sample from which a small portion was wire-eroded that + represents the sample that was then prepared for characterization with an electron microscope. + + The terms sample and specimen are here considered as exact synonyms. + + This field must not be used for an alias for the sample name. Instead, use name. + + In cases where multiple specimens were loaded into the microscope, the identifier has to resolve + the specific sample, whose results are stored by this :ref:`NXentry` instance, because a single + NXentry should be used for the characterization of a single specimen. + + Details about the specimen preparation should be stored in resources referring to identifier_parent. + + + + + + Identifier of the sample from which the sample was cut off or the string *None*. + I.e. the parent to this sample. + + The purpose of this field is to support functionalities for tracking + sample provenance in a research data management system. + + + + + + ISO 8601 time code with local time zone offset to UTC information + when the specimen was prepared. + + Ideally, report the end of the preparation, i.e. the last known timestamp when + the measured specimen surface was actively prepared. Ideally, this matches + the last timestamp that is mentioned in the digital resource pointed to by + identifier_parent. + + Knowing when the specimen was exposed to e.g. specific atmosphere is especially + required for material that is sensitive to the environment such as specimens that were + charged with fast diffusing elements or short-lived radioactive tracers. + + Additional time stamps prior to preparation_date are better placed in resources which + describe but do not pollute the description here with prose. Resolving these + connected metadata is considered the responsibility of the research data management + system and not the a NeXus file. + + + + + Specimen name + + + + + List of comma-separated elements from the periodic table that are contained in the sample. + If the sample substance has multiple components, all elements from each component + must be included in atom_types. + + The purpose of the field is to offer research data management systems an opportunity + to parse the relevant elements without having to interpret these from the resources + pointed to by identifier_parent or walk through eventually deeply nested groups in + individual data instances. + + + + + (Measured) sample thickness. + + The information is recorded to qualify if the beam used was likely + able to shine through the specimen. For scanning electron microscopy, + in many cases the specimen is typically thicker than what is + illuminatable by the electron beam. + + In this case the value should be set to the actual thickness of the specimen + viewed for an illumination situation where the nominal surface normal of the + specimen is parallel to the optical axis. + + + + + (Measured) density of the specimen. + + For multi-layered specimens this field should only be used to describe + the density of the excited volume. For scanning electron microscopy + the usage of this field is discouraged and instead an instance of a + region-of-interest connected to individual :ref:`NXevent_data_em` + instances can provide a cleaner description of the relevant details. + + + + + Discouraged free-text field to provide further detail. + + + + + + The conventions used when reporting crystal orientations. + We follow the best practices of the Material Science community + that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + Convention how a positive rotation angle is defined when viewing + from the end of the rotation unit vector towards its origin. + This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + Counter_clockwise is equivalent to a right-handed choice. + Clockwise is equivalent to a left-handed choice. + + + + + + + + + How are rotations interpreted into an orientation according to convention 3 + of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + + How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) + according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + The most frequently used convention in Materials Science is zxz, which is based on the work + of H.-J. Bunge but using other conventions is possible. Proper Euler angles are distinguished + from (improper) Tait-Bryan angles. + + + + + + + + + + + + + + + + + + + To which angular range is the rotation angle argument of an + axis-angle pair parameterization constrained according to + convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + Which sign convention is followed when converting orientations + between different parametrizations/representations according + to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + + + + + + + + + + + + + + + + + Location of the origin of the processing_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + + + + + + + + + + + + + + + + Direction of the positively pointing x-axis base vector of the + processing_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing y-axis base vector of the + processing_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing z-axis base vector of the + processing_reference_frame. + + + + + + + + + + + + + + + Reference to the specifically named :ref:`NXsample` instance(s) for + which these conventions apply (e.g. /entry1/sample1). + + + + + + + Location of the origin of the sample_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + + + + + + + + + + + + + + + + Direction of the positively pointing x-axis base vector of the + sample_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing y-axis base vector of the + sample_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing z-axis base vector of the + sample_reference_frame. + + + + + + + + + + + + + + The reference frame that is defined by a specific detector. + + + + Reference to the specifically named :ref:`NXdetector` instance for + which these conventions apply (e.g. /entry1/instrument/detector1). + + + + + + + Location of the origin of the detector_reference_frame. + + If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted + by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) + along respective base vector direction of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + + + + + + + + + + + + + + + + Direction of the positively pointing x-axis base vector of the + detector_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing y-axis base vector of the + detector_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing z-axis base vector of the + detector_reference_frame. + + + + + + + + + + + + + + + + + + + + + + + + + Details about the control program used for operating the microscope. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A spherical aberration corrector is a typical component in a transmission electron microscope. + Many instruments have only one, in this case the variadic suffix should be dropped. + If there are multiple instances these should be numbered starting from 1, i.e. corrector_cs1, + corrector_cs2. + + + + Use specifically when there are multiple instances. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. + + + + + + + + + + + + + + + + + + + + + Operation mode of the detector as displayed by the control software. + + + + + + + + + + + + + + Nominal current of the heater. + + + + + Nominal voltage of the heater. + + + + + + + + + + + + + + + + Documentation for a simulation of electron beam-matter interaction. + + + + The program with which the simulation was performed. + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + Configuration of the simulation + + + + + Results of the simulation + + + + + + + + + + + + + This concept is related to term `Region Of Interest`_ of the EMglossary standard. + + .. _Region Of Interest: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/applications/nyaml/NXapm.yaml b/applications/nyaml/NXapm.yaml new file mode 100644 index 0000000000..36936ed3ec --- /dev/null +++ b/applications/nyaml/NXapm.yaml @@ -0,0 +1,3131 @@ +category: application +doc: | + Application definition for real or simulated atom probe and field-ion microscopy experiments. + + Atom probe tomography and field-ion microscopy are methods for characterizing materials + through induced controlled extraction of individual atoms as ions and molecular ions from + a sharp needle-shaped specimen. + + Offering isotopic and nanometer-scale resolution, atom probe data enable quantification of + local chemical composition and computing of volumetric reconstructions which are models for + the atomic architecture of the small specimen volume analyzed. These reconstructions provide + input for characterization of atomic segregation at crystal defects. The term microstructural features + is considered as a narrow synonym for crystal defects. + + The aim of the NXapm application definition is to provide a general yet specific enough + solution to serialize artifacts for virtually all atom probe and field-ion microcopy experiments. + + Before summarizing the design of the base classes and the parts of the NXapm application definition, + it is worthwhile to recall and distinguish concepts that are related to atom extraction + events and the molecular ions that are frequently generated by the sequence of events: + + * An atom probe instrument uses laser or voltage pulsing events to trigger ion extraction events. + * These ions are accelerated in an electric field towards a position-sensitive detector system. + Physical events and corresponding signal on this detector is triggered by an ion hitting the detector. + Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. + * Note that only a part the specimen volume can be measured and finite detection efficiency means that + not all atoms in the measured volume will be detected. Neutral atoms can escape detection. Some ions + escape detection because they hit into walls of the analysis_chamber. + + Raw data are typically processed as follows: + + * Detector pulses and their timing are processed and discriminated into signal events of different quality levels. + High quality events might be considered in further processing to identify the corresponding molecular ion + and its original position in the reconstructed volume. + * Signal calibration and filtering steps are applied to convert raw time-of-flight data to calibrated + mass-to-charge state ratio values and obtain calibrated impact positions on the detector. + * Ranging and identifying an ion that corresponds to each detector event. + Isotopic abundance and theoretical models inform these ranging algorithms. + * Finally, such selected ion impact positions and iontypes are used to compute a reconstructed volume of + the specimen using backprojection algorithms. In effect, an atom probe measurement is a combination of + a data acquisition and a data analysis workflow. + + Not only in AMETEK/Cameca's APSuite/IVAS software, which the majority of atom probers use, these concepts + are well distinguished. However, the algorithms used to transform correlations between pulses and physical + events into actual events, the so-called detector hits of ions, is a proprietary one. This algorithm is also + referred to as the hit finding algorithm. + + Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting + schema where the course of the specimen evaporation is documented such that quantities are a function of + evaporation_id i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. + That is the evaporation_id values take the role of an implicit time and course of the experiment given that + ion extraction physically is a sequential process. + + This application definition includes fields that the atom probe community has decided to represent best practices + for reporting atom probe measurements. Exemplar mapping tables are provided for documents that reported these + best practices to translate technical term into concepts of the NXapm application definition. + + *The NeXus application definition NXapm defines a hierarchical data model with ten building blocks:* + + The data model represents a tree of concepts. The tree is constructed from groups of concepts representing + the branches, together with fields and attributes representing leaves. NXapm is defined by composing and + specializing base classes into the following ten categories: + + - The field ``definition`` specifies that the data schema is NXapm. In combination with + administrative metadata such as the attribute ``NeXus_version`` provided by :ref:`NXroot` this + specifies which version of NXapm the instance data in a NeXus/HDF5 file are compliant with. + - The fields ``run_number``, ``experiment_alias``, ``experiment_description`` and + the group ``userID`` provide concepts for storing organizational metadata that + contextualize the work within the research workflow and humans involved in this. + - The fields ``start_time``, ``end_time`` provide concepts for framing a temporal context for the research. + - The groups ``citeID``, ``noteID`` provide concepts for adding contextual details such as citations or notes + that are associated with the data, i.e. other artifacts that are deemed relevant when reporting about + a measurement or simulation. These groups are useful when NXapm is used as a serialization format for + technology-partner-agnostic archival of data and metadata that have been collected during a session with + an atom probe instrument. The terms run and session are understood as exact synonyms that refer to an + uninterrupted period of measurement. Resuming measurement on a specimen after an interruption is viewed + as a new run and the new data should not be appended to the previous run, but written to either a new NXentry, + or a new file. Removing the specimen from the instrument is an interruption. Changing evaporation conditions + while the specimen is remains in the analysis_chamber and resuming thereafter the measurement + is not considered as an interruption. It is a common strategy to probe the evaporation process for different + instrument parameters. Each individual collection should then though be stored in an own NXevent_data_apm + group. Parking the specimen to the buffer_chamber and resuming the measurement at a later stage is an interruption. + During a run, the microscope is used for a certain amount of time to characterize a single specimen. + - The groups ``sample`` and ``specimen`` provide concepts for storing metadata about the sample and the specimen, + i.e. the smaller part that was removed from the sample to be measured in the atom probe session. + The term "tip" in the context of atom probe research is considered jargon. + Specimen is an exact synonym for tip. + - The field ``operation_mode`` and group ``measurement`` provides concepts that + are useful for describing a measurement during a session with an atom probe or field-ion microscope. + This includes the chain of events of data and metadata that were collected during such a session. + - The group ``simulation`` provides concepts that are useful for describing a simulation of an + atom extraction, ionization, and ion trajectory simulation. Combined with ``measurement`` + this provides a data schema for defining a digital twin of the instrument and its setup. + - The groups ``consistent_rotations``, and ``NAMED_reference_frame`` provide concepts for + reporting coordinate systems (frames of reference) and rotation conventions that clarify how data + should be interpreted specifying the rotation of orientable objects in the microscope, its components, + or of crystals and crystal defects in the material analyzed. + - The group ``atom_probeID`` provides concepts for the computational workflows that were + used to convert raw detector data into reconstructed ion positions and documentation of + ranging definitions made. + - The group ``profiling`` provides concepts for reporting computational details such as + programs and libraries used, for documenting the libraries of virtual environments such as those used + by conda or python virtual environment, including details about the computing hardware used, and + documenting capabilities for performance analyses and benchmarking of the software or its parts. + + *Design choices:* + + Given that most atom probe instruments across the globe were built by AMETEK/Cameca and are delivered + with the AP Suite/IVAS software there is some homogeneity in how a measurement is performed and which data + artifacts and algorithms used for data processing. Complementary use of open-source software specifically for + the reconstruction, ranging, and later data processing stages contributes to a landscape of multiple tools in use. + Therefore, communication of atom probe research differs between user groups. This holds even more so true + for the sub community in atom probe which study physical mechanisms involved during ionization to the point that + here that almost each research work defines different simulation tools with different types of data artifacts. + + NXapm defines constraints on the existence and cardinality of concepts and its concept branches but seeks to + offer a compromise. The key design pattern followed is that most branches are made optional or at most recommended + but their child concepts are conditionally required. Thereby, NXapm can cover a variety of simple but also complex + use cases. An example of this parent-optional-but-childs-stronger-restricted design is the combination of the + optional group ``measurement`` with its required child ``measurement/instrument``: + Users which report simulations are not forced to document the instrument but users which have characterized + a specimen are motivated to report about the instrument. They are though not necessarily required to report all + the details of the instruments' components because the design pattern is applied recursively. + + *NXapm distinguishes and stores instance data based on how long they remain unchanged:* + + ``measurement`` provides two groups ``measurement/instrument`` and ``measurement/eventID``. + The first group is designed for storing metadata about the instrument that do not change over the course of the session. + Examples are the name of the technology partner who built the microscope or whether a laser or voltage pulser + and reflectron exists or not. The second group is designed for metadata and data that are collected during + the session with the instrument. These, are stored as instances of ``measurement/eventID``, + events that can be time-stamped individually. + Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose is to + store those specific state and settings of the instrument that was present during the collection of the event. + Thereby, changing conditions such as campaigns with different target detection rate can be stored. + + Noteworthy, such an approach of the atom probe detecting groups of events and storing these as groups has also + been in use in the proprietary software via CamecaRoot, a set of customized data structures and file formats that use + the CernRoot library. By virtue of design this reduces unnecessary repetition of metadata stored in the first group. + + ``atom_probeID`` offer classes for the each task relevant task in the data processing pipeline that converts raw detector + event data to calibrated mass-to-charge-state-ratio values and hit_position on the detector. These include + ``initial_specimen``, and ``final_specimen`` locations for storing images of the specimen prior/after the measurement as + considered best practice by AMETEK/Cameca, ``raw_data`` for delay-line timing data, ``hit_finding`` for details of the + hit finding algorithm, ``hit_spatial_filtering`` a process that filters hits of too low quality and those laying outside the about + to be computed reconstruction volume. Furthermore, group ``voltage_and_bowl`` offers a place for documenting calibrations + and processing non-linearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the + conversion from time-of-flight to mass-to-charge-state-ratio values. + + Finally, the groups ``reconstruction`` and ``ranging`` were designed to match and document the classical approaches how + from all the previous sources of input one can compute a reconstructed volume, and apply peak fitting routines on the + mass-to-charge-state-ratio histogram to label ions, i.e. range them for their isotopic identity. + Group ``atom_probeID/reconstruction/naive_discretization`` offers a standardized way to report simple + three-dimensional histograms. Group ``atom_probeID/ranging/peak_identification/ionID`` and its + complementing group ``atom_probeID/ranging/peak_identification/ionID/charge_state_analysis`` + solves the issue that the ranging definitions in classical file formats are not reported for always for their isotopic identity + and charge state. The field ``atom_probeID/ranging/peak_identification/iontypes`` provides a place for + storing a compact representation of the results of each ranging definition made at the level of each ion. + + *The compatibility of NXapm and NXem:** + + The design of NXapm mirrors that of :ref:`NXem`. This was an intentional choice to support the increasingly stronger connection between + these two materials characterization methods, especially in light of recent advances in the direct coupling of atom probe and + transmission electron microscopes and scanning transmission electron microscopes. +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. + n_ht: | + Number of hit qualities, the so-called hit types, distinguished. + n_dld: | + Number of delay-line-detector (DLD) wires of the detector. + n_bins: | + Number of bins used in the mass-to-charge-state-ratio spectrum. + p: | + Number of pulses collected in between start_time and end_time resolved by an + instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of + ions included in the reconstructed volume if the application definition is used + to store results of an already reconstructed dataset. + p_out: | + Number of pulses returned by the hit_finding algorithm. + Neither necessarily equal to p nor to n. + n: | + Number of ions spatially filtered from results of the hit_finding algorithm + from which an instance of a reconstructed volume has been generated. + These ions get new identifier assigned in the process, the so-called + evaporation_id. This identifier must not be confused with the pulse_id. + This value is typically smaller than both p and p_out. + m_r: | + Number of mass resolution values. +type: group +NXapm(NXobject): + (NXentry): + exists: ['min', '1', 'max', 'unbounded'] + definition(NX_CHAR): + \@version(NX_CHAR): + exists: optional + enumeration: [NXapm] + profiling(NXcs_profiling): + exists: optional + doc: | + The configuration of the software that was used to generate this NeXus file. + programID(NXprogram): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doc: | + A collection of all programs and libraries which are considered relevant + to understand with which software tools this NeXus file instance was + generated. Ideally, to enable a binary recreation from the input data. + + Examples include the name and version of the libraries used to write the + instance. Ideally, the software which writes these NXprogram instances + also includes the version of the set of NeXus classes i.e. the specific + set of base classes, application definitions, and contributed definitions + with which the here described concepts can be resolved. + + For the `pynxtools library `_ + which is used by the `NOMAD `_ + research data management system, it makes sense to store e.g. the GitHub + repository commit and respective submodule references used. + program(NX_CHAR): + \@version(NX_CHAR): + environment(NXcollection): + exists: recommended + doc: | + Programs and libraries representing the computational environment + (NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + program(NX_CHAR): + \@version(NX_CHAR): + run_number(NX_UINT): + exists: recommended + unit: NX_UNITLESS + doc: | + The identifier whereby the experiment is referred to in the control software. + + It is common practice in atom probe research to refer to a measurement on a single + specimen as a run. When working with AMETEK/Cameca instruments it is a common + practice also to store all data associated with such a run in files whose name + is composed from a prefix that details the type of instrument (e.g. R5076) followed + by the run_number. These filenames are often used as the specimen_name or + experiment_identifier. The terms run and session are understood as exact synonyms. + + For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, + or the instruments at GPM in Rouen, use the identifier which matches + best conceptually to the LEAP run number. + + The field does not have to be required, if the information is recoverable + in the dataset which for LEAP instruments is the case; provided these + RHIT or HITS files respectively are stored alongside a data artifact. + With NXapm the RHIT or HITS can be stored via NXnote in the + hit_finding algorithm section. + + As a destructive microscopy technique, a run can be performed only once. + It is possible, however, to interrupt a run and restart data acquisition + while still using the same specimen. In this case, each evaporation run + needs to be distinguished with different run numbers. + We follow this habit of most atom probe groups. Such interrupted runs + should be stored as individual :ref:`NXentry` instances in one NeXus file. + experiment_alias(NX_CHAR): + exists: optional + doc: | + Alias or short name which scientists can use to refer to this experiment. + experiment_description(NX_CHAR): + exists: optional + doc: | + Free-text description about the experiment. + + Users are strongly advised to parameterize the description of their experiment + by using respective groups and fields and base classes instead of writing prose + into the field. + start_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information + included when the atom probe session started. If the exact duration of + the measurement is not relevant, start_time only should be used. + + The start_time is required in order to ensure that at least one point in time + is provided for full temporal context to a measurement and simulation + when writing instance data using NXapm. Otherwise, the instance data + can not be sorted in order or even placed in a logical sequence to other + steps of the research workflow, which would disallow using functionalities + in research data management systems that rely on temporal context. + + Specifying start_time and end_time is useful for capturing more detailed + bookkeeping of the experiment. The user should be aware that even with + having both dates specified, it may not be possible to infer how long + the experiment took or for how long data were collected. + + More detailed timing data over the course of the experiment have to be + collected to compute this event chain during the experiment. For this + purpose the :ref:`NXevent_data_apm` instance should be used. + end_time(NX_DATE_TIME): + exists: recommended + doc: | + ISO 8601 time code with local time zone offset to UTC included + when the atom probe session ended. + + Writing the end_time can be a tricky in practice. If written at the start + of the experiment, it can only be an estimate. If written at the end, there + is the risk for having the computer crash or lose power. The absence of + end_time should not be interpreted as that the experiment was aborted. + Only, the field ``status`` should be used for communicating such abortion. + elapsed_time(NX_FLOAT): + exists: recommended + unit: NX_TIME + doc: | + How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime + citeID(NXcite): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doi(NX_CHAR): + noteID(NXnote): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + operation_mode(NX_CHAR): + doc: | + What type of atom probe experiment is performed to inform research data management + systems and allow filtering: + + * apt are experiments where the analysis_chamber has no imaging gas. + Experiments with LEAP instruments are typically with this operation_mode. + * fim are experiments where the analysis_chamber has an imaging gas, + which should be specified with the atmosphere in the analysis_chamber group. + * apt_fim should be used for combinations of the two imaging modes. + Few experiments of this type have been performed, as it can be detrimental + to LEAP systems (see `S. Katnagallu et al. `_). + enumeration: + open_enum: true + items: [apt, fim, apt_fim] + userID(NXuser): + exists: recommended + nameType: partial + identifierNAME(NX_CHAR): + nameType: partial + exists: recommended + \@type(NX_CHAR): + name(NX_CHAR): + exists: optional + sample(NXsample): + exists: recommended + doc: | + Description of the sample from which the specimen was prepared or + site-specifically cut out using e.g. a focused-ion beam instrument. + + In NXapm, a measurement is performed on a specimen. Since APM specimens + are very small, they are typically cut from a larger object with some + scientific significance, which NXapm refers to as a sample. + identifierNAME(NX_CHAR): + nameType: partial + exists: recommended + is_simulation(NX_BOOLEAN): + doc: | + False, if the sample is a real one. + True, if the sample is a virtual one. + alias(NX_CHAR): + doc: | + Given name/alias for the sample. + grain_diameter(NX_FLOAT): + exists: optional + unit: NX_LENGTH + doc: | + Qualitative information about the grain size, here specifically + described as the equivalent spherical diameter of an assumed + average grain size for the crystal ensemble. + + If the specimen does not contain many crystals average values + might be an unreliable descriptor. + + Reporting a grain size may be useful though as it allows + judging if specific features are expected to be found in the + detector hit map. + grain_diameter_errors(NX_FLOAT): + exists: optional + unit: NX_LENGTH + doc: | + Magnitude of the standard deviation of the grain_diameter. + heat_treatment_time(NX_FLOAT): + exists: optional + unit: NX_TIME + doc: | + An array of elapsed time, the independent axis, of a time-temperature curve. + + This field can be used in combination with heat_treatment_temperature and + heat_treatment_temperature_errors as well as heat_treatment_quenching_rate + and heat_treatment_quenching_rate_errors respectively. In this case, these fields + should also be stored as an array with the same dimensions as heat_treatment_time + to store the dependant axes of a time-temperature curve as well as its first derivative. + heat_treatment_temperature(NX_FLOAT): + exists: optional + unit: NX_TEMPERATURE + doc: | + If heat_treatment_time is absent, the temperature of the last heat treatment step + before quenching. + + Knowledge about this value can give an idea how the sample + was heat treated. However, if a documentation of the annealing + treatment as a function of time is available one should better + rely on this information and have it stored alongside the NeXus file. + + If heat_treatment_time is provided, the temperature. + Consult the docstring of heat_treatment_time. + heat_treatment_temperature_errors(NX_FLOAT): + exists: optional + unit: NX_TEMPERATURE + doc: | + Magnitude of the standard deviation of the heat_treatment_temperature. + + If heat_treatment_time is provided, the magnitude of the standard derivation of the + temperature. Consult the docstring of heat_treatment_time. + heat_treatment_quenching_rate(NX_FLOAT): + exists: optional + unit: NX_ANY + doc: | + If heat_treatment_time is absent, the rate of the last quenching step. + + Knowledge about this value can give an idea how the sample was heat treated. + However, there are many situations where one can imagine that the scalar value + for just the quenching rate is insufficient. + + If heat_treatment_time is provided, the first derivative of the time-temperature curve. + Consult the docstring of heat_treatment_time for further details. + heat_treatment_quenching_rate_errors(NX_FLOAT): + exists: optional + unit: NX_ANY + doc: | + Magnitude of the standard deviation of the heat_treatment_quenching_rate. + + If heat_treatment_time is provided, the magnitude of the standard deviation of + the first derivative of the time-temperature curve. + Consult the docstring of heat_treatment_time for further details. + description(NX_CHAR): + exists: optional + chemical_composition(NXchemical_composition): + exists: recommended + doc: | + The chemical composition of the sample. + + Typically, it is assumed that this more macroscopic composition is representative + for the material so that the composition of the typically substantially less + voluminous specimen probes from the more voluminous sample. + normalization(NX_CHAR): + ELEMENT(NXatom): + exists: ['min', '1', 'max', '118'] + nameType: any + chemical_symbol(NX_CHAR): + composition(NX_FLOAT): + composition_errors(NX_FLOAT): + exists: recommended + specimen(NXsample): + doc: | + Description of the specimen that was cut off from the sample. + + In atom probe jargon this is typically referred to as the tip. + identifierNAME(NX_CHAR): + nameType: partial + exists: recommended + is_simulation(NX_BOOLEAN): + doc: | + False, if the specimen is a real one. + True, if the specimen is a virtual one. + alias(NX_CHAR): + exists: recommended + doc: | + Given name or an alias. Better use identifierNAME and identifier_parent instead. + + A single NXentry should be used only for the characterization of a single specimen. + identifier_parent(NX_CHAR): + exists: recommended + doc: | + Identifier of the sample from which the specimen was cut or the string "n/a". + + The purpose of this field is to support functionalities for tracking sample + provenance via a research data management system. + preparation_date(NX_DATE_TIME): + exists: recommended + doc: | + ISO 8601 time code with local time zone offset to UTC information + when the specimen was prepared. + + Ideally, report the end of the preparation, i.e. the last known time + the measured specimen surface was actively prepared. Ideally, this + matches the last timestamp that is mentioned in the digital resource + pointed to by identifier_parent. + + Knowing when the specimen was exposed to e.g. specific atmosphere is + especially required for environmentally sensitive material such as + hydrogen charged specimens or experiments including tracers with a + short half time. + atom_types(NX_CHAR): + doc: | + List of comma-separated elements from the IUPAC periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by identifier_parent or walk through + eventually deeply nested groups in data instances. + description(NX_CHAR): + exists: optional + doc: | + Discouraged free-text field. + is_polycrystalline(NX_BOOLEAN): + exists: recommended + doc: | + True, if the specimen contains a grain or phase boundary. + False, if the specimen is a single crystal. + is_amorphous(NX_BOOLEAN): + exists: recommended + doc: | + True, if the specimen is amorphous. + False, if the specimen is not. + initial_radius(NX_FLOAT): + exists: recommended + unit: NX_LENGTH + doc: | + Ideally measured otherwise best elaborated guess of the initial radius of the + specimen. + shank_angle(NX_FLOAT): + exists: recommended + unit: NX_ANGLE + doc: | + Ideally measured, otherwise best estimate, of the initial shank angle. + + This is a measure of the specimen taper. + Define it in such a way that the base of the specimen is modelled + as a conical frustrum so that the shank angle is the smallest angle + between the specimen space z-axis and a vector on the lateral surface + of the cone. + consistent_rotations(NXparameters): + exists: recommended + doc: | + The conventions used when reporting crystal orientations. + We follow the best practices of the Material Science community + that are defined in reference ``_. + rotation_handedness(NX_CHAR): + doc: | + Convention how a positive rotation angle is defined when viewing + from the end of the rotation unit vector towards its origin. + This is in accordance with convention 2 of reference ``_. + + Counter_clockwise is equivalent to a right-handed choice. + Clockwise is equivalent to a left-handed choice. + enumeration: [counter_clockwise, clockwise] + rotation_convention(NX_CHAR): + doc: | + How are rotations interpreted into an orientation according to convention 3 + of reference ``_. + enumeration: [passive, active] + euler_angle_convention(NX_CHAR): + doc: | + How are Euler angles interpreted given that there are several choices e.g. zxz, xyz + according to convention 4 of reference ``_. + + The most frequently used convention in Materials Science is zxz, which is based on the work + of H.-J. Bunge but using other conventions is possible. Proper Euler angles are distinguished + from Tait-Bryan angles. + enumeration: [zxz, xyx, yzy, zyz, xzx, yxy, xyz, yzx, zxy, xzy, zyx, yxz] + axis_angle_convention(NX_CHAR): + doc: | + To which angular range is the rotation angle argument of an + axis-angle pair parameterization constrained according to + convention 5 of reference ``_. + enumeration: [rotation_angle_on_interval_zero_to_pi] + sign_convention(NX_CHAR): + doc: | + Which sign convention is followed when converting orientations + between different parametrizations/representations according + to convention 6 of reference ``_. + enumeration: [p_plus_one, p_minus_one] + NAMED_reference_frameID(NXcoordinate_system): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + doc: | + A coordinate system. Multiple instances require unique names. + + Several Euclidean coordinate systems (CS) are used in the field of atom probe: + + * World space; + a CS specifying a local coordinate system of the planet earth which + identifies into which direction gravity is pointing such that + the laboratory space CS can be rotated into this world CS. + * The laboratory space; + a CS specifying the room where the instrument is located in or + a physical landmark on the instrument, e.g. the direction of the + transfer rod where positive is the direction how the rod + has to be pushed during loading a specimen into the instrument. + In summary, this CS is defined by the chassis of the instrument. + Suggested name of the group ``laboratory_reference_frame``. + * The specimen space; + a CS affixed to either the base or the initial apex of the specimen, + whose z axis points towards the detector. + Suggested name of the group ``specimen_reference_frame``. + * The detector space; + a CS affixed to the detector plane whose xy plane is usually in the + detector and whose z axis points towards the specimen. + This is a distorted space with respect to the reconstructed ion + positions. + Suggested name of the group ``detector_reference_frame``. + * The reconstruction space; + a CS in which the reconstructed ion positions are defined. + The orientation depends on the analysis software used. + * Eventually further coordinate systems attached to the + flight path of individual ions might be defined. + Suggested name of the group ``reconstruction_reference_frame``. + + To achieve unique names, the prefix "NAMED" should be replaced to + with something derived from an alias for the coordinate system, + or the value of the "alias" field. + + Use the suffix _reference_frame when creating specific instances + of NXcoordinate_system e.g. laboratory_reference_frame, + reconstruction_reference_frame and so on and so forth. + + In atom probe microscopy a frequently used choice for the detector + space (CS) is discussed with the so-called detector space image + stack. This is a stack of two-dimensional histograms of detected ions + within a predefined evaporation identifier interval. Typically, the set of + ion evaporation sequence identifiers is grouped into chunks. + + For each chunk a histogram of the ion hit positions on the detector + is computed. This leaves the possibility for inconsistency between + the so-called detector space and the e.g. specimen space. + + To avoid these ambiguities, instances of :ref:`NXtransformations` should be used. + alias(NX_CHAR): + exists: optional + type(NX_CHAR): + origin(NX_CHAR): + exists: recommended + x(NX_NUMBER): + x_direction(NX_CHAR): + exists: recommended + y(NX_NUMBER): + y_direction(NX_CHAR): + exists: recommended + z(NX_NUMBER): + z_direction(NX_CHAR): + exists: recommended + measurement(NXapm_measurement): + exists: optional + status(NX_CHAR): + exists: recommended + quality(NX_CHAR): + exists: recommended + instrument(NXinstrument_apm): + type(NX_CHAR): + exists: recommended + location(NX_CHAR): + exists: recommended + flight_path(NX_FLOAT): + exists: recommended + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + reflectron(NXcomponent): + exists: optional + applied(NX_BOOLEAN): + local_electrode(NXelectromagnetic_lens): + exists: recommended + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + aperture_type(NX_CHAR): + exists: recommended + ion_detector(NXdetector): + exists: recommended + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + pulser(NXcomponent): + exists: recommended + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + sourceID(NXsource): + exists: ['min', '0', 'max', '2'] + nameType: partial + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + stage(NXmanipulator): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + analysis_chamber(NXcomponent): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + buffer_chamber(NXcomponent): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + load_lock_chamber(NXcomponent): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + getter_pump(NXpump): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + roughening_pump(NXpump): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + turbomolecular_pump(NXpump): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + eventID(NXevent_data_apm): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + start_time(NX_DATE_TIME): + exists: recommended + end_time(NX_DATE_TIME): + exists: recommended + instrument(NXinstrument_apm): + exists: recommended + reflectron(NXcomponent): + exists: recommended + voltage(NX_FLOAT): + local_electrode(NXelectromagnetic_lens): + exists: recommended + voltage(NX_FLOAT): + pulser(NXcomponent): + exists: recommended + pulse_mode(NX_CHAR): + pulse_frequency(NX_FLOAT): + pulse_fraction(NX_FLOAT): + pulse_voltage(NX_FLOAT): + exists: optional + dimensions: + rank: 1 + dim: (n,) + pulse_number(NX_UINT): + exists: optional + dimensions: + rank: 1 + dim: (n,) + standing_voltage(NX_FLOAT): + exists: optional + dimensions: + rank: 1 + dim: (n,) + sourceID(NXsource): + exists: ['min', '0', 'max', '2'] + nameType: partial + wavelength(NX_FLOAT): + exists: recommended + unit: NX_WAVELENGTH + power(NX_FLOAT): + unit: NX_POWER + pulse_energy(NX_FLOAT): + dimensions: + rank: 1 + dim: (n,) + stage(NXmanipulator): + temperature_sensor(NXsensor): + measurement(NX_CHAR): + value(NX_FLOAT): + analysis_chamber(NXcomponent): + pressure_sensor(NXsensor): + measurement(NX_CHAR): + value(NX_FLOAT): + control(NXparameters): + exists: recommended + evaporation_control(NX_CHAR): + target_detection_rate(NX_NUMBER): + simulation(NXapm_simulation): + exists: optional + atom_probeID(NXroi_process): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doc: | + A region-of-interest analyzed either during or after the session for which + specific processed data of the measured or simulated data are available. + + If a single instance is required the group should be named atom_probe. + If multiple groups are required these should be named atom_probe1, atom_probe2, + and so on and so forth. + initial_specimen(NXimage): + exists: recommended + doc: | + SEM or TEM image of the initial specimen taken before the measurement. + image_2d(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + real(NX_NUMBER): + axis_j(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_j,) + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_i,) + \@long_name(NX_CHAR): + final_specimen(NXimage): + exists: recommended + doc: | + SEM or TEM image of the final specimen taken after completion of the + measurement. + image_2d(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + real(NX_NUMBER): + axis_j(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_j,) + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_i,) + \@long_name(NX_CHAR): + raw_data(NXprocess): + exists: optional + doc: | + Document the control software that was used on the instrument with which raw data + were collected. + + For almost all atom probe instruments, the recorded raw data and metadata follow + proprietary semantics. Therefore, this group can currently often not be filled with + more than the control software and some pointing to digital artifacts (e.g. proprietary files) + that have been collected during the measurement in an effort to document as best as + possible all steps of an analysis workflow. + + The physical quantities measured in an atom probe experiment are time-of-flight and + tuples of arrival_time_pairs as a function of the event chain on the pulser. + From these tuples, hits are computed in a process called hit_finding. + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doc: | + The control software that was used for running the measurement. + + At least the main software should be reported. If this is the only program + to report name the group "program" and use its below fields program and + version to detail the version used. E.g. program AP Suite, version 6.3 + + It is recommended to report multiple programs though, i.e. also the libraries + and dependencies of the software. In the case of AP Suite/IVAS this can be used + to document the AP Suite GUI, LAS, CamecaRoot, and CernRoot versions. + In this case always name the program groups program1, program2, ... + with program one being AP Suite/IVAS. + + In the case of an open-source instrument, like P. Felfer's Oxcart or G. Schmitz's + M-TAP instruments, also use program1, program2, ... with program1 representing + the control software e.g. `M. Monajem and P. Felfer pyCCAPT `_. + Further instances (program2, ...) can be used to list the dependencies, the + python virtual environment. + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: recommended + doc: | + Possibility to point to files that contain raw data. + + Exemplar files that could be pointed to here when working with + AMETEK/Cameca instruments are the proprietary STR, RRAW, or HITS + files that AP Suite/IVAS generates. + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + number_of_dld_wires(NX_UINT): + exists: recommended + unit: NX_UNITLESS + doc: | + The number of delay-line-detector (DLD) wires present. + enumeration: [1, 2, 3] + dld_wire_names(NX_CHAR): + exists: optional + doc: | + Alias tuple, typical for the begin and the end of each DLD wire + of the detector. Order follows arrival_time_pairs. + + The order of the first dimension should match that of the + second dimension of the arrival_time_pairs field. + dimensions: + rank: 2 + dim: (n_dld, 2) + arrival_time_pairs(NX_NUMBER): + exists: optional + unit: NX_TIME + doc: | + Raw readings from the analog-to-digital-converter + timing circuits of the detector wires. + dimensions: + rank: 3 + dim: (p, n_dld, 2) + hit_finding(NXprocess): + exists: recommended + doc: | + The configuration of a hit finding algorithm and its output. + + Hit finding is the process of deciding which detector signals are significant + and assigning specific ions colliding with the detector + to each observed event. + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + config(NXnote): + exists: recommended + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + hit_positions(NX_NUMBER): + exists: recommended + unit: NX_LENGTH + doc: | + Evaluated ion impact coordinates on the detector. + Use the depends_on field to specify which reference + frame the positions are defined in. + dimensions: + rank: 2 + dim: (p_out, 2) + \@depends_on(NX_CHAR): + doc: | + Contains the path to an instance of NX_coordinate_system + in which the positions are defined. + total_event_golden(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + Number of events of type "golden" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventGolden + field of a CamecaRoot RHIT/HITS file. + total_event_incomplete(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + Number of events of type "incomplete" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventIncomplete + field of a CamecaRoot RHIT/HITS file. + total_event_multiple(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + Number of events of type "multiple" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventMultiple + field of a CamecaRoot RHIT/HITS file. + total_event_partials(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + Number of events of type "partials" when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventPartials + field of a CamecaRoot RHIT/HITS file. + total_event_record(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + Number of events when APSuite/IVAS was used as the + software with which the measurement was performed. + + The value can be extracted from the CRunHeader.fTotalEventRecords + field of a CamecaRoot RHIT/HITS file. + hit_quality_type(NX_CHAR): + exists: optional + doc: | + Hit quality is an integer that specifies which category/type a hit was assigned to. + This field lists the human-readable, possibly though proprietary types distinguished. + The indices of this array are used in hit_quality to encode hit_quality for each + pulse in a more efficient way than by repeating the string that is used for each + type as it is provided in this field. + + As an example, assume two types, "golden" and "partial", are distinguished. + If hit_quality_type stores the array "golden", "partial", the index 0 + in hit_quality identifies all those pulses of category "golden", + while the index 1 in hit_quality identifies all of category "partial". + dimensions: + rank: 1 + dim: (n_ht,) + hit_quality(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + Hit quality identifier for each pulse. + Identifier has to be within hit_quality_type. + dimensions: + rank: 1 + dim: (p_out,) + hit_multiplicity(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + The number of ions determined to have been collected on the same pulse. + These ions may hit different pixels, or even the same detector pixel. + The hit_multiplicity is not related to the makeup of the ions and should not be + confused with the number of atoms or elements that constitute a molecular ion. + dimensions: + rank: 1 + dim: (p_out,) + hit_spatial_filtering(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: optional + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + evaporation_id_offset(NX_INT): + unit: NX_UNITLESS + doc: | + Integer which defines the first evaporation_id. + Typically, this is either zero or one. + evaporation_id(NX_INT): + unit: NX_UNITLESS + doc: | + There are two possibilities to report evaporation_id values: + + If evaporation_id_offset is provided, the evaporation_id values are defined + by the sequence :math:`[evaporation\_id\_offset, evaporation\_id\_offset + n]` + with :math:`n` the number of ions in the reconstructed volume. + + Alternatively, evaporation_id_offset is not provided but instead a + a sequence of :math:`n` values is defined, these integer values + do not need to be sorted. + dimensions: + rank: 1 + dim: (n,) + hit_filter(NXcs_filter_boolean_mask): + exists: recommended + number_of_objects(NX_UINT): + bitdepth(NX_UINT): + mask(NX_UINT): + + # at this point the set of events p_out has been filtered down to n + voltage_and_bowl(NXprocess): + exists: recommended + doc: | + Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. + + The voltage-and-bowl correction is a data post-processing step to correct ion impact + positions for flight path differences, detector bias, and nonlinearities. + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: optional + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + config(NXparameters): + correction_peak(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + Reference mass-to-charge state ratio value + + For example 16 Da as mentioned by `T. Blum et al. `_ (page 371). + raw_tof(NX_FLOAT): + exists: recommended + doc: | + Raw time-of-flight data without corrections. + dimensions: + rank: 1 + dim: (n,) + tof_zero_estimate(NX_FLOAT): + exists: optional + unit: NX_TIME + doc: | + The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate + calibrated_tof(NX_FLOAT): + exists: recommended + doc: | + Calibrated time-of-flight. + dimensions: + rank: 1 + dim: (n,) + mass_to_charge_conversion(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: recommended + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + config(NXparameters): + mass_calibration(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + Mass calibration with unit peaks/interp. as mentioned by `T. Blum et al. + `_ (page 371). + mass_resolution(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + Inverse of the mass resolution :math:`\frac{M}{\Delta M}` as mentioned by `T. Blum et al. `_ (page 371). + + Multiple values can be reported but reporting each is only useful when stating also: + + * The full width at which :math:`{\Delta M}_{fw}` fraction of maximum this value was defined. + Examples are at tenth :math:`{\Delta M}_{10}` or at half maximum (FWHM). + Consequently, mass_resolution_fw should needs to be a vector of the same length + and using the same order like used for mass_resolution, i.e. the first mass resolution was + defined at the maximum as defined by the first value from mass_resolution_fw. + * The reference molecular ion e.g. :math:`^{16}{O_{2}}^{+}` + As many instances of mass_resolutionION should be used with instances + numbered starting from 1 up to the length of the mass_resolution vector. + dimensions: + rank: 1 + dim: (m_r,) + mass_resolution_fw(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + The full width at which :math:`{\Delta M}_{fw}` fraction of maximum this value was defined. + Examples are at tenth :math:`{\Delta M}_{10}` or at half maximum (FWHM). + Consequently, mass_resolution_fw should needs to be a vector of the same length + and using the same order like used for mass_resolution, i.e. the first mass resolution was + defined at the maximum as defined by the first value from mass_resolution_fw. + dimensions: + rank: 1 + dim: (m_r,) + mass_resolutionION(NXatom): + nameType: partial + exists: recommended + doc: | + The reference molecular ion e.g. :math:`^{16}{O_{2}}^{+}` + As many instances of mass_resolutionION should be used with instances + numbered starting from 1 up to the length of the mass_resolution vector. + nuclide_hash(NX_UINT): + exists: recommended + name(NX_CHAR): + mass_to_charge(NX_FLOAT): + dimensions: + rank: 1 + dim: (n,) + reconstruction(NXapm_reconstruction): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: recommended + doc: | + For LEAP and APSuite/IVAS-based analyses the root file which stores + the settings whereby an RHIT/HITS file can be used to regenerate the + reconstructed volume that is here referred to. + + The respective RHIT/HITS file should ideally be specified in the serialized + group of the hit_finding section of this application definition. + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + results(NXnote): + exists: recommended + doc: | + For LEAP and APSuite/IVAS-based analyses the resulting typically + file with the reconstructed positions and calibrated mass-to-charge- + state ratio values. + + For other data collection/analysis software the data artifact which comes + closest conceptually to AMETEK/Cameca's typical file formats. + + These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, + which should be stored alongside this record in the research data + management system. + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + config(NXparameters): + exists: recommended + voltage_filter_initial(NX_FLOAT): + exists: recommended + voltage_filter_final(NX_FLOAT): + exists: recommended + protocol_name(NX_CHAR): + exists: recommended + primary_element(NX_CHAR): + exists: recommended + efficiency(NX_FLOAT): + exists: recommended + flight_path(NX_FLOAT): + exists: recommended + evaporation_field(NX_CHAR): + exists: recommended + image_compression(NX_FLOAT): + exists: recommended + kfactor(NX_FLOAT): + exists: recommended + shank_angle(NX_FLOAT): + exists: recommended + ion_volume(NX_FLOAT): + exists: recommended + crystallographic_calibration(NX_CHAR): + exists: recommended + comment(NX_CHAR): + exists: recommended + reconstructed_positions(NX_FLOAT): + dimensions: + rank: 2 + dim: (n, 3) + naive_discretization(NXprocess): + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + (NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + dimensions: + rank: 3 + dim: (n_z, n_y, n_x) + axis_z(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_z,) + \@long_name(NX_CHAR): + axis_y(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_y,) + \@long_name(NX_CHAR): + axis_x(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_x,) + \@long_name(NX_CHAR): + volume(NX_FLOAT): + exists: recommended + field_of_view(NX_FLOAT): + exists: recommended + ranging(NXapm_ranging): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: recommended + doc: | + The respective ranging definitions file RNG/RRNG/ENV/HDF5. + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + mass_to_charge_distribution(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + min_mass_to_charge(NX_FLOAT): + max_mass_to_charge(NX_FLOAT): + n_mass_to_charge(NX_POSINT): + mass_spectrum(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_bins,) + \@long_name(NX_CHAR): + axis_mass_to_charge(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_bins,) + \@long_name(NX_CHAR): + background_quantification(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + background(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + (Out-of-sync, time-independent) background levels in ppm/ns + reported by e.g. APSuite/IVAS for LEAP systems. + mrp_value(NX_FLOAT): + exists: recommended + unit: NX_DIMENSIONLESS + doc: | + The mass-resolving power (MRP) value + + `D. Larson et al. `_ report Eq. D.8 in page 282: + + :math:`MRP = \frac{1}{2\delta t} \cdot \sqrt{\frac{m}{n}\frac{1}{2eV}L}`, + + with :math:`\delta t` representing the timing imprecision, :math:`\frac{m}{n}` the mass-to-charge state ratio, + :math:`e` the elementary charge, :math:`V` the potential difference, and :math:`L` the flight path length. + + Timing imprecision is caused by variations of flight path length and voltage, + the fact that the precision of electronics is finite and a spread of the + time-of-departure of individual ions is observed. + mrp_mass_to_charge(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + Mass-to-charge state ratio :math:`\frac{m}{n}` at which mrp_value was specified. + mrp_voltage(NX_FLOAT): + exists: recommended + unit: NX_VOLTAGE + doc: | + Potential difference :math:`V` at which mrp_value was specified. + mrp_flight_path_length(NX_FLOAT): + exists: recommended + unit: NX_LENGTH + doc: | + Flight path length :math:`L` at which mrp_value was specified. + peak_search(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + peakID(NXpeak): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + label(NX_CHAR): + exists: recommended + description(NX_CHAR): + exists: recommended + category(NX_CHAR): + exists: recommended + doc: | + Category for the peak offering a qualitative statement of the location of the peak + in light of limited mass-resolving power that is relevant for + composition quantification. See `D. Larson et al. (p172) `_ + for examples of each category: + + * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` + * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` + * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states + * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` + * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` + * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` + enumeration: [0, 1, 2, 3, 4, 5] + position(NX_NUMBER): + + # peak deconvolution(NXprocess): + peak_identification(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + number_of_ion_types(NX_UINT): + maximum_number_of_atoms_per_molecular_ion(NX_UINT): + ionID(NXatom): + nameType: partial + exists: ['min', '1', 'max', '256'] + doc: | + Ions that were ranged. + + The value zero is reserved for documenting that an ion was unranged. + Identifier for ranged ions need to start at 1 up to number_of_ion_types. + nuclide_hash(NX_UINT): + charge_state(NX_INT): + charge_state_analysis(NXapm_charge_state_analysis): + exists: optional + config(NXparameters): + nuclides(NX_UINT): + mass_to_charge_range(NX_FLOAT): + min_half_life(NX_FLOAT): + min_abundance(NX_FLOAT): + sacrifice_isotopic_uniqueness(NX_BOOLEAN): + charge_state(NX_INT): + nuclide_hash(NX_UINT): + mass(NX_FLOAT): + natural_abundance_product(NX_FLOAT): + shortest_half_life(NX_FLOAT): + mass_to_charge_range(NX_FLOAT): + nuclide_list(NX_UINT): + exists: recommended + name(NX_CHAR): + exists: recommended + iontypes(NX_UINT): + exists: recommended + unit: NX_UNITLESS + doc: | + The iontype identifier for each ion that was best matching; + stored in the order of the evaporation_id. + + The value zero is reserved for documenting that an ion was unranged. + Identifier for ranged ions need to start at 1 up to number_of_ion_types. + dimensions: + rank: 1 + dim: (n,) + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 1b00d2191b69e2bfe0c99007cdf2cd0e6215b63bf90f5f7f4940d5651953763a +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of hit qualities, the so-called hit types, distinguished. +# +# +# +# +# Number of delay-line-detector (DLD) wires of the detector. +# +# +# +# +# Number of bins used in the mass-to-charge-state-ratio spectrum. +# +# +# +# +# Number of pulses collected in between start_time and end_time resolved by an +# instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of +# ions included in the reconstructed volume if the application definition is used +# to store results of an already reconstructed dataset. +# +# +# +# +# Number of pulses returned by the hit_finding algorithm. +# Neither necessarily equal to p nor to n. +# +# +# +# +# Number of ions spatially filtered from results of the hit_finding algorithm +# from which an instance of a reconstructed volume has been generated. +# These ions get new identifier assigned in the process, the so-called +# evaporation_id. This identifier must not be confused with the pulse_id. +# This value is typically smaller than both p and p_out. +# +# +# +# +# Number of mass resolution values. +# +# +# +# +# Application definition for real or simulated atom probe and field-ion microscopy experiments. +# +# Atom probe tomography and field-ion microscopy are methods for characterizing materials +# through induced controlled extraction of individual atoms as ions and molecular ions from +# a sharp needle-shaped specimen. +# +# Offering isotopic and nanometer-scale resolution, atom probe data enable quantification of +# local chemical composition and computing of volumetric reconstructions which are models for +# the atomic architecture of the small specimen volume analyzed. These reconstructions provide +# input for characterization of atomic segregation at crystal defects. The term microstructural features +# is considered as a narrow synonym for crystal defects. +# +# The aim of the NXapm application definition is to provide a general yet specific enough +# solution to serialize artifacts for virtually all atom probe and field-ion microcopy experiments. +# +# Before summarizing the design of the base classes and the parts of the NXapm application definition, +# it is worthwhile to recall and distinguish concepts that are related to atom extraction +# events and the molecular ions that are frequently generated by the sequence of events: +# +# * An atom probe instrument uses laser or voltage pulsing events to trigger ion extraction events. +# * These ions are accelerated in an electric field towards a position-sensitive detector system. +# Physical events and corresponding signal on this detector is triggered by an ion hitting the detector. +# Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. +# * Note that only a part the specimen volume can be measured and finite detection efficiency means that +# not all atoms in the measured volume will be detected. Neutral atoms can escape detection. Some ions +# escape detection because they hit into walls of the analysis_chamber. +# +# Raw data are typically processed as follows: +# +# * Detector pulses and their timing are processed and discriminated into signal events of different quality levels. +# High quality events might be considered in further processing to identify the corresponding molecular ion +# and its original position in the reconstructed volume. +# * Signal calibration and filtering steps are applied to convert raw time-of-flight data to calibrated +# mass-to-charge state ratio values and obtain calibrated impact positions on the detector. +# * Ranging and identifying an ion that corresponds to each detector event. +# Isotopic abundance and theoretical models inform these ranging algorithms. +# * Finally, such selected ion impact positions and iontypes are used to compute a reconstructed volume of +# the specimen using backprojection algorithms. In effect, an atom probe measurement is a combination of +# a data acquisition and a data analysis workflow. +# +# Not only in AMETEK/Cameca's APSuite/IVAS software, which the majority of atom probers use, these concepts +# are well distinguished. However, the algorithms used to transform correlations between pulses and physical +# events into actual events, the so-called detector hits of ions, is a proprietary one. This algorithm is also +# referred to as the hit finding algorithm. +# +# Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting +# schema where the course of the specimen evaporation is documented such that quantities are a function of +# evaporation_id i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. +# That is the evaporation_id values take the role of an implicit time and course of the experiment given that +# ion extraction physically is a sequential process. +# +# This application definition includes fields that the atom probe community has decided to represent best practices +# for reporting atom probe measurements. Exemplar mapping tables are provided for documents that reported these +# best practices to translate technical term into concepts of the NXapm application definition. +# +# *The NeXus application definition NXapm defines a hierarchical data model with ten building blocks:* +# +# The data model represents a tree of concepts. The tree is constructed from groups of concepts representing +# the branches, together with fields and attributes representing leaves. NXapm is defined by composing and +# specializing base classes into the following ten categories: +# +# - The field ``definition`` specifies that the data schema is NXapm. In combination with +# administrative metadata such as the attribute ``NeXus_version`` provided by :ref:`NXroot` this +# specifies which version of NXapm the instance data in a NeXus/HDF5 file are compliant with. +# - The fields ``run_number``, ``experiment_alias``, ``experiment_description`` and +# the group ``userID`` provide concepts for storing organizational metadata that +# contextualize the work within the research workflow and humans involved in this. +# - The fields ``start_time``, ``end_time`` provide concepts for framing a temporal context for the research. +# - The groups ``citeID``, ``noteID`` provide concepts for adding contextual details such as citations or notes +# that are associated with the data, i.e. other artifacts that are deemed relevant when reporting about +# a measurement or simulation. These groups are useful when NXapm is used as a serialization format for +# technology-partner-agnostic archival of data and metadata that have been collected during a session with +# an atom probe instrument. The terms run and session are understood as exact synonyms that refer to an +# uninterrupted period of measurement. Resuming measurement on a specimen after an interruption is viewed +# as a new run and the new data should not be appended to the previous run, but written to either a new NXentry, +# or a new file. Removing the specimen from the instrument is an interruption. Changing evaporation conditions +# while the specimen is remains in the analysis_chamber and resuming thereafter the measurement +# is not considered as an interruption. It is a common strategy to probe the evaporation process for different +# instrument parameters. Each individual collection should then though be stored in an own NXevent_data_apm +# group. Parking the specimen to the buffer_chamber and resuming the measurement at a later stage is an interruption. +# During a run, the microscope is used for a certain amount of time to characterize a single specimen. +# - The groups ``sample`` and ``specimen`` provide concepts for storing metadata about the sample and the specimen, +# i.e. the smaller part that was removed from the sample to be measured in the atom probe session. +# The term "tip" in the context of atom probe research is considered jargon. +# Specimen is an exact synonym for tip. +# - The field ``operation_mode`` and group ``measurement`` provides concepts that +# are useful for describing a measurement during a session with an atom probe or field-ion microscope. +# This includes the chain of events of data and metadata that were collected during such a session. +# - The group ``simulation`` provides concepts that are useful for describing a simulation of an +# atom extraction, ionization, and ion trajectory simulation. Combined with ``measurement`` +# this provides a data schema for defining a digital twin of the instrument and its setup. +# - The groups ``consistent_rotations``, and ``NAMED_reference_frame`` provide concepts for +# reporting coordinate systems (frames of reference) and rotation conventions that clarify how data +# should be interpreted specifying the rotation of orientable objects in the microscope, its components, +# or of crystals and crystal defects in the material analyzed. +# - The group ``atom_probeID`` provides concepts for the computational workflows that were +# used to convert raw detector data into reconstructed ion positions and documentation of +# ranging definitions made. +# - The group ``profiling`` provides concepts for reporting computational details such as +# programs and libraries used, for documenting the libraries of virtual environments such as those used +# by conda or python virtual environment, including details about the computing hardware used, and +# documenting capabilities for performance analyses and benchmarking of the software or its parts. +# +# *Design choices:* +# +# Given that most atom probe instruments across the globe were built by AMETEK/Cameca and are delivered +# with the AP Suite/IVAS software there is some homogeneity in how a measurement is performed and which data +# artifacts and algorithms used for data processing. Complementary use of open-source software specifically for +# the reconstruction, ranging, and later data processing stages contributes to a landscape of multiple tools in use. +# Therefore, communication of atom probe research differs between user groups. This holds even more so true +# for the sub community in atom probe which study physical mechanisms involved during ionization to the point that +# here that almost each research work defines different simulation tools with different types of data artifacts. +# +# NXapm defines constraints on the existence and cardinality of concepts and its concept branches but seeks to +# offer a compromise. The key design pattern followed is that most branches are made optional or at most recommended +# but their child concepts are conditionally required. Thereby, NXapm can cover a variety of simple but also complex +# use cases. An example of this parent-optional-but-childs-stronger-restricted design is the combination of the +# optional group ``measurement`` with its required child ``measurement/instrument``: +# Users which report simulations are not forced to document the instrument but users which have characterized +# a specimen are motivated to report about the instrument. They are though not necessarily required to report all +# the details of the instruments' components because the design pattern is applied recursively. +# +# *NXapm distinguishes and stores instance data based on how long they remain unchanged:* +# +# ``measurement`` provides two groups ``measurement/instrument`` and ``measurement/eventID``. +# The first group is designed for storing metadata about the instrument that do not change over the course of the session. +# Examples are the name of the technology partner who built the microscope or whether a laser or voltage pulser +# and reflectron exists or not. The second group is designed for metadata and data that are collected during +# the session with the instrument. These, are stored as instances of ``measurement/eventID``, +# events that can be time-stamped individually. +# Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose is to +# store those specific state and settings of the instrument that was present during the collection of the event. +# Thereby, changing conditions such as campaigns with different target detection rate can be stored. +# +# Noteworthy, such an approach of the atom probe detecting groups of events and storing these as groups has also +# been in use in the proprietary software via CamecaRoot, a set of customized data structures and file formats that use +# the CernRoot library. By virtue of design this reduces unnecessary repetition of metadata stored in the first group. +# +# ``atom_probeID`` offer classes for the each task relevant task in the data processing pipeline that converts raw detector +# event data to calibrated mass-to-charge-state-ratio values and hit_position on the detector. These include +# ``initial_specimen``, and ``final_specimen`` locations for storing images of the specimen prior/after the measurement as +# considered best practice by AMETEK/Cameca, ``raw_data`` for delay-line timing data, ``hit_finding`` for details of the +# hit finding algorithm, ``hit_spatial_filtering`` a process that filters hits of too low quality and those laying outside the about +# to be computed reconstruction volume. Furthermore, group ``voltage_and_bowl`` offers a place for documenting calibrations +# and processing non-linearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the +# conversion from time-of-flight to mass-to-charge-state-ratio values. +# +# Finally, the groups ``reconstruction`` and ``ranging`` were designed to match and document the classical approaches how +# from all the previous sources of input one can compute a reconstructed volume, and apply peak fitting routines on the +# mass-to-charge-state-ratio histogram to label ions, i.e. range them for their isotopic identity. +# Group ``atom_probeID/reconstruction/naive_discretization`` offers a standardized way to report simple +# three-dimensional histograms. Group ``atom_probeID/ranging/peak_identification/ionID`` and its +# complementing group ``atom_probeID/ranging/peak_identification/ionID/charge_state_analysis`` +# solves the issue that the ranging definitions in classical file formats are not reported for always for their isotopic identity +# and charge state. The field ``atom_probeID/ranging/peak_identification/iontypes`` provides a place for +# storing a compact representation of the results of each ranging definition made at the level of each ion. +# +# *The compatibility of NXapm and NXem:** +# +# The design of NXapm mirrors that of :ref:`NXem`. This was an intentional choice to support the increasingly stronger connection between +# these two materials characterization methods, especially in light of recent advances in the direct coupling of atom probe and +# transmission electron microscopes and scanning transmission electron microscopes. +# +# +# +# +# +# +# +# +# +# +# The configuration of the software that was used to generate this NeXus file. +# +# +# +# A collection of all programs and libraries which are considered relevant +# to understand with which software tools this NeXus file instance was +# generated. Ideally, to enable a binary recreation from the input data. +# +# Examples include the name and version of the libraries used to write the +# instance. Ideally, the software which writes these NXprogram instances +# also includes the version of the set of NeXus classes i.e. the specific +# set of base classes, application definitions, and contributed definitions +# with which the here described concepts can be resolved. +# +# For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ +# which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ +# research data management system, it makes sense to store e.g. the GitHub +# repository commit and respective submodule references used. +# +# +# +# +# +# +# +# Programs and libraries representing the computational environment +# +# +# +# +# +# +# +# +# +# +# The identifier whereby the experiment is referred to in the control software. +# +# It is common practice in atom probe research to refer to a measurement on a single +# specimen as a run. When working with AMETEK/Cameca instruments it is a common +# practice also to store all data associated with such a run in files whose name +# is composed from a prefix that details the type of instrument (e.g. R5076) followed +# by the run_number. These filenames are often used as the specimen_name or +# experiment_identifier. The terms run and session are understood as exact synonyms. +# +# For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, +# or the instruments at GPM in Rouen, use the identifier which matches +# best conceptually to the LEAP run number. +# +# The field does not have to be required, if the information is recoverable +# in the dataset which for LEAP instruments is the case; provided these +# RHIT or HITS files respectively are stored alongside a data artifact. +# With NXapm the RHIT or HITS can be stored via NXnote in the +# hit_finding algorithm section. +# +# As a destructive microscopy technique, a run can be performed only once. +# It is possible, however, to interrupt a run and restart data acquisition +# while still using the same specimen. In this case, each evaporation run +# needs to be distinguished with different run numbers. +# We follow this habit of most atom probe groups. Such interrupted runs +# should be stored as individual :ref:`NXentry` instances in one NeXus file. +# +# +# +# +# Alias or short name which scientists can use to refer to this experiment. +# +# +# +# +# Free-text description about the experiment. +# +# Users are strongly advised to parameterize the description of their experiment +# by using respective groups and fields and base classes instead of writing prose +# into the field. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# included when the atom probe session started. If the exact duration of +# the measurement is not relevant, start_time only should be used. +# +# The start_time is required in order to ensure that at least one point in time +# is provided for full temporal context to a measurement and simulation +# when writing instance data using NXapm. Otherwise, the instance data +# can not be sorted in order or even placed in a logical sequence to other +# steps of the research workflow, which would disallow using functionalities +# in research data management systems that rely on temporal context. +# +# Specifying start_time and end_time is useful for capturing more detailed +# bookkeeping of the experiment. The user should be aware that even with +# having both dates specified, it may not be possible to infer how long +# the experiment took or for how long data were collected. +# +# More detailed timing data over the course of the experiment have to be +# collected to compute this event chain during the experiment. For this +# purpose the :ref:`NXevent_data_apm` instance should be used. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC included +# when the atom probe session ended. +# +# Writing the end_time can be a tricky in practice. If written at the start +# of the experiment, it can only be an estimate. If written at the end, there +# is the risk for having the computer crash or lose power. The absence of +# end_time should not be interpreted as that the experiment was aborted. +# Only, the field ``status`` should be used for communicating such abortion. +# +# +# +# +# How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime +# +# +# +# +# +# +# +# +# +# +# +# +# +# What type of atom probe experiment is performed to inform research data management +# systems and allow filtering: +# +# * apt are experiments where the analysis_chamber has no imaging gas. +# Experiments with LEAP instruments are typically with this operation_mode. +# * fim are experiments where the analysis_chamber has an imaging gas, +# which should be specified with the atmosphere in the analysis_chamber group. +# * apt_fim should be used for combinations of the two imaging modes. +# Few experiments of this type have been performed, as it can be detrimental +# to LEAP systems (see `S. Katnagallu et al. <https://doi.org/10.1017/S1431927621012381>`_). +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Description of the sample from which the specimen was prepared or +# site-specifically cut out using e.g. a focused-ion beam instrument. +# +# In NXapm, a measurement is performed on a specimen. Since APM specimens +# are very small, they are typically cut from a larger object with some +# scientific significance, which NXapm refers to as a sample. +# +# +# +# +# False, if the sample is a real one. +# True, if the sample is a virtual one. +# +# +# +# +# Given name/alias for the sample. +# +# +# +# +# Qualitative information about the grain size, here specifically +# described as the equivalent spherical diameter of an assumed +# average grain size for the crystal ensemble. +# +# If the specimen does not contain many crystals average values +# might be an unreliable descriptor. +# +# Reporting a grain size may be useful though as it allows +# judging if specific features are expected to be found in the +# detector hit map. +# +# +# +# +# Magnitude of the standard deviation of the grain_diameter. +# +# +# +# +# An array of elapsed time, the independent axis, of a time-temperature curve. +# +# This field can be used in combination with heat_treatment_temperature and +# heat_treatment_temperature_errors as well as heat_treatment_quenching_rate +# and heat_treatment_quenching_rate_errors respectively. In this case, these fields +# should also be stored as an array with the same dimensions as heat_treatment_time +# to store the dependant axes of a time-temperature curve as well as its first derivative. +# +# +# +# +# If heat_treatment_time is absent, the temperature of the last heat treatment step +# before quenching. +# +# Knowledge about this value can give an idea how the sample +# was heat treated. However, if a documentation of the annealing +# treatment as a function of time is available one should better +# rely on this information and have it stored alongside the NeXus file. +# +# If heat_treatment_time is provided, the temperature. +# Consult the docstring of heat_treatment_time. +# +# +# +# +# Magnitude of the standard deviation of the heat_treatment_temperature. +# +# If heat_treatment_time is provided, the magnitude of the standard derivation of the +# temperature. Consult the docstring of heat_treatment_time. +# +# +# +# +# If heat_treatment_time is absent, the rate of the last quenching step. +# +# Knowledge about this value can give an idea how the sample was heat treated. +# However, there are many situations where one can imagine that the scalar value +# for just the quenching rate is insufficient. +# +# If heat_treatment_time is provided, the first derivative of the time-temperature curve. +# Consult the docstring of heat_treatment_time for further details. +# +# +# +# +# Magnitude of the standard deviation of the heat_treatment_quenching_rate. +# +# If heat_treatment_time is provided, the magnitude of the standard deviation of +# the first derivative of the time-temperature curve. +# Consult the docstring of heat_treatment_time for further details. +# +# +# +# +# +# The chemical composition of the sample. +# +# Typically, it is assumed that this more macroscopic composition is representative +# for the material so that the composition of the typically substantially less +# voluminous specimen probes from the more voluminous sample. +# +# +# +# +# +# +# +# +# +# +# +# Description of the specimen that was cut off from the sample. +# +# In atom probe jargon this is typically referred to as the tip. +# +# +# +# +# False, if the specimen is a real one. +# True, if the specimen is a virtual one. +# +# +# +# +# Given name or an alias. Better use identifierNAME and identifier_parent instead. +# +# A single NXentry should be used only for the characterization of a single specimen. +# +# +# +# +# Identifier of the sample from which the specimen was cut or the string "n/a". +# +# The purpose of this field is to support functionalities for tracking sample +# provenance via a research data management system. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# when the specimen was prepared. +# +# Ideally, report the end of the preparation, i.e. the last known time +# the measured specimen surface was actively prepared. Ideally, this +# matches the last timestamp that is mentioned in the digital resource +# pointed to by identifier_parent. +# +# Knowing when the specimen was exposed to e.g. specific atmosphere is +# especially required for environmentally sensitive material such as +# hydrogen charged specimens or experiments including tracers with a +# short half time. +# +# +# +# +# List of comma-separated elements from the IUPAC periodic table that are +# contained in the specimen. If the specimen substance has multiple +# components, all elements from each component must be included in +# `atom_types`. +# +# The purpose of the field is to offer research data management systems an +# opportunity to parse the relevant elements without having to interpret +# these from the resources pointed to by identifier_parent or walk through +# eventually deeply nested groups in data instances. +# +# +# +# +# Discouraged free-text field. +# +# +# +# +# True, if the specimen contains a grain or phase boundary. +# False, if the specimen is a single crystal. +# +# +# +# +# True, if the specimen is amorphous. +# False, if the specimen is not. +# +# +# +# +# Ideally measured otherwise best elaborated guess of the initial radius of the +# specimen. +# +# +# +# +# Ideally measured, otherwise best estimate, of the initial shank angle. +# +# This is a measure of the specimen taper. +# Define it in such a way that the base of the specimen is modelled +# as a conical frustrum so that the shank angle is the smallest angle +# between the specimen space z-axis and a vector on the lateral surface +# of the cone. +# +# +# +# +# +# The conventions used when reporting crystal orientations. +# We follow the best practices of the Material Science community +# that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# Convention how a positive rotation angle is defined when viewing +# from the end of the rotation unit vector towards its origin. +# This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# Counter_clockwise is equivalent to a right-handed choice. +# Clockwise is equivalent to a left-handed choice. +# +# +# +# +# +# +# +# +# How are rotations interpreted into an orientation according to convention 3 +# of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# +# +# +# +# +# How are Euler angles interpreted given that there are several choices e.g. zxz, xyz +# according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# The most frequently used convention in Materials Science is zxz, which is based on the work +# of H.-J. Bunge but using other conventions is possible. Proper Euler angles are distinguished +# from Tait-Bryan angles. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# To which angular range is the rotation angle argument of an +# axis-angle pair parameterization constrained according to +# convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# +# +# +# +# Which sign convention is followed when converting orientations +# between different parametrizations/representations according +# to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# +# +# +# +# +# +# A coordinate system. Multiple instances require unique names. +# +# Several Euclidean coordinate systems (CS) are used in the field of atom probe: +# +# * World space; +# a CS specifying a local coordinate system of the planet earth which +# identifies into which direction gravity is pointing such that +# the laboratory space CS can be rotated into this world CS. +# * The laboratory space; +# a CS specifying the room where the instrument is located in or +# a physical landmark on the instrument, e.g. the direction of the +# transfer rod where positive is the direction how the rod +# has to be pushed during loading a specimen into the instrument. +# In summary, this CS is defined by the chassis of the instrument. +# Suggested name of the group ``laboratory_reference_frame``. +# * The specimen space; +# a CS affixed to either the base or the initial apex of the specimen, +# whose z axis points towards the detector. +# Suggested name of the group ``specimen_reference_frame``. +# * The detector space; +# a CS affixed to the detector plane whose xy plane is usually in the +# detector and whose z axis points towards the specimen. +# This is a distorted space with respect to the reconstructed ion +# positions. +# Suggested name of the group ``detector_reference_frame``. +# * The reconstruction space; +# a CS in which the reconstructed ion positions are defined. +# The orientation depends on the analysis software used. +# * Eventually further coordinate systems attached to the +# flight path of individual ions might be defined. +# Suggested name of the group ``reconstruction_reference_frame``. +# +# To achieve unique names, the prefix "NAMED" should be replaced to +# with something derived from an alias for the coordinate system, +# or the value of the "alias" field. +# +# Use the suffix _reference_frame when creating specific instances +# of NXcoordinate_system e.g. laboratory_reference_frame, +# reconstruction_reference_frame and so on and so forth. +# +# In atom probe microscopy a frequently used choice for the detector +# space (CS) is discussed with the so-called detector space image +# stack. This is a stack of two-dimensional histograms of detected ions +# within a predefined evaporation identifier interval. Typically, the set of +# ion evaporation sequence identifiers is grouped into chunks. +# +# For each chunk a histogram of the ion hit positions on the detector +# is computed. This leaves the possibility for inconsistency between +# the so-called detector space and the e.g. specimen space. +# +# To avoid these ambiguities, instances of :ref:`NXtransformations` should be used. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# A region-of-interest analyzed either during or after the session for which +# specific processed data of the measured or simulated data are available. +# +# If a single instance is required the group should be named atom_probe. +# If multiple groups are required these should be named atom_probe1, atom_probe2, +# and so on and so forth. +# +# +# +# SEM or TEM image of the initial specimen taken before the measurement. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# SEM or TEM image of the final specimen taken after completion of the +# measurement. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Document the control software that was used on the instrument with which raw data +# were collected. +# +# For almost all atom probe instruments, the recorded raw data and metadata follow +# proprietary semantics. Therefore, this group can currently often not be filled with +# more than the control software and some pointing to digital artifacts (e.g. proprietary files) +# that have been collected during the measurement in an effort to document as best as +# possible all steps of an analysis workflow. +# +# The physical quantities measured in an atom probe experiment are time-of-flight and +# tuples of arrival_time_pairs as a function of the event chain on the pulser. +# From these tuples, hits are computed in a process called hit_finding. +# +# +# +# +# The control software that was used for running the measurement. +# +# At least the main software should be reported. If this is the only program +# to report name the group "program" and use its below fields program and +# version to detail the version used. E.g. program AP Suite, version 6.3 +# +# It is recommended to report multiple programs though, i.e. also the libraries +# and dependencies of the software. In the case of AP Suite/IVAS this can be used +# to document the AP Suite GUI, LAS, CamecaRoot, and CernRoot versions. +# In this case always name the program groups program1, program2, ... +# with program one being AP Suite/IVAS. +# +# In the case of an open-source instrument, like P. Felfer's Oxcart or G. Schmitz's +# M-TAP instruments, also use program1, program2, ... with program1 representing +# the control software e.g. `M. Monajem and P. Felfer pyCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_. +# Further instances (program2, ...) can be used to list the dependencies, the +# python virtual environment. +# +# +# +# +# +# +# +# Possibility to point to files that contain raw data. +# +# Exemplar files that could be pointed to here when working with +# AMETEK/Cameca instruments are the proprietary STR, RRAW, or HITS +# files that AP Suite/IVAS generates. +# +# +# +# +# +# +# +# +# The number of delay-line-detector (DLD) wires present. +# +# +# +# +# +# +# +# +# +# Alias tuple, typical for the begin and the end of each DLD wire +# of the detector. Order follows arrival_time_pairs. +# +# The order of the first dimension should match that of the +# second dimension of the arrival_time_pairs field. +# +# +# +# +# +# +# +# +# Raw readings from the analog-to-digital-converter +# timing circuits of the detector wires. +# +# +# +# +# +# +# +# +# +# +# The configuration of a hit finding algorithm and its output. +# +# Hit finding is the process of deciding which detector signals are significant +# and assigning specific ions colliding with the detector +# to each observed event. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Evaluated ion impact coordinates on the detector. +# Use the depends_on field to specify which reference +# frame the positions are defined in. +# +# +# +# +# +# +# +# Contains the path to an instance of NX_coordinate_system +# in which the positions are defined. +# +# +# +# +# +# Number of events of type "golden" when APSuite/IVAS was used as the +# software with which the measurement was performed. +# +# The value can be extracted from the CRunHeader.fTotalEventGolden +# field of a CamecaRoot RHIT/HITS file. +# +# +# +# +# Number of events of type "incomplete" when APSuite/IVAS was used as the +# software with which the measurement was performed. +# +# The value can be extracted from the CRunHeader.fTotalEventIncomplete +# field of a CamecaRoot RHIT/HITS file. +# +# +# +# +# Number of events of type "multiple" when APSuite/IVAS was used as the +# software with which the measurement was performed. +# +# The value can be extracted from the CRunHeader.fTotalEventMultiple +# field of a CamecaRoot RHIT/HITS file. +# +# +# +# +# Number of events of type "partials" when APSuite/IVAS was used as the +# software with which the measurement was performed. +# +# The value can be extracted from the CRunHeader.fTotalEventPartials +# field of a CamecaRoot RHIT/HITS file. +# +# +# +# +# Number of events when APSuite/IVAS was used as the +# software with which the measurement was performed. +# +# The value can be extracted from the CRunHeader.fTotalEventRecords +# field of a CamecaRoot RHIT/HITS file. +# +# +# +# +# Hit quality is an integer that specifies which category/type a hit was assigned to. +# This field lists the human-readable, possibly though proprietary types distinguished. +# The indices of this array are used in hit_quality to encode hit_quality for each +# pulse in a more efficient way than by repeating the string that is used for each +# type as it is provided in this field. +# +# As an example, assume two types, "golden" and "partial", are distinguished. +# If hit_quality_type stores the array "golden", "partial", the index 0 +# in hit_quality identifies all those pulses of category "golden", +# while the index 1 in hit_quality identifies all of category "partial". +# +# +# +# +# +# +# +# Hit quality identifier for each pulse. +# Identifier has to be within hit_quality_type. +# +# +# +# +# +# +# +# The number of ions determined to have been collected on the same pulse. +# These ions may hit different pixels, or even the same detector pixel. +# The hit_multiplicity is not related to the makeup of the ions and should not be +# confused with the number of atoms or elements that constitute a molecular ion. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Integer which defines the first evaporation_id. +# Typically, this is either zero or one. +# +# +# +# +# There are two possibilities to report evaporation_id values: +# +# If evaporation_id_offset is provided, the evaporation_id values are defined +# by the sequence :math:`[evaporation\_id\_offset, evaporation\_id\_offset + n]` +# with :math:`n` the number of ions in the reconstructed volume. +# +# Alternatively, evaporation_id_offset is not provided but instead a +# a sequence of :math:`n` values is defined, these integer values +# do not need to be sorted. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. +# +# The voltage-and-bowl correction is a data post-processing step to correct ion impact +# positions for flight path differences, detector bias, and nonlinearities. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Reference mass-to-charge state ratio value +# +# For example 16 Da as mentioned by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). +# +# +# +# +# +# Raw time-of-flight data without corrections. +# +# +# +# +# +# +# +# The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate +# +# +# +# +# Calibrated time-of-flight. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Mass calibration with unit peaks/interp. as mentioned by `T. Blum et al. +# <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). +# +# +# +# +# Inverse of the mass resolution :math:`\frac{M}{\Delta M}` as mentioned by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). +# +# Multiple values can be reported but reporting each is only useful when stating also: +# +# * The full width at which :math:`{\Delta M}_{fw}` fraction of maximum this value was defined. +# Examples are at tenth :math:`{\Delta M}_{10}` or at half maximum (FWHM). +# Consequently, mass_resolution_fw should needs to be a vector of the same length +# and using the same order like used for mass_resolution, i.e. the first mass resolution was +# defined at the maximum as defined by the first value from mass_resolution_fw. +# * The reference molecular ion e.g. :math:`^{16}{O_{2}}^{+}` +# As many instances of mass_resolutionION should be used with instances +# numbered starting from 1 up to the length of the mass_resolution vector. +# +# +# +# +# +# +# +# The full width at which :math:`{\Delta M}_{fw}` fraction of maximum this value was defined. +# Examples are at tenth :math:`{\Delta M}_{10}` or at half maximum (FWHM). +# Consequently, mass_resolution_fw should needs to be a vector of the same length +# and using the same order like used for mass_resolution, i.e. the first mass resolution was +# defined at the maximum as defined by the first value from mass_resolution_fw. +# +# +# +# +# +# +# +# The reference molecular ion e.g. :math:`^{16}{O_{2}}^{+}` +# As many instances of mass_resolutionION should be used with instances +# numbered starting from 1 up to the length of the mass_resolution vector. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# For LEAP and APSuite/IVAS-based analyses the root file which stores +# the settings whereby an RHIT/HITS file can be used to regenerate the +# reconstructed volume that is here referred to. +# +# The respective RHIT/HITS file should ideally be specified in the serialized +# group of the hit_finding section of this application definition. +# +# +# +# +# +# +# +# +# For LEAP and APSuite/IVAS-based analyses the resulting typically +# file with the reconstructed positions and calibrated mass-to-charge- +# state ratio values. +# +# For other data collection/analysis software the data artifact which comes +# closest conceptually to AMETEK/Cameca's typical file formats. +# +# These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, +# which should be stored alongside this record in the research data +# management system. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# The respective ranging definitions file RNG/RRNG/ENV/HDF5. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# (Out-of-sync, time-independent) background levels in ppm/ns +# reported by e.g. APSuite/IVAS for LEAP systems. +# +# +# +# +# The mass-resolving power (MRP) value +# +# `D. Larson et al. <https://doi.org/10.1007/978-1-4614-8721-0>`_ report Eq. D.8 in page 282: +# +# :math:`MRP = \frac{1}{2\delta t} \cdot \sqrt{\frac{m}{n}\frac{1}{2eV}L}`, +# +# with :math:`\delta t` representing the timing imprecision, :math:`\frac{m}{n}` the mass-to-charge state ratio, +# :math:`e` the elementary charge, :math:`V` the potential difference, and :math:`L` the flight path length. +# +# Timing imprecision is caused by variations of flight path length and voltage, +# the fact that the precision of electronics is finite and a spread of the +# time-of-departure of individual ions is observed. +# +# +# +# +# Mass-to-charge state ratio :math:`\frac{m}{n}` at which mrp_value was specified. +# +# +# +# +# Potential difference :math:`V` at which mrp_value was specified. +# +# +# +# +# Flight path length :math:`L` at which mrp_value was specified. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Category for the peak offering a qualitative statement of the location of the peak +# in light of limited mass-resolving power that is relevant for +# composition quantification. See `D. Larson et al. (p172) <https://doi.org/10.1007/978-1-4614-8721-0>`_ +# for examples of each category: +# +# * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` +# * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` +# * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states +# * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` +# * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` +# * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Ions that were ranged. +# +# The value zero is reserved for documenting that an ion was unranged. +# Identifier for ranged ions need to start at 1 up to number_of_ion_types. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# The iontype identifier for each ion that was best matching; +# stored in the order of the evaporation_id. +# +# The value zero is reserved for documenting that an ion was unranged. +# Identifier for ranged ions need to start at 1 up to number_of_ion_types. +# +# +# +# +# +# +# +# +# +# diff --git a/applications/nyaml/NXem.yaml b/applications/nyaml/NXem.yaml new file mode 100644 index 0000000000..914509a7e3 --- /dev/null +++ b/applications/nyaml/NXem.yaml @@ -0,0 +1,3583 @@ +category: application +doc: | + Application definition for normalized representation of electron microscopy research. + + This application definition is a comprehensive, general description for the + standardization of data and metadata collected using electron microscopy. + + NXem is designed to be used for documenting experiments or computer simulations in which + controlled electron beams are used to study electron-beam matter interactions, to simulate this, + to explore physical mechanisms and phenomena, or to characterize materials. + + *The NeXus application definition NXem defines a hierarchical data model with ten building blocks:* + + The data model represents a tree of concepts. The tree is constructed from groups of concepts + representing the branches surplus fields and attributes representing leafs. + + *NXem an introduction for typical use cases in material characterization and simulation:* + + Transmission electron microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) + Scanning Electron Microscopy (SEM) + Scanning Electron Microscopy combined a Focused-Ion Beam (SEM/FIB) + + *A deeper dive into the branches of NXem:* + + NXem is constructed from composing and specializing base classes into the following ten categories: + + - The field ``definition`` specifies that the data schema is NXem. In combination with + administrative metadata such as the ``NeXus_version`` provided by :ref:`NXroot` this + specifies which version of NXem the instance data in a NeXus/HDF5 file are compliant with. + - The fields ``identifier_experiment``, ``experiment_alias``, ``experiment_description`` and + the group ``userID`` provide concepts for storing organizational metadata that + contextualize the work within the research workflow and humans involved in this. + - The fields ``start_time``, ``end_time`` provide concepts for framing a temporal context for the research. + - The groups ``citeID``, ``noteID`` provide concepts for adding contextual details such as citations + that are associated with or notes, i.e. other artifacts that are deemed relevant when reporting about a measurement + or simulation. These groups are useful when NXem is used as a serialization format for technology-partner-agnostic + archival of data and metadata that have been collected during a session with an electron microscope or when a + simulation was performed. + - The group ``sampleID`` provides concepts for storing metadata about the sample that was + characterized or simulated during the session. + - The group ``measurement`` provides concepts that are useful for describing a measurement + during a session with an electron microscope. This includes the chain of events of data and metadata that + were collected during such a session. + - The group``simulation`` provides concepts that are useful for describing a simulation of an + electron beam that interacts with matter. Combined with ``measurement`` this provides a data schema + for defining a digital twin of the microscope and its optical setup. + - The groups ``consistent_rotations``, ``NAMED_reference_frame`` provide concepts for + reporting coordinate systems (frames of reference) and rotation conventions that clarify how data + should be interpreted specifying the rotation of orientable objects in the microscope, its components, + or of crystals and crystal defects in the material analyzed. These metadata support interpretation for + downstream or on-the-fly data analyses which electron microscopes typically nowadays perform + during a session. Examples are the indexing of diffraction patterns, image analysis in general, or + analyses of the chemical composition. + - The group ``roiID`` provides concepts for reporting several domain- and technique-specific + configuration parameter and results of data processing steps that were applied. + - The group ``profiling`` provides concepts for reporting computational details such as + programs and libraries used, for documenting the libraries of virtual environments such as those used + by conda or python virtual environment, including details about the computing hardware used, and + documenting capabilities for performance analyses and benchmarking of the software or its parts. + + *Design choices:* + + Specific details about how an electron microscope was used and eventually its configuration modified differ + between user groups. This holds also true for computer simulations of electron-beam matter interaction. + Different peer groups in different sub-domains in electron microscopy consider different data and metadata + relevant. NXem defines constraints on the existence and cardinality of concepts and its concept branches + but seeks to offer a compromise. The key design pattern followed is that most branches are made optional + or at most recommended but their child concepts conditional required. Thereby, NXem can cover a variety + of simple but also complex use cases. An example of this parent-optional-but-childs-stronger-restricted design + is the combination of the optional group ``measurement`` with its required child + ``measurement/instrument``: Users which report simulations are not forced to document the instrument + but users which have characterized a sample are motivated to report about the instrument. They are though not + necessarily required to report all the details of the instruments' components because the design pattern is-used + applied recursively. + + *Inclusive design, one schema for scanning, focused-ion beam, and transmission electron microscopes:* + + Contrary to many other proposals of a data schema for electron microscopy, NXem seeks to highlight the similarity + of the three fundamental types of electron microscopes that are nowadays used most routinely in academia and + industry: An electron microscope is a beamline that provides a controlled beam of electrons combined with eventually + beams of other particles (ions) to investigate electron/ion(-beam) matter interaction. + This design of per-particle-type concept branches is realized in the base classes ``NXebeam_column`` and ``NXibeam_column``. + These provide concepts for reporting the technical components that are typically used for generating a controllable + (and typically scanning) beam of particles such as electrons or ions. + + Focused-ion beam capabilities are modelled by adding an optional group ``measurement/instrument/ibeam_column``. + We foresee that this design is beneficial also in the future when research should be documented where photon-electron + interactions via an electron microscope are combined. The current proposal though does not include such a + ``NXpbeam_column`` base class that could be used for photon-/light-beam, i.e. laser plus optical + beam path descriptions and components. + + We acknowledge that scanning and transmission electron microscopes are different types of instruments that have distinct differences + in the electron-optical setup and the components used. What remains the same from the perspective of an observer who monitors the + experiment inside the electron-matter interaction volume, i.e. in, on, or close to the surface of the specimen is the imaginary split + into an upper and a lower half-space. In the upper half-space a specific but eventually differently shaped electron beam illuminates + the specimen when comparing a scanning with a transmission electron microscope. In the lower half-space the beam or particles exit + the specimen or end up thermalized in thick specimens. + + *NXem distinguishes and stores instance data based on how long they remain unchanged:* + + ``measurement`` provides two groups ``measurement/instrument`` and ``measurement/eventID``. + The first group is designed for storing metadata about the instrument which do not change over the course of the session. Examples are + the name of the technology partner who built the microscope, the microscope's serial number, or the type of lenses mounted, etc. + The second group is designed for metadata and data that are collected during the microscope session. For these, specializations of + ``NXdata`` specifically ``NXimage`` and ``NXspectrum`` are provided. Each ``measurement/eventID`` event can be time-stamped + individually. Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose + is to store those specific state and settings of the microscope that was present during the collection of the event. + This includes lens settings, apertures used, aberrations, and other components, etc. + By virtue of design this reduces unnecessary repetition of metadata stored in the first group like is often observed + in image-based archival formats like TIFF, PNG, etc. + + *NXem offers domain-specific classes for standardized reporting of method-specific configurations, data processing, and results:* + + These include ``NXem_img`` for generic and specific imaging including diffraction, ``NXem_eds`` for energy-dispersive X-ray spectroscopy, + ``NXem_ebsd`` for electron backscatter diffraction, as well as ``NXem_eels`` for electron energy loss spectroscopy. These branches provide + examples that proof how NeXus can be used for combining session-centric data storage with data processing. These examples are naturally + incomplete but show at different levels of technical depth and breath how standardization can be useful even to report specifically formatted + data representations like multi-dimensional plotting. Thereby, downstream processing using software for data analyses or research data + management can take advantage of a standardized reporting rather than demanding for a zoo of parsers that interconvert + between many representations. + + *NXem within the ecosystem of data schemata for electron microscopy:** + + We support the statement that substantially fewer standardized rather than many ad hoc schemata are required to facilitate the + documentation and exchange of knowledge within electron microscopy. We tailored NXem to serve the materials science and + materials engineering usage of electron microscopy to provide a complementary coverage to what OMERO has established for + the bio- and life science usage of electron microscopy. +type: group +NXem(NXobject): + (NXentry): + exists: ['min', '1', 'max', 'unbounded'] + definition(NX_CHAR): + enumeration: [NXem] + profiling(NXcs_profiling): + exists: optional + doc: | + The configuration of the software that was used to generate this NeXus file. + programID(NXprogram): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + doc: | + A collection of all programs and libraries used to generate this NeXus file. + Ideally, this would enable a binary recreation from the input data. + + Examples include the name and version of the libraries used to write the + instance. Ideally, the software which writes these NXprogram instances + also includes the version of the set of NeXus classes i.e. the specific set + of base classes, application definitions, and contributed definitions + with which the here described concepts can be resolved. + + For the `pynxtools library `_ + which is used by the `NOMAD `_ + research data management system, it makes sense to store e.g. the GitHub + repository commit and respective submodule references used. + + Instances can also be used to document the modules and libraries that + are offered by the computational environment such as those parsed + from conda or python virtualenv environments. + program(NX_CHAR): + \@version(NX_CHAR): + identifier_experiment(NX_CHAR): + exists: optional + doc: | + A (globally) unique persistent identifier for referring to this experiment. + experiment_alias(NX_CHAR): + exists: optional + doc: | + Alias (short name) which scientists can use to refer to this experiment. + experiment_description(NX_CHAR): + exists: optional + doc: | + Free-text description about the experiment. + + Users are strongly advised to parameterize the description of their experiment + by using respective groups and fields and base classes instead of writing prose + into the field. + start_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information included + when the microscope session started. If the application demands that time + codes in this section of the application definition should only be used + for specifying when the experiment was performed - and the exact + duration is not relevant - use this start_time field. + + Often though it is useful to specify a time interval via setting both a start_time + and an end_time because this enables software tools and users to collect a + more detailed bookkeeping of the experiment. + + Users should be aware though that even using only start_time and end_time + may not be sufficient to infer how long the experiment took or for how long + data were acquired. To bookkeep more fine-grained timestamps over the + course of the experiment is possible with start_time and end_time fields + of respective :ref:`NXevent_data_em` instances. + end_time(NX_DATE_TIME): + exists: recommended + doc: | + ISO 8601 time code with local time zone offset to UTC included when + the microscope session ended. + + See docstring of the start_time field to see how to use the + start_time and end_time together. + citeID(NXcite): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + noteID(NXnote): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doc: | + Collection of serialized resources associated with the experiment. + Examples of such resources are files which are formatted using proprietary + data models of technology partners as those generated by the control software + of the microscope during the instrument session. + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + userID(NXuser): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doc: | + Information about persons who performed or were involved in the microscope + session or simulation run. + identifierNAME(NX_CHAR): + nameType: partial + exists: recommended + \@type(NX_CHAR): + name(NX_CHAR): + exists: optional + doc: | + Given (first) name and surname. + affiliation(NX_CHAR): + exists: optional + doc: | + Name of the affiliation at the point in time when the experiment was performed. + address(NX_CHAR): + exists: optional + doc: | + Postal address of the affiliation. + email(NX_CHAR): + exists: optional + doc: | + Email address at the point in time when the experiment was performed. + + Writing the most permanently used email is recommended. + telephone_number(NX_CHAR): + exists: optional + doc: | + Telephone number at the point in time when the experiment was performed. + role(NX_CHAR): + exists: optional + doc: | + User role at the point in time when the experiment was performed. + + Examples are technician operating the microscope, student, postdoc, + principle investigator, or guest. + sampleID(NXsample): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + doc: + - | + A physical entity which contains material intended to be investigated. + Sample and specimen are treated as de facto synonyms. + Samples can be real or virtual ones as annotated via is_simulation. + - | + The suggested best practice is to call this group sample. In those cases when + multiple samples need to be grouped inside one entry, these SAMPLE groups + should be named using the prefix sample followed an index starting from 1, i.e. + (sample1, sample2). + - | + There are at least two strategies how to store (meta)data when one analyzes multiple + samples - not different ROIs on a single sample though - in one session. + - | + One strategy is to store each sample and its results under an own NXem/ENTRY. + This is one of the most frequent use cases as during most sessions typically only a + single sample is investigated. In this case the name of this group should be sample. + - | + If multiple samples are investigated storing each of them in their own ENTRY group eventually will + demand unnecessary duplication of instrument details. + - | + This can be avoided by using another strategy for storing samples and their results. + Namely, by using only one instance of NXem/ENTRY. That NXem/ENTRY should then be named, + like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., + i.e. instances should use sample as a name prefix. + - | + In this case the collection of events should use identifier_sample to state clearly for which + of the samples loaded the (characterization) event was detected. + - | + xref: + spec: EMglossary + term: Specimen + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 + is_simulation(NX_BOOLEAN): + doc: | + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). + physical_form: + exists: recommended + enumeration: + open_enum: true + items: [bulk, foil, thin_film, powder] + identifier_sample(NX_CHAR): + exists: recommended + doc: | + Ideally, (globally) unique persistent identifier which distinguishes this sample from all others + and especially the predecessor/origin from where that sample was cut off. An example of cutting off + is a steel sheet that is the parent sample from which a small portion was wire-eroded that + represents the sample that was then prepared for characterization with an electron microscope. + + The terms sample and specimen are here considered as exact synonyms. + + This field must not be used for an alias for the sample name. Instead, use name. + + In cases where multiple specimens were loaded into the microscope, the identifier has to resolve + the specific sample, whose results are stored by this :ref:`NXentry` instance, because a single + NXentry should be used for the characterization of a single specimen. + + Details about the specimen preparation should be stored in resources referring to identifier_parent. + \@type(NX_CHAR): + identifier_parent(NX_CHAR): + exists: recommended + doc: | + Identifier of the sample from which the sample was cut off or the string *None*. + I.e. the parent to this sample. + + The purpose of this field is to support functionalities for tracking + sample provenance in a research data management system. + \@type(NX_CHAR): + preparation_date(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information + when the specimen was prepared. + + Ideally, report the end of the preparation, i.e. the last known timestamp when + the measured specimen surface was actively prepared. Ideally, this matches + the last timestamp that is mentioned in the digital resource pointed to by + identifier_parent. + + Knowing when the specimen was exposed to e.g. specific atmosphere is especially + required for material that is sensitive to the environment such as specimens that were + charged with fast diffusing elements or short-lived radioactive tracers. + + Additional time stamps prior to preparation_date are better placed in resources which + describe but do not pollute the description here with prose. Resolving these + connected metadata is considered the responsibility of the research data management + system and not the a NeXus file. + name(NX_CHAR): + exists: recommended + doc: | + Specimen name + atom_types(NX_CHAR): + doc: | + List of comma-separated elements from the periodic table that are contained in the sample. + If the sample substance has multiple components, all elements from each component + must be included in atom_types. + + The purpose of the field is to offer research data management systems an opportunity + to parse the relevant elements without having to interpret these from the resources + pointed to by identifier_parent or walk through eventually deeply nested groups in + individual data instances. + thickness(NX_NUMBER): + exists: optional + unit: NX_LENGTH + doc: | + (Measured) sample thickness. + + The information is recorded to qualify if the beam used was likely + able to shine through the specimen. For scanning electron microscopy, + in many cases the specimen is typically thicker than what is + illuminatable by the electron beam. + + In this case the value should be set to the actual thickness of the specimen + viewed for an illumination situation where the nominal surface normal of the + specimen is parallel to the optical axis. + density(NX_NUMBER): + exists: optional + unit: NX_ANY + doc: | + (Measured) density of the specimen. + + For multi-layered specimens this field should only be used to describe + the density of the excited volume. For scanning electron microscopy + the usage of this field is discouraged and instead an instance of a + region-of-interest connected to individual :ref:`NXevent_data_em` + instances can provide a cleaner description of the relevant details. + description(NX_CHAR): + exists: optional + doc: | + Discouraged free-text field to provide further detail. + consistent_rotations(NXparameters): + exists: recommended + doc: | + The conventions used when reporting crystal orientations. + We follow the best practices of the Material Science community + that are defined in reference ``_. + rotation_handedness(NX_CHAR): + doc: | + Convention how a positive rotation angle is defined when viewing + from the end of the rotation unit vector towards its origin. + This is in accordance with convention 2 of reference ``_. + + Counter_clockwise is equivalent to a right-handed choice. + Clockwise is equivalent to a left-handed choice. + enumeration: [counter_clockwise, clockwise] + rotation_convention(NX_CHAR): + doc: | + How are rotations interpreted into an orientation according to convention 3 + of reference ``_. + enumeration: [passive, active] + euler_angle_convention(NX_CHAR): + doc: | + How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) + according to convention 4 of reference ``_. + + The most frequently used convention in Materials Science is zxz, which is based on the work + of H.-J. Bunge but using other conventions is possible. Proper Euler angles are distinguished + from (improper) Tait-Bryan angles. + enumeration: [zxz, xyx, yzy, zyz, xzx, yxy, xyz, yzx, zxy, xzy, zyx, yxz] + axis_angle_convention(NX_CHAR): + doc: | + To which angular range is the rotation angle argument of an + axis-angle pair parameterization constrained according to + convention 5 of reference ``_. + enumeration: [rotation_angle_on_interval_zero_to_pi] + sign_convention(NX_CHAR): + doc: | + Which sign convention is followed when converting orientations + between different parametrizations/representations according + to convention 6 of reference ``_. + enumeration: [p_plus_one, p_minus_one] + NAMED_reference_frameID(NXcoordinate_system): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + alias(NX_CHAR): + exists: optional + type(NX_CHAR): + origin(NX_CHAR): + exists: recommended + x(NX_NUMBER): + x_direction(NX_CHAR): + exists: recommended + y(NX_NUMBER): + y_direction(NX_CHAR): + exists: recommended + z(NX_NUMBER): + z_direction(NX_CHAR): + exists: recommended + processing_reference_frame(NXcoordinate_system): + exists: recommended + alias(NX_CHAR): + exists: optional + type(NX_CHAR): + origin(NX_CHAR): + exists: recommended + doc: | + Location of the origin of the processing_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + enumeration: + open_enum: true + items: [front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] + x(NX_NUMBER): + x_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing x-axis base vector of the + processing_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + y(NX_NUMBER): + y_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing y-axis base vector of the + processing_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + z(NX_NUMBER): + z_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing z-axis base vector of the + processing_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + sample_reference_frame(NXcoordinate_system): + exists: recommended + depends_on(NX_CHAR): + exists: optional + doc: | + Reference to the specifically named :ref:`NXsample` instance(s) for + which these conventions apply (e.g. /entry1/sample1). + alias(NX_CHAR): + exists: optional + type(NX_CHAR): + origin(NX_CHAR): + exists: recommended + doc: | + Location of the origin of the sample_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + enumeration: + open_enum: true + items: [front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] + x(NX_NUMBER): + x_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing x-axis base vector of the + sample_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + y(NX_NUMBER): + y_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing y-axis base vector of the + sample_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + z(NX_NUMBER): + z_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing z-axis base vector of the + sample_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + detector_reference_frameID(NXcoordinate_system): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + doc: | + The reference frame that is defined by a specific detector. + depends_on(NX_CHAR): + exists: optional + doc: | + Reference to the specifically named :ref:`NXdetector` instance for + which these conventions apply (e.g. /entry1/instrument/detector1). + alias(NX_CHAR): + exists: optional + type(NX_CHAR): + origin(NX_CHAR): + exists: recommended + doc: | + Location of the origin of the detector_reference_frame. + + If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted + by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) + along respective base vector direction of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + enumeration: + open_enum: true + items: [front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] + x(NX_NUMBER): + x_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing x-axis base vector of the + detector_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + y(NX_NUMBER): + y_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing y-axis base vector of the + detector_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + z(NX_NUMBER): + z_direction(NX_CHAR): + exists: recommended + doc: | + Direction of the positively pointing z-axis base vector of the + detector_reference_frame. + enumeration: + open_enum: true + items: [north, east, south, west, in, out] + measurement(NXem_measurement): + exists: optional + + # voltage like all other dynamic quantities should better be placed in instances of NXevent_data_em + instrument(NXinstrument_em): + name(NX_CHAR): + exists: recommended + location(NX_CHAR): + exists: recommended + type(NX_CHAR): + exists: recommended + fabrication(NXfabrication): + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + programID(NXprogram): + exists: recommended + nameType: partial + doc: | + Details about the control program used for operating the microscope. + program(NX_CHAR): + \@version(NX_CHAR): + ebeam_column(NXebeam_column): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + electron_source(NXsource): + exists: recommended + emitter_type(NX_CHAR): + probe(NX_CHAR): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + lensID(NXelectromagnetic_lens): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + apertureID(NXaperture): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + deflectorID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + blankerID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + monochromatorID(NXmonochromator): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + type(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + corrector_csID(NXcorrector_cs): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + doc: | + A spherical aberration corrector is a typical component in a transmission electron microscope. + Many instruments have only one, in this case the variadic suffix should be dropped. + If there are multiple instances these should be numbered starting from 1, i.e. corrector_cs1, + corrector_cs2. + name(NX_CHAR): + exists: recommended + doc: | + Use specifically when there are multiple instances. + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + corrector_ax(NXcomponent): + exists: ['min', '0', 'max', '1'] + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + biprismID(NXcomponent): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + phaseplateID(NXcomponent): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + type(NX_CHAR): + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + sensorID(NXsensor): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + actuatorID(NXactuator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + beamID(NXbeam): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + scan_controller(NXscan_controller): + exists: optional + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + ibeam_column(NXibeam_column): + exists: ['min', '0', 'max', '1'] + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + ion_source(NXsource): + emitter_type(NX_CHAR): + probe(NXatom): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + lensID(NXelectromagnetic_lens): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + apertureID(NXaperture): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + deflectorID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + blankerID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + monochromatorID(NXmonochromator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + type(NX_CHAR): + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + + # device for correcting axial astigmatism of ion beam? + sensorID(NXsensor): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + actuatorID(NXactuator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + beamID(NXbeam): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + scan_controller(NXscan_controller): + exists: optional + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + detectorID(NXdetector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + gas_injector(NXcomponent): + exists: optional + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + stageID(NXmanipulator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + design(NX_CHAR): + exists: recommended + + # add enumeration values from old NXstage_lab + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + nanoprobeID(NXmanipulator): + nameType: partial + exists: optional + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + pumpID(NXpump): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + design(NX_CHAR): + sensorID(NXsensor): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + actuatorID(NXactuator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + eventID(NXevent_data_em): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + start_time(NX_DATE_TIME): + exists: recommended + end_time(NX_DATE_TIME): + exists: recommended + identifier_sample(NX_CHAR): + exists: recommended + + # above field is another example for lacking support to define conditional existence constraints + imageID(NXimage): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + (NXprocess): + exists: recommended + input(NXnote): + exists: recommended + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + context(NX_CHAR): + detector_identifier(NX_CHAR): + image_1d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + real(NX_NUMBER): + \@long_name(NX_CHAR): + imag(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + intensity(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + complex(NX_COMPLEX): + exists: optional + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + image_2d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + real(NX_NUMBER): + \@long_name(NX_CHAR): + imag(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + intensity(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + magnitude(NX_COMPLEX): + exists: optional + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + image_3d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + real(NX_NUMBER): + \@long_name(NX_CHAR): + imag(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + intensity(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + complex(NX_COMPLEX): + exists: optional + \@long_name(NX_CHAR): + axis_k(NX_NUMBER): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + image_4d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + real(NX_NUMBER): + \@long_name(NX_CHAR): + imag(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + intensity(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + complex(NX_COMPLEX): + exists: optional + \@long_name(NX_CHAR): + axis_m(NX_NUMBER): + \@long_name(NX_CHAR): + axis_k(NX_NUMBER): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + stack_1d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + real(NX_NUMBER): + \@long_name(NX_CHAR): + imag(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + intensity(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + complex(NX_COMPLEX): + exists: optional + \@long_name(NX_CHAR): + indices_group(NX_INT): + exists: optional + \@long_name(NX_CHAR): + indices_image(NX_INT): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + stack_2d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + real(NX_NUMBER): + \@long_name(NX_CHAR): + imag(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + intensity(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + complex(NX_COMPLEX): + exists: optional + \@long_name(NX_CHAR): + indices_group(NX_INT): + exists: optional + \@long_name(NX_CHAR): + indices_image(NX_INT): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + stack_3d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + real(NX_NUMBER): + \@long_name(NX_CHAR): + imag(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + intensity(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + complex(NX_COMPLEX): + exists: optional + \@long_name(NX_CHAR): + indices_group(NX_INT): + exists: optional + \@long_name(NX_CHAR): + indices_image(NX_INT): + \@long_name(NX_CHAR): + axis_k(NX_NUMBER): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + spectrumID(NXspectrum): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + (NXprocess): + exists: recommended + input(NXnote): + exists: recommended + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + context(NX_CHAR): + detector_identifier(NX_CHAR): + spectrum_0d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + spectrum_1d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + spectrum_2d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + spectrum_3d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + axis_k(NX_NUMBER): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + stack_0d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + indices_spectrum(NX_INT): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + stack_1d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + indices_spectrum(NX_INT): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + stack_2d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + indices_spectrum(NX_INT): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + stack_3d(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + \@long_name(NX_CHAR): + indices_spectrum(NX_INT): + \@long_name(NX_CHAR): + axis_k(NX_NUMBER): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + axis_energy(NX_NUMBER): + \@long_name(NX_CHAR): + instrument(NXinstrument_em): + exists: recommended + ebeam_column(NXebeam_column): + operation_mode(NX_CHAR): + exists: recommended + electron_source(NXsource): + exists: optional + voltage(NX_NUMBER): + extraction_voltage(NX_NUMBER): + exists: optional + emission_current(NX_NUMBER): + exists: optional + filament_current(NX_NUMBER): + exists: optional + lensID(NXelectromagnetic_lens): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + power_setting(NX_CHAR_OR_NUMBER): + apertureID(NXaperture): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + setting(NX_CHAR_OR_NUMBER): + exists: recommended + doc: | + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. + deflectorID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + blankerID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + monochromatorID(NXmonochromator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + applied(NX_BOOLEAN): + dispersion(NX_NUMBER): + exists: recommended + voltage(NX_NUMBER): + exists: recommended + corrector_csID(NXcorrector_cs): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + applied(NX_BOOLEAN): + exists: recommended + tableauID(NXprocess): + nameType: partial + exists: ['min', '1', 'max', 'unbounded'] + + # model(NX_CHAR): + + # ceos + c_1(NXaberration): + exists: optional + magnitude(NX_NUMBER): + a_1(NXaberration): + exists: optional + magnitude(NX_NUMBER): + b_2(NXaberration): + exists: optional + magnitude(NX_NUMBER): + a_2(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_3(NXaberration): + exists: optional + magnitude(NX_NUMBER): + s_3(NXaberration): + exists: optional + magnitude(NX_NUMBER): + a_3(NXaberration): + exists: optional + magnitude(NX_NUMBER): + b_4(NXaberration): + exists: optional + magnitude(NX_NUMBER): + d_4(NXaberration): + exists: optional + magnitude(NX_NUMBER): + a_4(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5(NXaberration): + exists: optional + magnitude(NX_NUMBER): + s_5(NXaberration): + exists: optional + magnitude(NX_NUMBER): + r_5(NXaberration): + exists: optional + magnitude(NX_NUMBER): + a_6(NXaberration): + exists: optional + magnitude(NX_NUMBER): + + # nion + c_1_0(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_1_2_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_1_2_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_2_1_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_2_1_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_2_3_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_2_3_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_3_0(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_3_2_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_3_2_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_3_4_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_3_4_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_4_1_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_4_1_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_4_3_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_4_3_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_4_5_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_4_5_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5_0(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5_2_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5_2_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5_4_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5_4_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5_6_a(NXaberration): + exists: optional + magnitude(NX_NUMBER): + c_5_6_b(NXaberration): + exists: optional + magnitude(NX_NUMBER): + + # we could write down how to store the aberrations but we should not force to add aberrations + # basically optional use of NXaberration therein at least some value required + corrector_ax(NXcomponent): + exists: optional + applied(NX_BOOLEAN): + value_x(NX_NUMBER): + value_y(NX_NUMBER): + biprismID(NXcomponent): + nameType: partial + exists: optional + phaseplateID(NXcomponent): + nameType: partial + exists: optional + sensorID(NXsensor): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + actuatorID(NXactuator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + beamID(NXbeam): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + scan_controller(NXscan_controller): + exists: recommended + scan_schema(NX_CHAR): + dwell_time(NX_NUMBER): + ibeam_column(NXibeam_column): + exists: optional + operation_mode(NX_CHAR): + exists: recommended + ion_source(NXsource): + probe(NXatom): + voltage(NX_NUMBER): + flux(NX_NUMBER): + lensID(NXelectromagnetic_lens): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + power_setting(NX_CHAR_OR_NUMBER): + apertureID(NXaperture): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + setting(NX_CHAR_OR_NUMBER): + doc: | + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. + deflectorID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + blankerID(NXdeflector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + monochromatorID(NXmonochromator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + applied(NX_BOOLEAN): + sensorID(NXsensor): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + actuatorID(NXactuator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + beamID(NXbeam): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + scan_controller(NXscan_controller): + exists: recommended + scan_schema(NX_CHAR): + dwell_time(NX_NUMBER): + optics(NXem_optical_system): + exists: recommended + detectorID(NXdetector): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + operation_mode(NX_CHAR): + doc: | + Operation mode of the detector as displayed by the control software. + stageID(NXmanipulator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + design(NX_CHAR): + exists: recommended + tilt1(NX_NUMBER): + tilt2(NX_NUMBER): + rotation(NX_NUMBER): + position(NX_NUMBER): + sample_heater(NXactuator): + exists: optional + physical_quantity(NX_CHAR): + heater_current(NX_NUMBER): + exists: optional + unit: NX_CURRENT + doc: | + Nominal current of the heater. + heater_voltage(NX_NUMBER): + exists: optional + unit: NX_VOLTAGE + doc: | + Nominal voltage of the heater. + heater_power(NX_NUMBER): + unit: NX_POWER + nanoprobeID(NXmanipulator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + gas_injector(NXcomponent): + exists: optional + pumpID(NXpump): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + sensorID(NXsensor): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + actuatorID(NXactuator): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + simulation(NXem_simulation): + exists: optional + doc: | + Documentation for a simulation of electron beam-matter interaction. + programID(NXprogram): + nameType: partial + exists: recommended + doc: | + The program with which the simulation was performed. + program(NX_CHAR): + \@version(NX_CHAR): + environment(NXcollection): + exists: recommended + doc: | + Programs and libraries representing the computational environment + (NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + program(NX_CHAR): + \@version(NX_CHAR): + config(NXparameters): + exists: optional + doc: | + Configuration of the simulation + results(NXprocess): + exists: optional + doc: | + Results of the simulation + (NXimage): + exists: ['min', '0', 'max', 'unbounded'] + (NXspectrum): + exists: ['min', '0', 'max', 'unbounded'] + interaction_volumeID(NXem_interaction_volume): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + (NXdata): + exists: recommended + (NXprocess): + exists: recommended + + # relevant research result post-processed for specific community methods + # but normalized in its representation ready to be consumed for + # research data management systems + roiID(NXroi_process): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + doc: | + xref: + spec: EMglossary + term: Region Of Interest + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 + + # as soon as one entry is here constrained further + # an RDM can be sure to find specific pieces of information in a + # specific way but then every user of this application definition + # is required to provide such information in this way! + img(NXem_img): + exists: optional + imageID(NXimage): + nameType: partial + exists: ['min', '1', 'max', 'unbounded'] + imaging_mode(NX_CHAR): + microstructureID(NXmicrostructure): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + + # exists: optional + ebsd(NXem_ebsd): + exists: optional + gnomonic_reference_frame(NXcoordinate_system): + exists: recommended + alias(NX_CHAR): + exists: optional + type(NX_CHAR): + origin(NX_CHAR): + x(NX_NUMBER): + x_direction(NX_CHAR): + exists: recommended + y(NX_NUMBER): + y_direction(NX_CHAR): + exists: recommended + z(NX_NUMBER): + z_direction(NX_CHAR): + exists: recommended + pattern_center(NXprocess): + exists: recommended + x_boundary_convention(NX_CHAR): + x_normalization_direction(NX_CHAR): + y_boundary_convention(NX_CHAR): + y_normalization_direction(NX_CHAR): + measurement(NXprocess): + exists: optional + depends_on(NX_CHAR): + source(NXnote): + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + simulation(NXprocess): + exists: optional + depends_on(NX_CHAR): + source(NXnote): + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + calibration(NXprocess): + exists: recommended + indexing(NXprocess): + exists: optional + number_of_scan_points(NX_UINT): + indexing_rate(NX_NUMBER): + exists: recommended + source(NXnote): + exists: optional + type(NX_CHAR): + exists: recommended + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + + # per scan point quantities (identifier_phase, matching_phase, positions, etc.) + # just using the implicit optional, for the database example in NOMAD we do + # not wish to duplicate all payload data + phaseID(NXphase): + nameType: partial + exists: ['min', '0', 'max', 'unbounded'] + name(NX_CHAR): + exists: recommended + number_of_scan_points(NX_UINT): + unit_cell(NXunit_cell): + a(NX_NUMBER): + b(NX_NUMBER): + c(NX_NUMBER): + alpha(NX_NUMBER): + beta(NX_NUMBER): + gamma(NX_NUMBER): + space_group(NX_CHAR): + + # phase-specific texture + ipfID(NXmicrostructure_ipf): + nameType: partial + exists: ['min', '1', 'max', 'unbounded'] + color_model(NX_CHAR): + projection_direction(NX_NUMBER): + map(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + data(NX_NUMBER): + \@long_name(NX_CHAR): + axis_x(NX_NUMBER): + \@long_name(NX_CHAR): + axis_y(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + axis_z(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + legend(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + data(NX_NUMBER): + \@long_name(NX_CHAR): + axis_x(NX_NUMBER): + \@long_name(NX_CHAR): + axis_y(NX_NUMBER): + \@long_name(NX_CHAR): + odfID(NXmicrostructure_odf): + nameType: partial + exists: optional + pfID(NXmicrostructure_pf): + nameType: partial + exists: optional + + # microstructure of the entire ROI + microstructureID(NXmicrostructure): + nameType: partial + exists: optional + roi(NXdata): + exists: recommended + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + descriptor(NX_CHAR): + exists: recommended + data(NX_NUMBER): + axis_z(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): + axis_y(NX_NUMBER): + \@long_name(NX_CHAR): + axis_x(NX_NUMBER): + \@long_name(NX_CHAR): + eds(NXem_eds): + exists: optional + + # remains to be discussed based on examples + indexing(NXprocess): + summary(NXdata): + exists: optional + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + axis_energy(NX_CHAR): + \@long_name(NX_CHAR): + atom_types(NX_CHAR): + ELEMENT_SPECIFIC_MAP(NXimage): + nameType: any + exists: ['min', '0', 'max', '118'] + iupac_line_candidates(NX_CHAR): + exists: recommended + energy_range(NX_NUMBER): + image_2d(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_UINT): + nameType: partial + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + axis_i(NX_NUMBER): + \@long_name(NX_CHAR): + axis_j(NX_NUMBER): + \@long_name(NX_CHAR): + eels(NXem_eels): + exists: optional + + # see an example how to map e.g. the following flat schema https://www.zenodo.org/record/6513745 to NXem + # in https://github.com/FAIRmat-NFDI/nexus_definitions/commit/0b928c4352bc5636f673b5fb25ce990f1af8a099 + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 42a56668edd9f76ee1df14d019beb4787653b981334951075cbcfd69c72b3af4 +# +# +# +# +# +# Application definition for normalized representation of electron microscopy research. +# +# This application definition is a comprehensive, general description for the +# standardization of data and metadata collected using electron microscopy. +# +# NXem is designed to be used for documenting experiments or computer simulations in which +# controlled electron beams are used to study electron-beam matter interactions, to simulate this, +# to explore physical mechanisms and phenomena, or to characterize materials. +# +# *The NeXus application definition NXem defines a hierarchical data model with ten building blocks:* +# +# The data model represents a tree of concepts. The tree is constructed from groups of concepts +# representing the branches surplus fields and attributes representing leafs. +# +# *NXem an introduction for typical use cases in material characterization and simulation:* +# +# Transmission electron microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) +# Scanning Electron Microscopy (SEM) +# Scanning Electron Microscopy combined a Focused-Ion Beam (SEM/FIB) +# +# *A deeper dive into the branches of NXem:* +# +# NXem is constructed from composing and specializing base classes into the following ten categories: +# +# - The field ``definition`` specifies that the data schema is NXem. In combination with +# administrative metadata such as the ``NeXus_version`` provided by :ref:`NXroot` this +# specifies which version of NXem the instance data in a NeXus/HDF5 file are compliant with. +# - The fields ``identifier_experiment``, ``experiment_alias``, ``experiment_description`` and +# the group ``userID`` provide concepts for storing organizational metadata that +# contextualize the work within the research workflow and humans involved in this. +# - The fields ``start_time``, ``end_time`` provide concepts for framing a temporal context for the research. +# - The groups ``citeID``, ``noteID`` provide concepts for adding contextual details such as citations +# that are associated with or notes, i.e. other artifacts that are deemed relevant when reporting about a measurement +# or simulation. These groups are useful when NXem is used as a serialization format for technology-partner-agnostic +# archival of data and metadata that have been collected during a session with an electron microscope or when a +# simulation was performed. +# - The group ``sampleID`` provides concepts for storing metadata about the sample that was +# characterized or simulated during the session. +# - The group ``measurement`` provides concepts that are useful for describing a measurement +# during a session with an electron microscope. This includes the chain of events of data and metadata that +# were collected during such a session. +# - The group``simulation`` provides concepts that are useful for describing a simulation of an +# electron beam that interacts with matter. Combined with ``measurement`` this provides a data schema +# for defining a digital twin of the microscope and its optical setup. +# - The groups ``consistent_rotations``, ``NAMED_reference_frame`` provide concepts for +# reporting coordinate systems (frames of reference) and rotation conventions that clarify how data +# should be interpreted specifying the rotation of orientable objects in the microscope, its components, +# or of crystals and crystal defects in the material analyzed. These metadata support interpretation for +# downstream or on-the-fly data analyses which electron microscopes typically nowadays perform +# during a session. Examples are the indexing of diffraction patterns, image analysis in general, or +# analyses of the chemical composition. +# - The group ``roiID`` provides concepts for reporting several domain- and technique-specific +# configuration parameter and results of data processing steps that were applied. +# - The group ``profiling`` provides concepts for reporting computational details such as +# programs and libraries used, for documenting the libraries of virtual environments such as those used +# by conda or python virtual environment, including details about the computing hardware used, and +# documenting capabilities for performance analyses and benchmarking of the software or its parts. +# +# *Design choices:* +# +# Specific details about how an electron microscope was used and eventually its configuration modified differ +# between user groups. This holds also true for computer simulations of electron-beam matter interaction. +# Different peer groups in different sub-domains in electron microscopy consider different data and metadata +# relevant. NXem defines constraints on the existence and cardinality of concepts and its concept branches +# but seeks to offer a compromise. The key design pattern followed is that most branches are made optional +# or at most recommended but their child concepts conditional required. Thereby, NXem can cover a variety +# of simple but also complex use cases. An example of this parent-optional-but-childs-stronger-restricted design +# is the combination of the optional group ``measurement`` with its required child +# ``measurement/instrument``: Users which report simulations are not forced to document the instrument +# but users which have characterized a sample are motivated to report about the instrument. They are though not +# necessarily required to report all the details of the instruments' components because the design pattern is-used +# applied recursively. +# +# *Inclusive design, one schema for scanning, focused-ion beam, and transmission electron microscopes:* +# +# Contrary to many other proposals of a data schema for electron microscopy, NXem seeks to highlight the similarity +# of the three fundamental types of electron microscopes that are nowadays used most routinely in academia and +# industry: An electron microscope is a beamline that provides a controlled beam of electrons combined with eventually +# beams of other particles (ions) to investigate electron/ion(-beam) matter interaction. +# This design of per-particle-type concept branches is realized in the base classes ``NXebeam_column`` and ``NXibeam_column``. +# These provide concepts for reporting the technical components that are typically used for generating a controllable +# (and typically scanning) beam of particles such as electrons or ions. +# +# Focused-ion beam capabilities are modelled by adding an optional group ``measurement/instrument/ibeam_column``. +# We foresee that this design is beneficial also in the future when research should be documented where photon-electron +# interactions via an electron microscope are combined. The current proposal though does not include such a +# ``NXpbeam_column`` base class that could be used for photon-/light-beam, i.e. laser plus optical +# beam path descriptions and components. +# +# We acknowledge that scanning and transmission electron microscopes are different types of instruments that have distinct differences +# in the electron-optical setup and the components used. What remains the same from the perspective of an observer who monitors the +# experiment inside the electron-matter interaction volume, i.e. in, on, or close to the surface of the specimen is the imaginary split +# into an upper and a lower half-space. In the upper half-space a specific but eventually differently shaped electron beam illuminates +# the specimen when comparing a scanning with a transmission electron microscope. In the lower half-space the beam or particles exit +# the specimen or end up thermalized in thick specimens. +# +# *NXem distinguishes and stores instance data based on how long they remain unchanged:* +# +# ``measurement`` provides two groups ``measurement/instrument`` and ``measurement/eventID``. +# The first group is designed for storing metadata about the instrument which do not change over the course of the session. Examples are +# the name of the technology partner who built the microscope, the microscope's serial number, or the type of lenses mounted, etc. +# The second group is designed for metadata and data that are collected during the microscope session. For these, specializations of +# ``NXdata`` specifically ``NXimage`` and ``NXspectrum`` are provided. Each ``measurement/eventID`` event can be time-stamped +# individually. Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose +# is to store those specific state and settings of the microscope that was present during the collection of the event. +# This includes lens settings, apertures used, aberrations, and other components, etc. +# By virtue of design this reduces unnecessary repetition of metadata stored in the first group like is often observed +# in image-based archival formats like TIFF, PNG, etc. +# +# *NXem offers domain-specific classes for standardized reporting of method-specific configurations, data processing, and results:* +# +# These include ``NXem_img`` for generic and specific imaging including diffraction, ``NXem_eds`` for energy-dispersive X-ray spectroscopy, +# ``NXem_ebsd`` for electron backscatter diffraction, as well as ``NXem_eels`` for electron energy loss spectroscopy. These branches provide +# examples that proof how NeXus can be used for combining session-centric data storage with data processing. These examples are naturally +# incomplete but show at different levels of technical depth and breath how standardization can be useful even to report specifically formatted +# data representations like multi-dimensional plotting. Thereby, downstream processing using software for data analyses or research data +# management can take advantage of a standardized reporting rather than demanding for a zoo of parsers that interconvert +# between many representations. +# +# *NXem within the ecosystem of data schemata for electron microscopy:** +# +# We support the statement that substantially fewer standardized rather than many ad hoc schemata are required to facilitate the +# documentation and exchange of knowledge within electron microscopy. We tailored NXem to serve the materials science and +# materials engineering usage of electron microscopy to provide a complementary coverage to what OMERO has established for +# the bio- and life science usage of electron microscopy. +# +# +# +# +# +# +# +# +# +# The configuration of the software that was used to generate this NeXus file. +# +# +# +# A collection of all programs and libraries used to generate this NeXus file. +# Ideally, this would enable a binary recreation from the input data. +# +# Examples include the name and version of the libraries used to write the +# instance. Ideally, the software which writes these NXprogram instances +# also includes the version of the set of NeXus classes i.e. the specific set +# of base classes, application definitions, and contributed definitions +# with which the here described concepts can be resolved. +# +# For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ +# which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ +# research data management system, it makes sense to store e.g. the GitHub +# repository commit and respective submodule references used. +# +# Instances can also be used to document the modules and libraries that +# are offered by the computational environment such as those parsed +# from conda or python virtualenv environments. +# +# +# +# +# +# +# +# +# A (globally) unique persistent identifier for referring to this experiment. +# +# +# +# +# Alias (short name) which scientists can use to refer to this experiment. +# +# +# +# +# Free-text description about the experiment. +# +# Users are strongly advised to parameterize the description of their experiment +# by using respective groups and fields and base classes instead of writing prose +# into the field. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information included +# when the microscope session started. If the application demands that time +# codes in this section of the application definition should only be used +# for specifying when the experiment was performed - and the exact +# duration is not relevant - use this start_time field. +# +# Often though it is useful to specify a time interval via setting both a start_time +# and an end_time because this enables software tools and users to collect a +# more detailed bookkeeping of the experiment. +# +# Users should be aware though that even using only start_time and end_time +# may not be sufficient to infer how long the experiment took or for how long +# data were acquired. To bookkeep more fine-grained timestamps over the +# course of the experiment is possible with start_time and end_time fields +# of respective :ref:`NXevent_data_em` instances. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC included when +# the microscope session ended. +# +# See docstring of the start_time field to see how to use the +# start_time and end_time together. +# +# +# +# +# +# Collection of serialized resources associated with the experiment. +# Examples of such resources are files which are formatted using proprietary +# data models of technology partners as those generated by the control software +# of the microscope during the instrument session. +# +# +# +# +# +# +# +# +# Information about persons who performed or were involved in the microscope +# session or simulation run. +# +# +# +# +# +# +# Given (first) name and surname. +# +# +# +# +# Name of the affiliation at the point in time when the experiment was performed. +# +# +# +# +# Postal address of the affiliation. +# +# +# +# +# Email address at the point in time when the experiment was performed. +# +# Writing the most permanently used email is recommended. +# +# +# +# +# Telephone number at the point in time when the experiment was performed. +# +# +# +# +# User role at the point in time when the experiment was performed. +# +# Examples are technician operating the microscope, student, postdoc, +# principle investigator, or guest. +# +# +# +# +# +# A physical entity which contains material intended to be investigated. +# Sample and specimen are treated as de facto synonyms. +# Samples can be real or virtual ones as annotated via is_simulation. +# +# The suggested best practice is to call this group sample. In those cases when +# multiple samples need to be grouped inside one entry, these SAMPLE groups +# should be named using the prefix sample followed an index starting from 1, i.e. +# (sample1, sample2). +# +# There are at least two strategies how to store (meta)data when one analyzes multiple +# samples - not different ROIs on a single sample though - in one session. +# +# One strategy is to store each sample and its results under an own NXem/ENTRY. +# This is one of the most frequent use cases as during most sessions typically only a +# single sample is investigated. In this case the name of this group should be sample. +# +# If multiple samples are investigated storing each of them in their own ENTRY group eventually will +# demand unnecessary duplication of instrument details. +# +# This can be avoided by using another strategy for storing samples and their results. +# Namely, by using only one instance of NXem/ENTRY. That NXem/ENTRY should then be named, +# like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., +# i.e. instances should use sample as a name prefix. +# +# In this case the collection of events should use identifier_sample to state clearly for which +# of the samples loaded the (characterization) event was detected. +# +# This concept is related to term `Specimen`_ of the EMglossary standard. +# +# .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 +# +# +# +# Qualifier whether the sample is a real (in which case is_simulation should be set to false) +# or a virtual one (in which case is_simulation should be set to true). +# +# +# +# +# +# +# +# +# +# +# +# +# Ideally, (globally) unique persistent identifier which distinguishes this sample from all others +# and especially the predecessor/origin from where that sample was cut off. An example of cutting off +# is a steel sheet that is the parent sample from which a small portion was wire-eroded that +# represents the sample that was then prepared for characterization with an electron microscope. +# +# The terms sample and specimen are here considered as exact synonyms. +# +# This field must not be used for an alias for the sample name. Instead, use name. +# +# In cases where multiple specimens were loaded into the microscope, the identifier has to resolve +# the specific sample, whose results are stored by this :ref:`NXentry` instance, because a single +# NXentry should be used for the characterization of a single specimen. +# +# Details about the specimen preparation should be stored in resources referring to identifier_parent. +# +# +# +# +# +# Identifier of the sample from which the sample was cut off or the string *None*. +# I.e. the parent to this sample. +# +# The purpose of this field is to support functionalities for tracking +# sample provenance in a research data management system. +# +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# when the specimen was prepared. +# +# Ideally, report the end of the preparation, i.e. the last known timestamp when +# the measured specimen surface was actively prepared. Ideally, this matches +# the last timestamp that is mentioned in the digital resource pointed to by +# identifier_parent. +# +# Knowing when the specimen was exposed to e.g. specific atmosphere is especially +# required for material that is sensitive to the environment such as specimens that were +# charged with fast diffusing elements or short-lived radioactive tracers. +# +# Additional time stamps prior to preparation_date are better placed in resources which +# describe but do not pollute the description here with prose. Resolving these +# connected metadata is considered the responsibility of the research data management +# system and not the a NeXus file. +# +# +# +# +# Specimen name +# +# +# +# +# List of comma-separated elements from the periodic table that are contained in the sample. +# If the sample substance has multiple components, all elements from each component +# must be included in atom_types. +# +# The purpose of the field is to offer research data management systems an opportunity +# to parse the relevant elements without having to interpret these from the resources +# pointed to by identifier_parent or walk through eventually deeply nested groups in +# individual data instances. +# +# +# +# +# (Measured) sample thickness. +# +# The information is recorded to qualify if the beam used was likely +# able to shine through the specimen. For scanning electron microscopy, +# in many cases the specimen is typically thicker than what is +# illuminatable by the electron beam. +# +# In this case the value should be set to the actual thickness of the specimen +# viewed for an illumination situation where the nominal surface normal of the +# specimen is parallel to the optical axis. +# +# +# +# +# (Measured) density of the specimen. +# +# For multi-layered specimens this field should only be used to describe +# the density of the excited volume. For scanning electron microscopy +# the usage of this field is discouraged and instead an instance of a +# region-of-interest connected to individual :ref:`NXevent_data_em` +# instances can provide a cleaner description of the relevant details. +# +# +# +# +# Discouraged free-text field to provide further detail. +# +# +# +# +# +# The conventions used when reporting crystal orientations. +# We follow the best practices of the Material Science community +# that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# Convention how a positive rotation angle is defined when viewing +# from the end of the rotation unit vector towards its origin. +# This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# Counter_clockwise is equivalent to a right-handed choice. +# Clockwise is equivalent to a left-handed choice. +# +# +# +# +# +# +# +# +# How are rotations interpreted into an orientation according to convention 3 +# of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# +# +# +# +# +# How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) +# according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# The most frequently used convention in Materials Science is zxz, which is based on the work +# of H.-J. Bunge but using other conventions is possible. Proper Euler angles are distinguished +# from (improper) Tait-Bryan angles. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# To which angular range is the rotation angle argument of an +# axis-angle pair parameterization constrained according to +# convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# +# +# +# +# Which sign convention is followed when converting orientations +# between different parametrizations/representations according +# to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Location of the origin of the processing_reference_frame. +# +# It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. +# Edges are interpreted by inspecting the direction of their outer unit normals +# (which point either parallel or antiparallel) along respective base vector direction +# of the reference frame. +# +# If any of these assumptions is not met, the user is required to explicitly state this. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing x-axis base vector of the +# processing_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing y-axis base vector of the +# processing_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing z-axis base vector of the +# processing_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Reference to the specifically named :ref:`NXsample` instance(s) for +# which these conventions apply (e.g. /entry1/sample1). +# +# +# +# +# +# +# Location of the origin of the sample_reference_frame. +# +# It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. +# Edges are interpreted by inspecting the direction of their outer unit normals +# (which point either parallel or antiparallel) along respective base vector direction +# of the reference frame. +# +# If any of these assumptions is not met, the user is required to explicitly state this. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing x-axis base vector of the +# sample_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing y-axis base vector of the +# sample_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing z-axis base vector of the +# sample_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# The reference frame that is defined by a specific detector. +# +# +# +# Reference to the specifically named :ref:`NXdetector` instance for +# which these conventions apply (e.g. /entry1/instrument/detector1). +# +# +# +# +# +# +# Location of the origin of the detector_reference_frame. +# +# If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted +# by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) +# along respective base vector direction of the reference frame. +# +# If any of these assumptions is not met, the user is required to explicitly state this. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing x-axis base vector of the +# detector_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing y-axis base vector of the +# detector_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Direction of the positively pointing z-axis base vector of the +# detector_reference_frame. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Details about the control program used for operating the microscope. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# A spherical aberration corrector is a typical component in a transmission electron microscope. +# Many instruments have only one, in this case the variadic suffix should be dropped. +# If there are multiple instances these should be numbered starting from 1, i.e. corrector_cs1, +# corrector_cs2. +# +# +# +# Use specifically when there are multiple instances. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Descriptor for the aperture setting when the exact technical details +# are unknown or not directly controllable as the control software of +# the microscope does not enable or was not configured to display these +# values for users. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Descriptor for the aperture setting when the exact technical details +# are unknown or not directly controllable as the control software of +# the microscope does not enable or was not configured to display these +# values for users. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Operation mode of the detector as displayed by the control software. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Nominal current of the heater. +# +# +# +# +# Nominal voltage of the heater. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Documentation for a simulation of electron beam-matter interaction. +# +# +# +# The program with which the simulation was performed. +# +# +# +# +# +# +# +# Programs and libraries representing the computational environment +# +# +# +# +# +# +# +# +# +# Configuration of the simulation +# +# +# +# +# Results of the simulation +# +# +# +# +# +# +# +# +# +# +# +# +# This concept is related to term `Region Of Interest`_ of the EMglossary standard. +# +# .. _Region Of Interest: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# diff --git a/contributed_definitions/NXaberration.nxdl.xml b/base_classes/NXaberration.nxdl.xml similarity index 55% rename from contributed_definitions/NXaberration.nxdl.xml rename to base_classes/NXaberration.nxdl.xml index c2fb7388f0..faca9e7310 100644 --- a/contributed_definitions/NXaberration.nxdl.xml +++ b/base_classes/NXaberration.nxdl.xml @@ -1,4 +1,4 @@ - + - Quantified aberration coefficient in an aberration_model. + Quantified aberration coefficient in an aberration_model. + + For an introduction in the aberrations in electron microscopy + see `R. Dunin-Borkowski et al. <https://doi.org/10.1017/9781316337455.022>`_ and + `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) + for different definitions available and further details. + Table 7-2 of Ibid. publication (page 305ff) documents how to convert from the Nion to the CEOS definitions. + Conversion tables are also summarized by `Y. Liao <https://www.globalsino.com/EM/page3740.html>`_ an introduction. - Magnitude of the aberration + Magnitude of the aberration - Uncertainty of the magnitude of the aberration + Uncertainty of the magnitude of the aberration - Free-text description how magnitude_errors was quantified - e.g. via the 95% confidence interval, variance, standard deviation, - using which algorithm or statistical model. + Free-text description how magnitude_errors was quantified + e.g. via the 95% confidence interval, variance, standard deviation, + using which algorithm or statistical model. - Time elapsed since the last measurement. + Time elapsed since the last measurement. - For the CEOS definitions the C aberrations are radial-symmetric and have - no angle entry, while the A, B, D, S, or R aberrations are n-fold - symmetric and have an angle entry. - For the NION definitions the coordinate system differs to the one - used in CEOS and instead two aberration coefficients a and b are used. + For the CEOS definitions the C aberrations are radial-symmetric and have + no angle entry, while the A, B, D, S, or R aberrations are n-fold + symmetric and have an angle entry. + For the NION definitions the coordinate system differs to the one + used in CEOS and instead two aberration coefficients a and b are used. - Given name to this aberration. + Given name to this aberration. - Alias also used to name and refer to this specific type of aberration. + Alias to name or refer to this specific type of aberration. diff --git a/base_classes/NXactuator.nxdl.xml b/base_classes/NXactuator.nxdl.xml index e0b8907b34..68c87a0e66 100644 --- a/base_classes/NXactuator.nxdl.xml +++ b/base_classes/NXactuator.nxdl.xml @@ -1,4 +1,4 @@ - + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The number of ion candidates. + + + + + Maximum number of allowed atoms per ion. + + + + + Number of entries + + + + + Base class to document the parameters, configuration, and results of a processing for recovering + the charge state and nuclide composition of an ion from ranging definitions as used in the research + field of atom probe microscopy. + + A ranging definition classically reports only the mass-to-charge-state-ratio interval plus the + elemental composition, but not necessarily the nuclide that compose the ion. + + As the mass-resolving-power in an atom probe instrument is finite and typically lower + than for cutting edge tandem mass spectrometry it is possible that different combinations of nuclides + are indistinguishable and thus multiple ions in eventually even different charge states can be valid + labels for a given mass-to-charge-state-ratio peak. Enumerating the possible combinations + is a programmatic approach that can help with peak identification. + + + + Parameters for the algorithm used to recover which combinations of nuclides + have a mass and charge that matches a set of constraints. + + Each parameter in this group is defines one constraint. + + + + Parameter that defines the elements considered in the combinatorial search. + The array contains nuclides as many times as their multiplicity and must not be empty. + Nuclides are encoded using the hashing rule that is defined in by nuclide_hash of :ref:`NXatom`. + + Constraining the elements or nuclides instead of providing all nuclides + reduces the time to perform an exhaustive combinatorial search. + + + + + + + + Parameter that defines the interval :math:`[{\frac{m}{q}}_{min}, {\frac{m}{q}}_{max}]` within which + ions with given mass-to-charge-state-ratio qualify as candidates. + + + + + + + + Parameter that defines the minimum half life for how long each nuclide of each + ion needs to be stable such that the ion qualifies as a candidate. + + + + + Parameter that defines the minimum natural abundance of each nuclide of each + ion such that the ion qualifies as a candidate. + + + + + If the value is false, it means that non-unique solutions are accepted. + These are solutions where multiple candidates have been built from + different nuclide instances but the charge_state of all the ions is the same. + + + + + + Signed charge, i.e. integer multiple of the elementary + charge of each candidate. + + + + + + + + Table of nuclide instances of which each candidate is composed. + Each row vector is sorted in descending order. + Unused entries in the matrix should be set to 0. + Use the hashing rule that is defined in nuclide_hash of :ref:`NXatom`. + + + + + + + + + Accumulated mass of the nuclides in each candidate. + Not corrected for quantum effects. + + + + + + + + The product of the natural abundances of the nuclides for each candidate. + + + + + + + + For each candidate the half life of the nuclide that has the + shortest half life. + + + + + + diff --git a/base_classes/NXapm_measurement.nxdl.xml b/base_classes/NXapm_measurement.nxdl.xml new file mode 100644 index 0000000000..c536a2daf1 --- /dev/null +++ b/base_classes/NXapm_measurement.nxdl.xml @@ -0,0 +1,70 @@ + + + + + + Base class for collecting a run with a real or a simulated atom probe or field-ion microscope. + + The term run is understood as an exact synonym for session, i.e. the usage of a real or simulated + tomograph or microscope for a certain amount of time during which one characterizes a single specimen. + + Research workflows for experiments and simulations of atom probe and related field-evaporation + evolve continuously and become increasingly connected with other methods used for material + characterization specifically electron microscopy. A few examples in this direction are: + + * `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_ + * `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_ + * `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_ + * `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_ + * `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ + + The majority of atom probe research is performed using the so-called Local Electrode Atom Probe (LEAP) instruments + from AMETEK/Cameca. In addition, several research groups have built their own instruments and shared different + aspects of the technical specifications and approaches including how these groups apply data processing e.g.: + + * `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_ + * `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ + * `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ + + to name but a few. + + + + A statement whether the measurement completed successfully, or was aborted. + + + + + + + + + Statement about the quality of the measurement. + + The value can be extracted from the CAnalysis.CResults.fQuality + field of a CamecaRoot ROOT file. + + + + + diff --git a/base_classes/NXapm_ranging.nxdl.xml b/base_classes/NXapm_ranging.nxdl.xml new file mode 100644 index 0000000000..86ac98719f --- /dev/null +++ b/base_classes/NXapm_ranging.nxdl.xml @@ -0,0 +1,118 @@ + + + + + + Base class for the configuration and results of ranging definitions. + + Ranging is a data post-processing step used in the research field of + atom probe during which elemental, isotopic, and/or molecular identities + are assigned to mass-to-charge-state ratios within certain intervals. + The documentation of these steps is based on ideas that + have been described in the literature: + + * `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ + * `D. Haley et al. <https://doi.org/10.1017/S1431927620024290>`_ + * `M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_ + + + + + + Specifies the mass-to-charge-state ratio histogram. + + + + + Smallest :math:`{\frac{m}{q}}_{min}` mass-to-charge-state ratio value. + + The lower (left-hand side) inclusive bound of the interval :math:`[{\frac{m}{q}}_{min}`, {\frac{m}{q}}_{max}]`. + + + + + Largest :math:`{\frac{m}{q}}_{max}` mass-to-charge-state ratio value. + + The upper (right-hand side) inclusive bound of the interval :math:`[{\frac{m}{q}}_{min}`, {\frac{m}{q}}_{max}]`. + + + + + The number of bins on the interval :math:`[{\frac{m}{q}}_{min}`, + {\frac{m}{q}}_{max}]`. + + + + + A default histogram aka mass spectrum of + the mass-to-charge-state ratio values. + + + + + + Details of the background model that was used to + correct the total counts per bin into counts. + + + + + Free-text field to describe how atom probers define a background model. + + Thereby, community feedback can be collected to inform an improved + version of this base class in the future. + + + + + + How were peaks in the mass-to-charge-state ratio histogram identified. + + + + + + + Details about how peaks, with taking into account + error models, were interpreted as ion types or not. + + + + + How many ion types are distinguished. If no ranging was performed, each + ion is of the special unknown type. The iontype ID of this unknown type + is 0 representing a reserved value. + + Consequently, start counting iontypes from 1. + + + + + Assumed maximum value that suffices to store all relevant molecular ions, + even the most complicated ones that one can typically observe and distinguish + typically. Currently, a value of 32 is used (see M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_). + + + + + diff --git a/base_classes/NXapm_reconstruction.nxdl.xml b/base_classes/NXapm_reconstruction.nxdl.xml new file mode 100644 index 0000000000..43068bd667 --- /dev/null +++ b/base_classes/NXapm_reconstruction.nxdl.xml @@ -0,0 +1,275 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of ions spatially filtered from results of the hit_finding algorithm + from which an instance of a reconstructed volume has been generated. + These ions get new identifier assigned in the process - the so-called + evaporation_id, which must not be confused with the pulse_id! + + + + + Base class for the configuration and results of a reconstruction algorithm. + + Generating a tomographic reconstruction of the specimen uses selected and + calibrated ion hit positions, the evaporation sequence, and voltage curve data. + Very often scientists use own software scripts according to published procedures, + so-called reconstruction protocols. + + + + + + + Parameters that configure a reconstruction algorithm which takes + hit data and mass-to-charge-state ratio values to construct a model + of the evaporated specimen. This model is called the reconstructed volume. + Researchers in the field of atom probe call these algorithms reconstruction + protocols. + + Different such protocols exist. Although these are qualitatively similar, + each protocol uses and interprets the parameters slightly differently. + + The majority of reconstructions is performed with the proprietary software + APSuite / IVAS, the source code for the reconstruction protocols that this + software implements in detail is not open but the parameters and their qualitative + effect on the reconstructed volume follows the protocols that are discussed in + the atom probe literature. This group allows to document these parameters in + a standardized manner. + + + + Lowest voltage at which an ion that is considered in the reconstructed + volume has been extracted from the specimen. + + + + + Highest voltage at which an ion that is considered in the reconstructed + volume has been extracted from the specimen. + + + + + Qualitative statement about which reconstruction protocol was used. + + For reconstructions performed with APSuite / IVAS the value "cameca" + should be used. + + + + + + + + + + + Assumed primary element based on which the reconstruction is calibrated. + + The value can be extracted from the CAnalysis.CSpatial.fPrimaryElement + field of a CamecaRoot ROOT file. + + + + + Assumed detection efficiency + + The value can be extracted from the CAnalysis.CSpatial.fEfficiency + field of a CamecaRoot ROOT file. + + + + + Nominal flight path + + The value can be extracted from the CAnalysis.CSpatial.fFlightPath + field of a CamecaRoot ROOT file. + + + + + Assumed evaporation electric field + + The value can be extracted from the CAnalysis.CSpatial.fEvaporationField + field of a CamecaRoot ROOT file. + + + + + Image compression factor (ICF) + + The value can be extracted from the CAnalysis.CSpatial.fImageCompression + field of a CamecaRoot ROOT file. + + + + + Sum of ion volumes + + The value can be extracted from the CAnalysis.CSpatial.fKfactor + field of a CamecaRoot ROOT file. + + + + + Shank angle + + The value can be extracted from the CAnalysis.CSpatial.fShankAngle + field of a CamecaRoot ROOT file. + + + + + Assumed atomic volume + + + + + The value can be extracted from the CAnalysis.CSpatial.fTipRadius + field of a CamecaRoot ROOT file. + + + + + The value can be extracted from the CAnalysis.CSpatial.fTipRadius0 + field of a CamecaRoot ROOT file. + + + + + The value can be extracted from the CAnalysis.CSpatial.fVoltage0 + field of a CamecaRoot ROOT file. + + + + + Different strategies for crystallographic calibration of the + reconstruction are possible. Therefore, we collect first such + feedback before parametrizing this further. + + If no crystallographic calibration was performed, the field + should be filled with the n/a, meaning not applied. + + + + + Possibility of a free text field that allows to report additional details related to + the reconstruction protocol. For LEAP systems and reconstructions that are + performed with APSuite / IVAS see also `B. Gault et al. <https://doi.org/10.1093/mam/ozae081>_` + and `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). + for best practices on the reporting of metadata in atom probe tomography. + + + + + + + Three-dimensional positions of the ions in the reconstructed volume. + + + + + + + + The instance of :ref:`NXcoordinate_system` in which the positions are defined. + + + + + + + + + Visual overview of the reconstructed dataset via a three-dimensional + histogram of ion counts. Ion counts are characterized using one nanometer + cubic bins without applying any smoothening of reconstructed positions + during the histogram computation. + + Such preview is useful to get an impression of the macroscopic shape of the + reconstructed volume. Visualizing by ion counts highlights density variations + the reconstructed volume that are signatures of features such as poles, + interfaces or irregularities of the specimen shape. + + + + + + Sum of ion volumes + + The value can be extracted from the CAnalysis.CSpatial.fRecoVolume + field of a CamecaRoot ROOT file. + + + + + + The nominal diameter of the specimen ROI which is measured in the + experiment. The physical specimen cannot be measured completely + because ions may launch but hit in locations other than the detector. + + + + + Tight, axis-aligned bounding box about the point cloud of the reconstruction. + + + + Minimum coordinate value along the x-direction + + + + + Maximum coordinate value along the x-direction + + + + + Minimum coordinate value along the y-direction + + + + + Maximum coordinate value along the y-direction + + + + + Minimum coordinate value along the z-direction + + + + + Maximum coordinate value along the z-direction + + + + diff --git a/base_classes/NXapm_simulation.nxdl.xml b/base_classes/NXapm_simulation.nxdl.xml new file mode 100644 index 0000000000..cd726f04c7 --- /dev/null +++ b/base_classes/NXapm_simulation.nxdl.xml @@ -0,0 +1,33 @@ + + + + + + Base class for simulation of ion extraction from matter via laser and/or voltage + pulsing. + + + + + + diff --git a/base_classes/NXatom.nxdl.xml b/base_classes/NXatom.nxdl.xml new file mode 100644 index 0000000000..b27c32ea21 --- /dev/null +++ b/base_classes/NXatom.nxdl.xml @@ -0,0 +1,223 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of atom positions. + + + + + Dimensionality + + + + + Maximum number of atoms/isotopes allowed per ion. + + + + + Number of mass-to-charge-state-ratio range intervals for ion type. + + + + + Base class for documenting a set of atoms. + + Atoms in the set may be bonded. The set may have + a net charge to represent an ion. + An ion can be a molecular ion. + + + + Given name for the set. + + This field could for example be used in the research field + of atom probe tomography to store a standardized human-readable + name of the element or ion like such as Al +++ or 12C +. + + + + + Given numerical identifier for the set. + + The identifier zero is reserved for the special unknown ion type. + + + + + Identifier used to refer to if the set of atoms represents a substance. + + + + + + + + Signed net (partial) charge of the (molecular) ion. + + Different methods for computing charge are in use. + Care needs to be exercised with respect to the integration. + `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. + + + + + Charge reported in multiples of the charge of an electron. + + For research using atom probe tomography the value should be set to + zero if the charge_state is unknown and irrecoverable. This can happen + when classical ranging definition files in formats like RNG, RRNG are used. + These file formats do not document the charge state explicitly but only + the number of atoms of each element per molecular ion surplus the + respective mass-to-charge-state-ratio interval. + + Details on ranging definition files in the literature are `M. K. Miller <https://doi.org/10.1002/sia.1719>`_. + + + + + Assumed volume affected by the set of atoms. + + Neither individual atoms nor a set of cluster of these have a volume + that is unique as a some cut-off criterion is required. + + + + + Index for each atom at locations as detailed by position. + Indices can be used as identifier and thus names for individual atoms. + + + + + + + + Nuclide information for each atom at locations as detailed by position. + + One `approach <https://doi.org/10.1017/S1431927621012241>`_ for storing nuclide information + efficiently is via individual hash values. + Consult the docstring of ``nuclide_hash`` for further details. + + + + + + + + Position of each atom. + + + + + + + + Path to an instance of :ref:`NXcoordinate_system` to document + the reference frame in which the positions are defined. + + This resolves ambiguity when the reference frame is different + to the NeXus default reference frame (McStas). + + + + + + Relative occupancy of the atom position. + + This field is useful for specifying the atomic motif in + instances of :ref:`NXunit_cell`. + + + + + + + + Vector of nuclide hash values. The vector is sorted in decreasing order. + + Individual hash values :math:`H` `encode <https://doi.org/10.1017/S1431927621012241>`_ + for each nuclide or element the number of protons :math:`Z` and a constant :math:`c` + via the following hashing rule :math:`H = Z + c \cdot 256`. :math:`Z` and :math:`c` must be 8-bit unsigned integers. + + The constant :math:`c` is either set to number of neutrons :math:`N` or to the special value 255. + The special value 255 is used to refer to all isotopes of an element from the IUPAC periodic table. + + Some examples: + + * The element hydrogen (meaning irrespective which isotope), its hash value is :math:`H = 1 + 255 \cdot 256 = 65281`. + * The :math:`^{1}H` hydrogen isotope (:math:`Z = 1, N = 0`), its hash value is :math:`H = 1 + 0 \cdot 256 = 1`. + * The :math:`^{2}H` deuterium isotope (:math:`Z = 1, N = 1`), its hash value is :math:`H = 1 + 1 \cdot 256 = 257`. + * The :math:`^{3}H` tritium isotope (:math:`Z = 1, N = 2`), its hash value is :math:`H = 1 + 2 \cdot 256 = 513`. + * The :math:`^{99}Tc` technetium isotope (:math:`Z = 43, N = 56`), its hash value is :math:`H = 43 + 56 \cdot 256 = 14379`. + + The special hash value :math:`0` is a placeholder. + + This hashing rule implements a bitshift operation. The benefit is that this enables encoding of all + currently known nuclides and elements efficiently into an 16-bit unsigned integer. Sufficient + unused indices remain to case situations when new elements will be discovered. + + + + + + + + Table which decodes the entries in nuclide_hash into a human-readable matrix + instances for either nuclids or elements. Specifically, the first row specifies the + nuclide mass number. When the nuclide_hash values are used this means + the row should report the sum :math:`Z + N` or 0. The value 0 documents that + an element from the IUPAC periodic table is meant. + The second row specifies the number of protons :math:`Z`. + The value 0 in this case documents a placeholder or that no element-specific + information is relevant. + + Taking a carbon-14 nuclide as an example the mass number is 14. + That is encoded as a column vector (14, 6). + The array is stored matching the order of nuclide_hash. + + + + + + + + + Associated lower :math:`{\frac{m}{q}}_{min}` and upper :math:`{\frac{m}{q}}_{max}` bounds of the + mass-to-charge-state ratio interval(s) :math:`[{\frac{m}{q}}_{min}, {\frac{m}{q}}_{max}]`. + (boundaries inclusive). This field is primarily of interest for documenting :ref:`NXprocess` + steps of indexing a ToF/mass-to-charge-state ratio histogram. + + + + + + + diff --git a/base_classes/NXcalibration.nxdl.xml b/base_classes/NXcalibration.nxdl.xml index a0714fb323..2e7bee9891 100644 --- a/base_classes/NXcalibration.nxdl.xml +++ b/base_classes/NXcalibration.nxdl.xml @@ -1,4 +1,4 @@ - + Although this description is storage efficient, it is not well-suited for topological analyses. In this case using a half-edge data structure is - an alternative. + an alternative. Having an own base class for the data structure how primitives are stored is useful to embrace both users with small or detailed specification demands. + + Indices can be used as identifier and thus names for individual instances. - + Number of vertices for each face. @@ -81,7 +83,7 @@ duplicate of an NXoff_geometry ?--> - + Number of edges for each face. @@ -92,12 +94,12 @@ duplicate of an NXoff_geometry ?--> - + Number of faces of the primitives. - + Integer offset whereby the identifier of the first member of the vertices differs from zero. @@ -106,7 +108,7 @@ duplicate of an NXoff_geometry ?--> Inspect the definition of NXcg_primitive for further details. - + Integer offset whereby the identifier of the first member of the edges differs from zero. @@ -115,7 +117,7 @@ duplicate of an NXoff_geometry ?--> Inspect the definition of NXcg_primitive for further details. - + Integer offset whereby the identifier of the first member of the faces differs from zero. @@ -124,7 +126,7 @@ duplicate of an NXoff_geometry ?--> Inspect the definition of NXcg_primitive for further details. - + Integer identifier to distinguish all vertices explicitly. @@ -132,7 +134,7 @@ duplicate of an NXoff_geometry ?--> - + Integer used to distinguish all edges explicitly. @@ -140,7 +142,7 @@ duplicate of an NXoff_geometry ?--> - + Integer used to distinguish all faces explicitly. @@ -216,6 +218,7 @@ duplicate of an NXoff_geometry ?--> * 0 - undefined * 1 - counter-clockwise (CCW) * 2 - clock-wise (CW) + diff --git a/contributed_definitions/NXcg_grid.nxdl.xml b/base_classes/NXcg_grid.nxdl.xml similarity index 98% rename from contributed_definitions/NXcg_grid.nxdl.xml rename to base_classes/NXcg_grid.nxdl.xml index abff32b117..07abb1001a 100644 --- a/contributed_definitions/NXcg_grid.nxdl.xml +++ b/base_classes/NXcg_grid.nxdl.xml @@ -1,4 +1,4 @@ - + - + Number of boundaries distinguished diff --git a/contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml b/base_classes/NXcg_half_edge_data_structure.nxdl.xml similarity index 92% rename from contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml rename to base_classes/NXcg_half_edge_data_structure.nxdl.xml index c88df09f51..91eb74bc44 100644 --- a/contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml +++ b/base_classes/NXcg_half_edge_data_structure.nxdl.xml @@ -1,4 +1,4 @@ - + - + Number of vertices for each face. @@ -72,7 +74,7 @@ - + Number of edges for each face. @@ -83,7 +85,7 @@ - + Integer offset whereby the identifier of the first member of the vertices differs from zero. @@ -92,7 +94,7 @@ Inspect the definition of :ref:`NXcg_primitive` for further details. - + Integer offset whereby the identifier of the first member of the edges differs from zero. @@ -101,7 +103,7 @@ Inspect the definition of :ref:`NXcg_primitive` for further details. - + Integer offset whereby the identifier of the first member of the faces differs from zero. @@ -110,7 +112,7 @@ Inspect the definition of :ref:`NXcg_primitive` for further details. - + The position of the vertices. diff --git a/contributed_definitions/NXcg_hexahedron.nxdl.xml b/base_classes/NXcg_hexahedron.nxdl.xml similarity index 95% rename from contributed_definitions/NXcg_hexahedron.nxdl.xml rename to base_classes/NXcg_hexahedron.nxdl.xml index d3442711e0..2684550116 100644 --- a/contributed_definitions/NXcg_hexahedron.nxdl.xml +++ b/base_classes/NXcg_hexahedron.nxdl.xml @@ -1,4 +1,4 @@ - + Combined storage of all primitives of all hexahedra. - + Individual storage of each hexahedron. - - Instances should use hexahedron as a name prefix. - + Individual storage of each hexahedron as a graph. - - Instances should use hexahedron_half_edge as a name prefix. diff --git a/base_classes/NXcg_parallelogram.nxdl.xml b/base_classes/NXcg_parallelogram.nxdl.xml new file mode 100644 index 0000000000..f54790ce5f --- /dev/null +++ b/base_classes/NXcg_parallelogram.nxdl.xml @@ -0,0 +1,101 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The cardinality of the set, i.e. the number of parallelograms. + + + + + Computational geometry description of a set of parallelograms. + + This class can also be used to describe rectangles or squares, irrespective + whether these are axis-aligned or not. The class represents different + access and description levels to embrace applied scientists and computational + geometry experts with their different views: + + * The simplest case is the communication of dimensions aka the size of a + region of interest in the 2D plane. In this case, communicating the + alignment with axes is maybe not as relevant as it is to report the area + of the ROI. + * In other cases the extent of the parallelogram is relevant though. + * Finally, in CAD models it should be possible to specify the polygons + which the parallelograms represent with exact numerical details. + + Parallelograms are important geometrical primitives as their usage for + describing many scanning experiments shows where typically parallelogram-shaped + ROIs are scanned across the surface of a sample. + + The term parallelogram will be used throughout this base class thus including + the important special cases rectangle, square, 2D box, axis-aligned bounding box + (AABB), or optimal bounding box (OBB) as analogous 2D variants to their 3D + counterparts. See :ref:`NXcg_hexahedron` for the generalization in 3D. + + An axis-aligned bounding box is a common data object in computational science + and simulation codes to represent a rectangle whose edges are aligned with the + axes of a coordinate system. As a part of binary trees AABBs are important data + objects for executing time- as well as space-efficient queries + of geometric primitives in techniques like kd-trees. + + An optimal bounding box is a common data object which provides the best, i.e. + most tightly fitting box about an arbitrary object. In general such boxes are + rotated. Other than in 3D dimensions, the rotation calipher method offers + a rigorous approach to compute an optimal bounding box to a point set in 2D. + + + + + To specify which parallelogram is a rectangle. + + + + + + + + Only to be used if is_rectangle is present. In this case, this field + describes whether parallelograms are rectangles whose primary edges + are parallel to the axes of the coordinate system. + + + + + + + + + Combined storage of all parallelograms. + + + + + Individual storage of each parallelogram. + + + diff --git a/contributed_definitions/NXcg_point.nxdl.xml b/base_classes/NXcg_point.nxdl.xml similarity index 98% rename from contributed_definitions/NXcg_point.nxdl.xml rename to base_classes/NXcg_point.nxdl.xml index 5fd37f9089..169abbe893 100644 --- a/contributed_definitions/NXcg_point.nxdl.xml +++ b/base_classes/NXcg_point.nxdl.xml @@ -1,4 +1,4 @@ - + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality, which has to be either 2 or 3. + + + + + The cardinality of the set, i.e. the number of polygons. + + + + + + The total number of vertices when visiting every polygon. + + + + + + Computational geometry description of a set of polygons in Euclidean space. + + Polygons are specialized polylines: + + * A polygon is a geometric primitive that is bounded by a closed polyline + * All vertices of this polyline lay in the d-1 dimensional plane. + whereas vertices of a polyline do not necessarily lay on a plane. + * A polygon has at least three vertices. + + Each polygon is built from a sequence of vertices (points with identifiers). + The members of a set of polygons may have a different number of vertices. + Sometimes a collection/set of polygons is referred to as a soup of polygons. + + As three-dimensional objects, a set of polygons can be used to define the + hull of what is effectively a polyhedron; however users are advised to use + the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed + polyhedra. Even more general complexes can be thought of. An example are the + so-called piecewise-linear complexes used in the TetGen library. + + As these complexes can have holes though, polyhedra without holes are one + subclass of such complexes, users should rather design their own base class + e.g. NXcg_polytope to describe such even more complex primitives instead + of abusing this base class for such purposes. + + + + The total number of vertices in the set. + + + + + + Combined storage of all primitives of all polygons. + + + + + Individual storage of the mesh of each polygon. + + + + + Individual storage of each polygon as a graph. + + + + + + For each polygon its accumulated length along its edges. + + + + + + + + Interior angles for each polygon. There are as many values per polygon + as there are number_of_vertices. + The angle is the angle at the specific vertex, i.e. between the adjoining + edges of the vertex according to the sequence in the polygons array. + Usually, the winding_order field is required to interpret the value. + + + + + + + + Curvature type: + + * 0 - unspecified, + * 1 - convex, + * 2 - concave + + + + + + diff --git a/contributed_definitions/NXcg_polyhedron.nxdl.xml b/base_classes/NXcg_polyhedron.nxdl.xml similarity index 78% rename from contributed_definitions/NXcg_polyhedron.nxdl.xml rename to base_classes/NXcg_polyhedron.nxdl.xml index 1a304a31ea..5e72d6070f 100644 --- a/contributed_definitions/NXcg_polyhedron.nxdl.xml +++ b/base_classes/NXcg_polyhedron.nxdl.xml @@ -1,4 +1,4 @@ - + - @@ -64,7 +54,7 @@ for clean graph-based descriptions of polyhedra.--> by creating customized instances of an :ref:`NXcg_polygon`. - + The number of faces for each polyhedron. Faces of adjoining polyhedra are counted for each polyhedron. @@ -81,7 +71,7 @@ for clean graph-based descriptions of polyhedra.--> - + The number of edges for each polyhedron. Edges of adjoining polyhedra are counted for each polyhedron. @@ -101,18 +91,14 @@ for clean graph-based descriptions of polyhedra.--> Combined storage of all primitives of all polyhedra. - + Individual storage of each polyhedron. - - Instances should use polyhedron as a name prefix. - + Individual storage of each polygon as a graph. - - Instances should use cluster_analysis as a name prefix. diff --git a/contributed_definitions/NXcg_polyline.nxdl.xml b/base_classes/NXcg_polyline.nxdl.xml similarity index 95% rename from contributed_definitions/NXcg_polyline.nxdl.xml rename to base_classes/NXcg_polyline.nxdl.xml index 50fec5fdc5..f5e247c756 100644 --- a/contributed_definitions/NXcg_polyline.nxdl.xml +++ b/base_classes/NXcg_polyline.nxdl.xml @@ -1,4 +1,4 @@ - + followed by the second vertex of the first polyline, until the last vertex of the first polyline. Thereafter, the first vertex of the second polyline, and so on and so forth. - Using the (cumulated) counts in number_of_vertices (:math:`n^v_i`), + Using the (cumulated) counts in number_of_vertices (:math:`n^v_i`), the vertices of the N-th polyline can be accessed on the array index interval :math:`[\sum_{i=0}^{i=N-1} n^v_i, \sum_{i=0}^{i=N} n^v_i]`. diff --git a/contributed_definitions/NXcg_primitive.nxdl.xml b/base_classes/NXcg_primitive.nxdl.xml similarity index 94% rename from contributed_definitions/NXcg_primitive.nxdl.xml rename to base_classes/NXcg_primitive.nxdl.xml index 4f5da5f2ae..2f096e316d 100644 --- a/contributed_definitions/NXcg_primitive.nxdl.xml +++ b/base_classes/NXcg_primitive.nxdl.xml @@ -1,9 +1,9 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. - Use the depends_on fields of the respective specialized - :ref:`NXcg_primitive` base class surplus - :ref:`NXcoordinate_system_set` with at least one instance of - :ref:`NXcoordinate_system` to define explicitly the reference frame in - which the primitives are defined. Alternatively, although - discouraged, one may use one :ref:`NXcoordinate_system_set` with with - only one :ref:`NXcoordinate_system` in the application definition to - specify implicitly in which reference frame the primitives are - defined. If none of these two possibilities is used all primitives - are assumed defined in the McStas coordinate system. + Use :ref:`NXcg_primitive` and :ref:`NXcoordinate_system` classes to + define explicitly the reference frame in which the primitives are + defined. diff --git a/contributed_definitions/NXcg_tetrahedron.nxdl.xml b/base_classes/NXcg_tetrahedron.nxdl.xml similarity index 88% rename from contributed_definitions/NXcg_tetrahedron.nxdl.xml rename to base_classes/NXcg_tetrahedron.nxdl.xml index 5288d9d0f4..95bf4e02dc 100644 --- a/contributed_definitions/NXcg_tetrahedron.nxdl.xml +++ b/base_classes/NXcg_tetrahedron.nxdl.xml @@ -1,4 +1,4 @@ - + - - - Constant to be used in the definition: the number of channels of the - circuit board. - - - - number of channels of the circuit board. - - - - Application definition for circuit devices. + Base class for documenting circuit devices. - Electronic circuits are hardware components connecting several electronic components to achieve + Electronic circuits are hardware components that connect several electronic components to achieve specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. - Hardware where the circuit is implanted; includes information about the hardware manufacturers and - type (e.g. part number) + Hardware where the circuit is implanted; includes information about the + hardware manufacturers and type (e.g. part number) All the elements below may be single numbers of an array of values with length N_channel describing multiple input and output channels. - + List of components used in the circuit, e.g., resistors, capacitors, transistors or any other complex components. - + Description of how components are interconnected, including connection points and wiring. - + Details of the power source for the circuit, including voltage and current ratings. - + Type of signal (input signal) the circuit is designed to handle, e.g., analog, digital, mixed-signal. @@ -74,9 +63,14 @@ - The operating frequency of the circuit, see also bandwidth below, which is possibly - centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth - amplifier at low, audio frequencies 1 - 20,000 Hz) + The operating frequency of the circuit, see also bandwidth, which is possibly + but not necessarily centered around this frequency (e.g. running a 100 kHz bandwidth + amplifier at low, audio frequencies 1 - 20,000 Hz). + + + + + The bandwidth of the frequency response of the circuit. @@ -92,18 +86,14 @@ - Gain of the circuit, if applicable, usually all instruments have a gain which might be - important or not. + Gain of the circuit, if applicable, usually all instruments have a gain + which might be important or not. - RMS noise level (in current or voltage) in the circuit in voltage or current. - - - - - The bandwidth of the frequency response of the circuit. + Root-mean-square (RMS) noise level (in current or voltage) + in the circuit in voltage or current. @@ -123,7 +113,7 @@ - Number of output channels collected to this circuit. Most probably N_channel. + Number of output channels connected to this circuit. Most probably N_channel. @@ -136,7 +126,7 @@ Power consumption of the circuit per unit time. - + Status indicators for the circuit, e.g., LEDs, display readouts. diff --git a/base_classes/NXcollectioncolumn.nxdl.xml b/base_classes/NXcollectioncolumn.nxdl.xml index 97d2aefce8..02fb82a7d5 100644 --- a/base_classes/NXcollectioncolumn.nxdl.xml +++ b/base_classes/NXcollectioncolumn.nxdl.xml @@ -91,7 +91,7 @@ Deflectors in the collection column section - + Individual lenses in the collection column section diff --git a/base_classes/NXcomponent.nxdl.xml b/base_classes/NXcomponent.nxdl.xml index 85ea0f7b81..d94bd41e56 100644 --- a/base_classes/NXcomponent.nxdl.xml +++ b/base_classes/NXcomponent.nxdl.xml @@ -1,4 +1,4 @@ - + - @@ -40,12 +38,14 @@ https://doi.org/10.1017/9781316337455.022--> Different technology partners use different conventions and models for quantifying the aberration coefficients. - The corrector in an electron microscope is composed of multiple lenses - and multipole stigmators with details that are specific for the technology partner - and microscope. Most technical details are proprietary knowledge. + Correctors in an electron microscope are composed of multiple lenses + and multipole stigmators. Their technical details are specific for the + technology partner as well as microscope. Most technical details are + proprietary knowledge. - If one component corrects for multiple types of aberrations (like it is the case reported - here `CEOS <https://www.ceos-gmbh.de/en/research/electrostat>`_) follow this design: + If one component corrects for multiple types of aberrations (like it is the case + reported here `CEOS <https://www.ceos-gmbh.de/en/research/electrostat>`_) follow this + design when using corrector and monochromator in an application definition: * Use :ref:`NXcorrector_cs` for spherical aberration * Use :ref:`NXmonochromator` for energy filtering or chromatic aberration @@ -57,9 +57,9 @@ https://doi.org/10.1017/9781316337455.022--> Was the corrector used? - + - Specific information about the alignment procedure that is a process during which + Specific information about the alignment procedure. This is a process during which the corrector is configured to enable calibrated usage of the instrument. This :ref:`NXprocess` group should also be used when one describes in a computer @@ -76,7 +76,8 @@ https://doi.org/10.1017/9781316337455.022--> The outer tilt angle of the beam in tableau acquisition. TODO: The relevant axes which span the tilt_angle need a - cleaner description. + cleaner description. Suggestions from the community are + welcome here for guiding an improvement of this base class. @@ -99,14 +100,14 @@ https://doi.org/10.1017/9781316337455.022--> - + Image(s) taken during the alignment procedure - Convention used for storing measured or estimated aberrations (for each image or final) + Convention used for storing measured or estimated aberrations (for each or the final image) via fields c_1, a_1, c_1_0, c_1_2_a, and so on and so forth. See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) @@ -162,46 +163,7 @@ https://doi.org/10.1017/9781316337455.022--> - - + diff --git a/base_classes/NXcs_computer.nxdl.xml b/base_classes/NXcs_computer.nxdl.xml new file mode 100644 index 0000000000..d02a32e4f4 --- /dev/null +++ b/base_classes/NXcs_computer.nxdl.xml @@ -0,0 +1,69 @@ + + + + + + Base class for reporting the description of a computer + + + + Given name/alias to the computing system, e.g. MyDesktop. + + + + + Name of the operating system, e.g. Windows, Linux, Mac, Android. + + + + Version plus build number, commit hash, or description of an ever + persistent resource where the source code of the program and build + instructions can be found so that the program can be configured in + such a manner that the result file is ideally recreatable yielding + the same results. + + + + + + + A globally unique persistent identifier of the computer, i.e. + the Universally Unique Identifier (UUID) of the computing node. + + + + + Multiple instances should be named processor1, processor2, etc. + + + + + Multiple instances should be named memory1, memory2, etc. + + + + + Multiple instances should be named storage1, storage2, etc. + + + diff --git a/base_classes/NXcs_filter_boolean_mask.nxdl.xml b/base_classes/NXcs_filter_boolean_mask.nxdl.xml new file mode 100644 index 0000000000..c4e453e028 --- /dev/null +++ b/base_classes/NXcs_filter_boolean_mask.nxdl.xml @@ -0,0 +1,86 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of entries (e.g. number of points or objects). + + + + + Number of bits assumed for the container datatype used. + + + + + Length of mask considering the eventual need for padding. + + + + + Base class for packing and unpacking booleans. + + The field mask should be constructed from packing a vector of booleans + (a bitfield) into unsigned integers with bytesize bitdepth. Padding to + an integer number of such integers is assumed. + + Thereby, this base class can be used to inform software about necessary modulo + operations to decode the mask to recover e.g. set membership of objects in sets + whose membership has been encoded as a vector of booleans. + + This is useful e.g. when processing object sets such as point cloud data. + If e.g. a spatial filter has been applied to a set of points, we may wish to document + memory-space efficiently which points were analyzed. An array of boolean values + is one option to achieve this. A value is true if the point is included and false otherwise. + + + + Possibility to refer to which set this mask applies. + + If depends_on is not provided, it is assumed that the mask + applies to its direct parent. + + + + + Number of objects represented by the mask. + + + + + Number of bits assumed matching on a default datatype. + (e.g. 8 bits for a C-style uint8). + + + + + The content of the mask. If padding is used, + padding bits have to be set to 0. + + + diff --git a/base_classes/NXcs_memory.nxdl.xml b/base_classes/NXcs_memory.nxdl.xml new file mode 100644 index 0000000000..0dfa2e171f --- /dev/null +++ b/base_classes/NXcs_memory.nxdl.xml @@ -0,0 +1,47 @@ + + + + + + Base class for reporting the description of the memory system of a computer. + + + + Typically, computers have multiple instances of memory. + + + + Qualifier for the type of random access memory. + + + + + + + + + Total amount of data which the medium can hold. + + + + diff --git a/base_classes/NXcs_prng.nxdl.xml b/base_classes/NXcs_prng.nxdl.xml new file mode 100644 index 0000000000..28303a0f6b --- /dev/null +++ b/base_classes/NXcs_prng.nxdl.xml @@ -0,0 +1,83 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Computer science description of pseudo-random number generator. + + The purpose of this base class is to identify if exactly the same sequence can be + reproduced, like for a PRNG or not, like for a true physically random source. + + + + Physical approach or algorithm whereby random numbers are generated. + + Different approaches for generating random numbers with a computer exists. + Some use a dedicated physical device whose the state is unpredictable + physically. Some use a strategy of mangling information from the system + clock. Also in this case the sequence is not reproducible without having + additional pieces of information. + + In most cases though so-called pseudo-random number generator (PRNG) + algorithms are used. These yield a deterministic sequence of practically + randomly appearing numbers. These algorithms differ in their quality in + how random the resulting sequences actually are, i.e. sequentially + uncorrelated. Nowadays one of the most commonly used algorithm is the + MersenneTwister (mt19937). + + + + + + + + + + + Name of the PRNG implementation and version. If such information is not + available or if the PRNG type was set to other the DOI to the publication + or the source code should be given. + + + + + Parameter of the PRNG controlling its initialization + and thus controlling the specific sequence generated. + + + + + Number of initial draws from the PRNG after its initialized with the seed. + These initial draws are typically discarded in an effort to equilibrate the + sequence. If no warmup was performed or if warmup procedures are unclear, + users should set the value to zero. + + + + diff --git a/base_classes/NXcs_processor.nxdl.xml b/base_classes/NXcs_processor.nxdl.xml new file mode 100644 index 0000000000..d4d3f7de48 --- /dev/null +++ b/base_classes/NXcs_processor.nxdl.xml @@ -0,0 +1,63 @@ + + + + + + Base class for reporting the description of processing units of a computer. + + Examples are e.g. classical so-called central processing units (CPUs), + coprocessors, graphic cards, accelerator processing units or a system of these. + + + + Typical examples for the granularization of processing units are: + + * A desktop computer with a single CPU; describe using one instance of NXcircuit. + * A dual-socket server; describe using two instances of NXcircuit. + * A server with two dual-socket server nodes; describe with four + instances of NXcircuit surplus a field that defines their level + in the hierarchy. + + + + General type of the processing unit e.g. + + * pu, processing core or hyper-threading core + * cpu, (multi-)core central processing unit + * gpu, (multi-)core general purpose processing unit + * fpga, field programmable gate array + + + + + + + + + + + Clock speed of the circuit + + + + diff --git a/base_classes/NXcs_profiling.nxdl.xml b/base_classes/NXcs_profiling.nxdl.xml new file mode 100644 index 0000000000..f934e98928 --- /dev/null +++ b/base_classes/NXcs_profiling.nxdl.xml @@ -0,0 +1,144 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Computer science description for performance and profiling data of an application. + + Performance monitoring and benchmarking of software is a task where questions + can be asked at various levels of detail. In general, there are three main + contributions to performance: + + * Hardware capabilities and configuration + * Software configuration and capabilities + * Dynamic effects of the system in operation and the system working together + with eventually multiple computers, especially when these have to exchange + information across a network and these are used usually by multiple users. + + At the most basic level users may wish to document how long e.g. a data + analysis with a scientific software, i.e. an app took. + A frequent idea is here to answer practical questions like how critical is the + effect on the workflow of the scientists, i.e. is the analysis possible in + a few seconds or would it take days if I were to run this analysis on a + comparable machine? + For this more qualitative performance monitoring, mainly the order of + magnitude is relevant, as well as how this was achieved using parallelization + (i.e. reporting the number of CPU and GPU resources used, the number of + processes and threads configured, and providing basic details about the computer). + + At more advanced levels benchmarks may go as deep as detailed temporal tracking + of individual processor instructions, their relation to other instructions, the + state of call stacks; in short eventually the entire app execution history + and hardware state history. Such analyses are mainly used for performance + optimization, i.e. by software and hardware developers as well as for + tracking bugs. Specialized software exists which documents such performance + data in specifically-formatted event log files or databases. + + This base class cannot and should not replace these specific solutions for now. + Instead, the intention of the base class is to serve scientists at the + basic level to enable simple monitoring of performance data and log profiling + data of key algorithmic steps or parts of computational workflows, so that + these pieces of information can guide users which order of magnitude differences + should be expected or not. + + Developers of application definitions should add additional fields and + references to e.g. more detailed performance data to which they wish to link + the metadata in this base class. + + + + + Path to the directory from which the tool was called. + + + + + Command line call with arguments if applicable. + + + + + ISO 8601 time code with local time zone offset to UTC information + included when the app was started. + + + + + ISO 8601 time code with local time zone offset to UTC information + included when the app terminated or crashed. + + + + + Wall-clock time how long the app execution took. This may be in principle + end_time minus start_time; however usage of eventually more precise timers + may warrant to use a finer temporal discretization, + and thus demands a more precise record of the wall-clock time. + + + + + The number of nominal processes that the app invoked at runtime. + + The main idea behind this field e.g. for apps which use e.g. MPI + (Message Passing Interface) parallelization is to communicate + how many processes were used. + + For sequentially running apps number_of_processes and number_of_threads + is one. If the app exclusively uses GPU parallelization, number_of_gpus + can be larger than one. If no GPU is used, number_of_gpus is zero, + even though the hardware may have GPUs installed. + + + + + The number of nominal threads that the app invoked at runtime. + Specifically here the maximum number of threads used for the + high-level threading library used (e.g. OMP_NUM_THREADS), posix. + + + + + The number of nominal GPUs that the app invoked at runtime. + + + + + A collection with one or more computing nodes each with own resources. + This can be as simple as a laptop or the nodes of a cluster computer. + + + + + A collection of individual profiling event data which detail e.g. how + much time the app took for certain computational steps and/or how much + memory was consumed during these operations. + ID is an increasing unsigned integer starting at 1. + + + diff --git a/contributed_definitions/NXcs_profiling_event.nxdl.xml b/base_classes/NXcs_profiling_event.nxdl.xml similarity index 50% rename from contributed_definitions/NXcs_profiling_event.nxdl.xml rename to base_classes/NXcs_profiling_event.nxdl.xml index ffc3e8285c..efcdb60e01 100644 --- a/contributed_definitions/NXcs_profiling_event.nxdl.xml +++ b/base_classes/NXcs_profiling_event.nxdl.xml @@ -1,4 +1,4 @@ - + + + + Base class for reporting the description of the I/O of a computer. + + + + + Qualifier for the type of storage medium used. + + + + + + + + + + + Total amount of data which the medium can hold. + + + + + Maximum read rate of the storage medium. + + + + + Maximum write rate of the storage medium. + + + + diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml index 826cd29158..8a87f560f3 100644 --- a/base_classes/NXdata.nxdl.xml +++ b/base_classes/NXdata.nxdl.xml @@ -1,4 +1,4 @@ - + - - - + Base class for an electro-magnetic lens or a compound lens. - + For :ref:`NXtransformations` the origin of the coordinate system is placed - in the center of the lens (its polepiece, pinhole, or another - point of reference). The origin should be specified in the :ref:`NXtransformations`. - - For details of electro-magnetic lenses in the literature see e.g. + in the center of the lens its polepiece, pinhole, or another point of reference. + The origin should be specified in the :ref:`NXtransformations`. + + For details of electro-magnetic lenses in the literature see e.g. * `L. Reimer: Scanning Electron Microscopy <https://doi.org/10.1007/978-3-540-38967-5>`_ * `P. Hawkes: Magnetic Electron Lenses <https://link.springer.com/book/10.1007/978-3-642-81516-4>`_ * `Y. Liao: Practical Electron Microscopy and Database <https://www.globalsino.com/EM/>`_ - @@ -51,7 +45,7 @@ with other research fields (MPES, XPS, OPT) could be useful--> Ideally, use instances of ``identifierNAME`` to point to a resource that provides further details. - + If such a resource does not exist or should not be used, use this free text, although it is not recommended. @@ -61,8 +55,8 @@ with other research fields (MPES, XPS, OPT) could be useful--> Descriptor for the lens excitation when the exact technical details are unknown or not directly controllable as the control software of the microscope does not enable or was not configured to display these - values (for end users). - + values for users. + Although this value does not document the exact physical voltage or excitation, it can still give useful context to reproduce the lens setting, provided a properly working instrument and software sets the lens @@ -75,7 +69,7 @@ with other research fields (MPES, XPS, OPT) could be useful--> Descriptor for the operation mode of the lens when other details are not directly controllable as the control software of the microscope does not enable or is not configured to display these values. - + Like value, the mode can only be interpreted for a specific microscope but can still be useful to guide users as to how to repeat the measurement. @@ -84,7 +78,7 @@ with other research fields (MPES, XPS, OPT) could be useful--> Excitation voltage of the lens. - + For dipoles it is a single number. For higher order multipoles, it is an array. @@ -92,7 +86,7 @@ with other research fields (MPES, XPS, OPT) could be useful--> Excitation current of the lens. - + For dipoles it is a single number. For higher-order multipoles, it is an array. @@ -111,4 +105,9 @@ with other research fields (MPES, XPS, OPT) could be useful--> + + + Qualitative description of the lens based on the number of pole pieces. + + diff --git a/base_classes/NXelectronanalyzer.nxdl.xml b/base_classes/NXelectronanalyzer.nxdl.xml index 6d0d4b6f15..1d990fec5e 100644 --- a/base_classes/NXelectronanalyzer.nxdl.xml +++ b/base_classes/NXelectronanalyzer.nxdl.xml @@ -272,7 +272,7 @@ Deflectors outside the main optics ensembles described by the subclasses - + Individual lenses outside the main optics ensembles described by the subclasses diff --git a/contributed_definitions/NXem_ebsd.nxdl.xml b/base_classes/NXem_ebsd.nxdl.xml similarity index 98% rename from contributed_definitions/NXem_ebsd.nxdl.xml rename to base_classes/NXem_ebsd.nxdl.xml index ade63a5774..55dcc79d88 100644 --- a/contributed_definitions/NXem_ebsd.nxdl.xml +++ b/base_classes/NXem_ebsd.nxdl.xml @@ -1,4 +1,4 @@ - + + An overview of the entire ROI. diff --git a/contributed_definitions/NXem_eds.nxdl.xml b/base_classes/NXem_eds.nxdl.xml similarity index 95% rename from contributed_definitions/NXem_eds.nxdl.xml rename to base_classes/NXem_eds.nxdl.xml index a39e52e717..31d4beb20c 100644 --- a/contributed_definitions/NXem_eds.nxdl.xml +++ b/base_classes/NXem_eds.nxdl.xml @@ -1,4 +1,4 @@ - + - @@ -108,9 +105,6 @@ energy typically the fastest direction--> However, a collection of instances of NXpeak with individual NXatom can be used to add isotopic information and other relevant context. - - - @@ -144,7 +138,7 @@ energy typically the fastest direction--> - + Individual element-specific EDS/EDX/EDXS/SXES mapping @@ -167,7 +161,7 @@ energy typically the fastest direction--> Discouraged free-text field to add additional information. - + Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that documents which elements and their specific lines are theoretically located within diff --git a/contributed_definitions/NXem_eels.nxdl.xml b/base_classes/NXem_eels.nxdl.xml similarity index 98% rename from contributed_definitions/NXem_eels.nxdl.xml rename to base_classes/NXem_eels.nxdl.xml index 42ce8a783f..f76b090dea 100644 --- a/contributed_definitions/NXem_eels.nxdl.xml +++ b/base_classes/NXem_eels.nxdl.xml @@ -1,4 +1,4 @@ - + diff --git a/base_classes/NXem_interaction_volume.nxdl.xml b/base_classes/NXem_interaction_volume.nxdl.xml new file mode 100644 index 0000000000..c7f6fe27ab --- /dev/null +++ b/base_classes/NXem_interaction_volume.nxdl.xml @@ -0,0 +1,56 @@ + + + + + + Base class to describe the volume of interaction for particle-matter interaction. + + Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam + interaction simulations can be used to qualify and (or) quantify the shape of + the interaction volume. Results of such simulations can be summary statistics + or single-particle-resolved sets of trajectories. + + Explicit or implicit descriptions of the geometry of this + interaction volume are possible: + + * An implicit description is via a set of electron/specimen interactions + represented ideally as trajectory data from the computer simulation. + * An explicit description is via iso-contour surface using either + a simulation grid or a triangulated surface mesh of the approximated + iso-contour surface evaluated at specific threshold values. + Iso-contours could be computed from electron or particle flux through + an imaginary control surface (the iso-surface) or energy-levels + (e.g. the case of X-rays). Details depend on the model. + * Another explicit description is via theoretical models which may + be relevant e.g. for X-ray spectroscopy + + Further details on how the interaction volume can be quantified + is available in the literature for example: + + * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ + * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ + * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ + + + + diff --git a/base_classes/NXem_measurement.nxdl.xml b/base_classes/NXem_measurement.nxdl.xml new file mode 100644 index 0000000000..4648fe57ac --- /dev/null +++ b/base_classes/NXem_measurement.nxdl.xml @@ -0,0 +1,30 @@ + + + + + + Base class for documenting a measurement with an electron microscope. + + + + diff --git a/contributed_definitions/NXoptical_system_em.nxdl.xml b/base_classes/NXem_optical_system.nxdl.xml similarity index 92% rename from contributed_definitions/NXoptical_system_em.nxdl.xml rename to base_classes/NXem_optical_system.nxdl.xml index c39440e874..73c90f0057 100644 --- a/contributed_definitions/NXoptical_system_em.nxdl.xml +++ b/base_classes/NXem_optical_system.nxdl.xml @@ -1,4 +1,4 @@ - + - + Base class for qualifying an electron optical system. @@ -73,12 +73,17 @@ .. _Working Distance: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 - + + Geometry of the cross-section formed when the primary beam shines onto the - specimen surface. + specimen surface. Reported as length of the semiaxes of the ellipsoidal + cross-section with semiaxes values sorted by decreasing length. - + + + + @@ -108,7 +113,7 @@ rank: 2--> - In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated + In the process of passing through an :ref:`NXelectromagnetic_lens` electrons are typically accelerated on a helical path about the optical axis. This causes an image rotation whose strength is affected by the magnification. diff --git a/base_classes/NXem_simulation.nxdl.xml b/base_classes/NXem_simulation.nxdl.xml new file mode 100644 index 0000000000..6ec01a7965 --- /dev/null +++ b/base_classes/NXem_simulation.nxdl.xml @@ -0,0 +1,32 @@ + + + + + + Base class for documenting a simulation of electron beam-matter interaction. + + + + + + diff --git a/base_classes/NXenergydispersion.nxdl.xml b/base_classes/NXenergydispersion.nxdl.xml index 1381cb6adc..0e42021f72 100644 --- a/base_classes/NXenergydispersion.nxdl.xml +++ b/base_classes/NXenergydispersion.nxdl.xml @@ -168,7 +168,7 @@ Deflectors in the energy dispersive section - + Individual lenses in the energy dispersive section diff --git a/base_classes/NXentry.nxdl.xml b/base_classes/NXentry.nxdl.xml index fffe80e6da..fbe7e00acc 100755 --- a/base_classes/NXentry.nxdl.xml +++ b/base_classes/NXentry.nxdl.xml @@ -128,7 +128,7 @@ Brief summary of the collection, including grouping criteria. - unique identifier for the measurement, defined by the facility. + Unique identifier for the measurement, defined by the facility. unique identifier for the measurement, defined by the facility. diff --git a/base_classes/NXevent_data_apm.nxdl.xml b/base_classes/NXevent_data_apm.nxdl.xml new file mode 100644 index 0000000000..820f061d95 --- /dev/null +++ b/base_classes/NXevent_data_apm.nxdl.xml @@ -0,0 +1,119 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of pulses collected in between start_time and end_time. + + + + + Base class to store state and (meta)data of events over the course of an atom probe experiment. + + Having at least one instance for an instance of NXapm is recommended. + + This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs + of atom probe research. Again static and dynamic quantities are split to avoid a duplication + of information. Specifically, the time interval considered is the entire time + starting at start_time until end_time during which we assume the pulser triggered pulses. + These pulses are identified via the pulse_id field. The point in time when each pulse was + fired can be recovered from analyzing start_time and delta_time. + + Which temporal granularity is adequate depends on the situation and research question. + Using a model which enables a collection of events offers the most flexible way to cater for + both atom probe experiments or simulation. To monitor the course of an ion extraction experiment + (or simulation) it makes sense to track time explicitly via time stamps or implicitly + via e.g. a clock inside the instrument, such as the clock of the pulser and respective pulse_id. + + + + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval started. + + If users wish to specify an interval of time that the snapshot should represent + during which the instrument was stable and configured using specific settings and + calibrations, the start_time is the start, the left bound of the time interval, while + the end_time specifies the end, the right bound of the time interval. + + + + + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval ended. + + + + + Delta time array which resolves for each pulse_id the time difference + between when that pulse was fired and start_time. + + In summary, using start_time, end_time, delta_time, pulse_id_offset, + and pulse_id provides temporal context information when a pulse was + fired relative to start_time and when it is relevant to translate this into + coordinated world time UTC. + + Note that pulses in reality have a shape and thus additional documentation + is required to assure that the entries in delta_time are always taken at + at points in time that, relative to the triggering of the pulse, represent an + as close as possible state of the pulse. + + + + + + + + Integer which defines the first pulse_id. + Typically, this is either zero or one. + + + + + An integer to identify a specific pulse in a sequence. + + There are two possibilities to report pulse_id values: + If pulse_id_offset is provided, the pulse_id values are defined + by the sequence :math:`[pulse\_id\_offset, pulse\_id\_offset + p]` + with :math:`p` the number of pulses collected in between + start_time and end_time. + + Alternatively, pulse_id_offset is not provided but instead + a sequence of :math:`p` values is defined. + These integer values do not need to be sorted. + + + + + + + + Place to store dynamic metadata of the instrument to document as close as possible + the state of the instrument during the event, i.e. in between start_time and end_time. + + + diff --git a/contributed_definitions/NXevent_data_em.nxdl.xml b/base_classes/NXevent_data_em.nxdl.xml similarity index 78% rename from contributed_definitions/NXevent_data_em.nxdl.xml rename to base_classes/NXevent_data_em.nxdl.xml index 5f8396228f..c26a78a7e6 100644 --- a/contributed_definitions/NXevent_data_em.nxdl.xml +++ b/base_classes/NXevent_data_em.nxdl.xml @@ -1,4 +1,4 @@ - + + + + Base class for a set of components equipping an instrument with FIB capabilities. + + Focused-ion-beam (FIB) capabilities turn especially scanning electron microscopes + into specimen preparation labs. FIB is a material preparation technique whereby + portions of the sample are illuminated with a focused ion beam with controlled + intensity. The beam is controlled such that it is intense, focused, and equipped + with sufficient ion having sufficient momentum to remove material in a controlled + manner. + + The fact that an electron microscope with FIB capabilities achieves these functionalities + via a second component (aka the ion gun) that has its own relevant control circuits, + focusing lenses, and other components, warrants the definition of an own base class + to group these components and distinguish them from the lenses and components for creating + and shaping the electron beam. + + For more details about the relevant physics and application examples + consult the literature, for example: + + * `L. A. Giannuzzi et al. <https://doi.org/10.1007/b101190>`_ + * `E. I. Preiß et al. <https://link.springer.com/content/pdf/10.1557/s43578-020-00045-w.pdf>`_ + * `J. F. Ziegler et al. <https://www.sciencedirect.com/science/article/pii/S0168583X10001862>`_ + * `J. Lili <https://www.osti.gov/servlets/purl/924801>`_ + * `N. Yao <https://doi.org/10.1017/CBO9780511600302>`_ + + + + Tech-partner, microscope-, and control-software-specific name of the + specific operation mode how the ibeam_column and its components are + controlled to achieve specific illumination conditions. + + In many cases the users of an instrument do not or can not be expected to know + all intricate spatiotemporal dynamics of their hardware. Instead, they rely on + assumptions that the instrument, its control software, and components work as + expected to focus on their research questions. + + For these cases, having a place for documenting the operation_mode is useful + in as much as at least some constraints on how the illumination conditions were + is documented. + + + + + The source which creates the ion beam. + + + + Given name/alias for the ion gun. + + + + + Emitter type used to create the ion beam. + + If the emitter type is other, give further + details in the description field. + + + + + + + + + + + Ideally, a (globally) unique persistent identifier, link, + or text to a resource which gives further details. + + + + + Which elements, ions, or molecular ions form the beam. + Examples are gallium, helium, neon, argon, krypton, + or xenon, O2+. + + + + + Average/nominal flux + + + + + Average/nominal brightness + + + + + + Charge current + + + + + Ion acceleration voltage upon source exit and + entering the vacuum flight path. + + + + + To be defined more specifically. Community suggestions are welcome. + + + + + + + + + A component for blanking the ion beam or generating pulsed ion beams. + + + + + + + + Individual characterization results for the position, shape, + and characteristics of the ion beam. + + :ref:`NXtransformations` should be used to specify the location or position + at which details about the ion beam are probed. + + + + + + diff --git a/contributed_definitions/NXimage.nxdl.xml b/base_classes/NXimage.nxdl.xml similarity index 67% rename from contributed_definitions/NXimage.nxdl.xml rename to base_classes/NXimage.nxdl.xml index 9bafb0b584..1bbf7b281e 100644 --- a/contributed_definitions/NXimage.nxdl.xml +++ b/base_classes/NXimage.nxdl.xml @@ -1,4 +1,4 @@ - + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of pulses collected in between start_time and end_time + inside a parent instance of :ref:`NXevent_data_apm`. + + + - Base class to document an instrument used for atom probe microscopy. + Base class for instrument-related details of a real or simulated + atom probe tomograph or field-ion microscope. - Inheriting from NXinstrument, this base class is designed to offer the same concepts about - instrument-centric metadata to be used in two places inside NXapm without demanding that - the application definition needs to define the concepts in two places as maintaining this is - prone to errors. This base class implements the key design idea behind the NXapm application - definition in that we would like to offer a design where all (meta)data which over the course - of a measurement remain static can be stored only once and without polluting the application - definition with another group with concepts that should be used for storing (meta)data about - the instrument during events that happen during the course of the measurement. + For collecting data and experiments which are simulations of an atom probe + microscope or a session with such instrument use the :ref:`NXapm` application definition + and the :ref:`NXevent_data_apm` groups it provides. - This design was inspired by NXem and electron microscopy where typically the instrument is - used in sessions and dozens of logical sets of data are collected under not necessarily always - the same instrument conditions. We do not want to repeat therefore the static (meta)data, as - this is redundant storage by virtue of design. The typical example is an electron microscope - where hundreds of images are taken and all static instrument data stored with each image. - This makes sense in cases when the image is used as a digital artifact that is exchanged across - different software applications or research data management systems but as in NeXus there - is either all information bundled into one artifact or there is a coordinating master artifact - that references related artifacts there is no point to store hundreds of times that always the - same microscope with the same lens setup was used to collect these images. + This base class implements the concept of :ref:`NXapm` whereby (meta)data are distinguished + whether these typically change during a session, so-called dynamic, or not, so-called static metadata. + This design allows to store e.g. hardware related concepts only once instead of demanding + that each image or spectrum from the session needs to be stored also with the static metadata. @@ -82,21 +83,27 @@ or volatile (meta)data.--> - + Location of the lab or place where the instrument is installed. Using GEOREF is preferred. + + + Nominal flight path + + The value can be extracted from the CAnalysis.CSpatial.fFlightPath + field of a CamecaRoot ROOT file. + + Device which reduces ToF differences of ions in ToF experiments. For atom probe the reflectron can be considered an energy compensation device. - Such a device can be realized technically for example with a Poschenrieder lens. + Such a device can be realized technically e.g. with a Poschenrieder lens. Consult the following U.S. patents for further details: @@ -114,15 +121,13 @@ Possibility to include a detailed computational geometry description of the inst - + A counter electrode of the LEAP 6000 series atom probes. - - + + A local electrode guiding the ion flight path. Also called counter or extraction electrode. @@ -132,13 +137,27 @@ according to A. Breen (UNSW)--> Acceleration voltage + + + The type of aperture used when the local_electrode has an aperture or acts as an aperture + in addition to acting as an extraction electrode. + + The local electrode is a component which combines functionalities + of :ref:`NXelectromagnetic_lens`, :ref:`NXaperture`, if not even :ref:`NXdeflector`: + + * "n/a", use when no aperture is present in the experiment + * "conical", conical aperture with a circular hole + * "feedthrough", an aperture where the specimen protrudes through a circular hole + * "custom", a user modified aperture, which is otherwise non-standard + + + + + + + + - Detector for taking raw time-of-flight and ion/hit impact positions data. @@ -148,8 +167,10 @@ NEW ISSUE: local electrode, baking strategies, storage--> Amplitude of the signal detected on the multi-channel plate (MCP). This field should be used for storing the signal amplitude quantity - within ATO files. The ATO file format is used primarily by the - atom probe groups of the GPM in Rouen, France. + within ATO files when the detector was an MCP. + + The ATO file format is used primarily by the atom probe group of the + GPM in Rouen, France. @@ -157,12 +178,14 @@ NEW ISSUE: local electrode, baking strategies, storage--> - CRunHeader.fMcpEfficiency + The value can be extracted from the CRunHeader.fMcpEfficiency + field of a CamecaRoot RHIT file. - CRunHeader.fMeshEfficiency + The value can be extracted from the CRunHeader.fMeshEfficiency + field of a CamecaRoot RHIT file. @@ -170,6 +193,22 @@ NEW ISSUE: local electrode, baking strategies, storage--> Laser- and/or voltage-pulsing device to trigger ion removal. + + When the base class NXinstrument_apm is used in the NXapm + application definition, the values for the following fields: + + * pulse_frequency + * pulse_fraction + * pulse_voltage + * pulse_number + * standing_voltage + * pulse_energy + * incidence_vector + * pinhole_position + * spot_position + + should be recorded in the order of, and assumed associated, + with the pulse_id in an instance of :ref:`NXevent_data_apm`. @@ -183,23 +222,10 @@ NEW ISSUE: local electrode, baking strategies, storage--> - Frequency with which the pulser fire(s). - - - Path to identifier_pulse - - @@ -210,11 +236,6 @@ case very efficiently we go for with an array of length 1xn_ions--> (as a function of standing voltage). Otherwise, this field should not be present. - - - Path to identifier_pulse - - Pulsed voltage, in laser pulsing mode this field can be omitted. - - - Path to identifier_pulse - - Absolute number of pulses starting from the beginning of the experiment. - - - Path to identifier_pulse - - - Direct current voltage between the specimen and the (local electrode) in the case of local electrode atom probe (LEAP) instrument. Otherwise, the standing voltage applied to the sample, relative to system ground. - - - Path to identifier_pulse - - - + - Atom probe microscopes use controlled laser, voltage, or a combination of - pulsing strategies to trigger ion extraction via exciting and eventual field evaporation + Group to store details about components that enable laser pulsing strategies. + + When multiple sources are available, these should be named source1, source2; + the LEAP 6000 series instruments have two sources. The majority of instruments + still has one source. In this case the variable part "ID" can be omitted. + Consequently the group should be named "source" when writing instance data. + + Atom probe microscopes use controlled laser, voltage, or a combination of pulsing + strategies to trigger ion extraction via exciting and eventual field evaporation field emission of ion at the specimen surface. @@ -274,11 +286,11 @@ existence constraint is independent of other values.--> - Path to identifier_pulse + Path to pulse_id - + Details about specific positions along the laser beam which illuminates the (atom probe) specimen. @@ -289,33 +301,18 @@ existence constraint is independent of other values.--> how the laser beam shines on the specimen, i.e. the mean vector is parallel to the laser propagation direction. - - - Path to identifier_pulse - - Track time-dependent settings over the course of the measurement where the laser beam exits the focusing optics. - - - Path to identifier_pulse - - Track time-dependent settings over the course of the measurement where the laser hits the specimen. - - - Path to identifier_pulse in an instance of :ref:`NXevent_data_apm`. - - @@ -332,7 +329,8 @@ existence constraint is independent of other values.--> - CRunHeader.CAnalysis.fSpecimenTemperature + The value can be extracted from the CRunHeader.CAnalysis.fSpecimenTemperature + field of a CamecaRoot RHIT file. @@ -353,7 +351,8 @@ existence constraint is independent of other values.--> - CRunHeader.CLasHeader.fAnalysisPressure + The value can be extracted from the CRunHeader.CLasHeader.fAnalysisPressure + field of a CamecaRoot RHIT file. @@ -368,24 +367,21 @@ existence constraint is independent of other values.--> Free-text field for additional comments. - + Relevant quantities during a measurement with a LEAP system as were suggested by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_. - Parameter set typically in the GUI of the control software which - defines the rules and control loops whereby the pulser and other - components of the instrument are controlled during evaporation. + Parameter that defines the rules and control loops whereby the pulser and + other components of the instrument are controlled during evaporation. - Control parameter set typically in the GUI relevant to assure that - the instrument internally controls its settings such to assure a - significant yet not too high ion influx on the detector to avoid - detection losses. + Parameter that assure maintenance of a significant yet not too high + ion influx on the detector to avoid detection losses. diff --git a/contributed_definitions/NXinstrument_em.nxdl.xml b/base_classes/NXinstrument_em.nxdl.xml similarity index 92% rename from contributed_definitions/NXinstrument_em.nxdl.xml rename to base_classes/NXinstrument_em.nxdl.xml index f0aee02a21..3e4b358e18 100644 --- a/contributed_definitions/NXinstrument_em.nxdl.xml +++ b/base_classes/NXinstrument_em.nxdl.xml @@ -1,9 +1,9 @@ - + - + Description of the type of the detector. @@ -87,8 +87,7 @@ direct electron, CMOS, or image plate to name but a few. - - + Stages in an electron microscope are multi-functional devices. @@ -96,8 +95,8 @@ on the specimen. Modern stages realize a hierarchy of components. A multi-axial tilt rotation holder is a good example where the control of each degree of freedom is technically implemented via providing instances - of either :ref:`NXpositioner`, :ref:`NXactuator`, or specialized :ref:`NXobject` - that achieve the rotating and positioning of the specimen. + of e.g. :ref:`NXpositioner` or :ref:`NXactuator` that achieve the rotating + and positioning of the specimen. The physical process of mounting a specimen on a stage in practice often comes with an own hierarchy of fixtures to bridge e.g. length scales technically. @@ -134,7 +133,6 @@ - Principal design of the stage. @@ -213,15 +211,20 @@ in a particular narrow community which work with that particular microscope--> - + - In contrast to the stage, the nanoprobe is an additional manipulator that is specifically + In contrast to the stage, the nanoprobe is an additional manipulator that is a specifically frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and - relocated portions of the specimen that have been cut free to realize specialized - geometries locally and enable site-specific measurements. + relocated portions of the specimen that have been cut off during site-specific lift-outs + and specimen preparation. + + + + + Gas injection systems (GIS) are components of microscopes that are equipped with focused-ion beam + capabilities. The component is used to introduce reactive neutral gases to the sample surface for + enhanced etching, preferential etching, or material deposition. - - diff --git a/base_classes/NXpeak.nxdl.xml b/base_classes/NXpeak.nxdl.xml index 1fe7e814ce..e23b87ca65 100644 --- a/base_classes/NXpeak.nxdl.xml +++ b/base_classes/NXpeak.nxdl.xml @@ -28,14 +28,14 @@ - Rank of the dependent and independent data arrays (for - multivariate scalar-valued fit.) + Rank of the dependent and independent data arrays + (for multivariate scalar-valued fit). Base class for describing a peak, its functional form, and support values - (i.e., the discretization (points) at which the function has been evaluated). + i.e., the discretization points at which the function has been evaluated. @@ -51,7 +51,7 @@ - The ``position`` field must have the same rank (``dimRank``) + The ``position`` field must have the same rank ``dimRank`` as the ``intensity`` field. Each individual dimension of ``position`` must have the same number of points as the corresponding dimension in the ``intensity`` field. @@ -64,7 +64,7 @@ - The ``intensity`` field must have the same rank (``dimRank``) + The ``intensity`` field must have the same rank ``dimRank`` as the ``intensity`` field. Each individual dimension of ``position`` must have the same number of points as the corresponding dimension in the ``position`` field. @@ -74,8 +74,8 @@ - The functional form of the peak. This could be a Gaussian, Lorentzian, - Voigt, etc. + The functional form of the peak. This could be a Gaussian, Lorentzian, Voigt, + etc. diff --git a/contributed_definitions/NXphase.nxdl.xml b/base_classes/NXphase.nxdl.xml similarity index 77% rename from contributed_definitions/NXphase.nxdl.xml rename to base_classes/NXphase.nxdl.xml index 756ad3edbe..1b2797b910 100644 --- a/contributed_definitions/NXphase.nxdl.xml +++ b/base_classes/NXphase.nxdl.xml @@ -1,4 +1,4 @@ - + - + + + + diff --git a/base_classes/NXprocess.nxdl.xml b/base_classes/NXprocess.nxdl.xml index 39e5da3bf8..8686b8890a 100644 --- a/base_classes/NXprocess.nxdl.xml +++ b/base_classes/NXprocess.nxdl.xml @@ -1,9 +1,9 @@ - + - Device to reduce an atmosphere (real or simulated) to a controlled pressure. + Device to reduce an atmosphere to a controlled pressure. Principle type of the pump. - + + + + + + + + + + The minimum pressure achievable in a chamber after + it has been pumped down for an extended period. + + + + + The material being moved by the pump. + + Pumps intending to create a vacuum should state "vacuum" as the medium, + while pumps having the primary purpose of creating a flow or pressure + of gas should state "gas" as the medium. + + + + + + + + + + Base class to report on the characterization of an area or volume of material. + + This area or volume of material is considered a region-of-interest (ROI). + + This base class should be used when the characterization was achieved by + processing data from experiment or computer simulations into models of + the microstructure of the material and the properties of the material or its + crystal defects within this ROI. Microstructural features is a narrow synonym + for these crystal defects. + + This base class can also be used to store data and metadata of the + representation of the ROI, i.e. its discretization and shape. + + Methods from computational geometry are typically used for + defining a discretization of the area and volume. + + Do not confuse this base class with :ref:`NXregion`. The purpose + of the :ref:`NXregion` base class is to document data access i.e. + I/O pattern on arrays. Therefore, concepts from :ref:`NXregion` operate + in data space rather than in real or simulated real space. + + + diff --git a/base_classes/NXroot.nxdl.xml b/base_classes/NXroot.nxdl.xml index 3aa87fb025..64e72f055a 100644 --- a/base_classes/NXroot.nxdl.xml +++ b/base_classes/NXroot.nxdl.xml @@ -102,7 +102,7 @@ A list of concepts in an application definition this file describes. This is for partially filling an application definition. If this attribute is not present the application definition is assumed - to be valid, if not only the specified concepts/paths are assumed to be valid. + to be valid, if not only the specified concepts/paths are assumed to be valid. diff --git a/base_classes/NXrotations.nxdl.xml b/base_classes/NXrotations.nxdl.xml new file mode 100644 index 0000000000..f931ac2591 --- /dev/null +++ b/base_classes/NXrotations.nxdl.xml @@ -0,0 +1,244 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The cardinality of the set, i.e. the number of value tuples. + + + + + How many phases with usually different crystal and symmetry are distinguished. + + + + + + Base class to detail a set of rotations, orientations, and disorientations. + + For getting a more detailed insight into the discussion of the + parameterized description of orientations in materials science see: + + * `H.-J. Bunge <https://doi.org/10.1016/C2013-0-11769-2>`_ + * `T. B. Britton et al. <https://doi.org/10.1016/j.matchar.2016.04.008>`_ + * `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_ + * `A. Morawiec <https://doi.org/10.1007/978-3-662-09156-2>`_ + + Once orientations are defined, one can continue to characterize the + misorientation and specifically the disorientation. The misorientation describes + the rotation that is required to register the lattices of two oriented objects + (like crystal lattice) into a crystallographic equivalent orientation: + + * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ + + The concepts of mis- and disorientation are relevant when analyzing the + crystallography of interfaces. + + + + Reference to an instance of :ref:`NXcoordinate_system` which contextualizes + how the here reported parameterized quantities can be interpreted. + + + + + Point group which defines the symmetry of the crystal. + + This has to be at least a single string. If crystal_symmetry is not + provided, point group 1 is assumed. + + In the case that misorientation or disorientation fields are used + and the two crystal sets resolve for phases with a different + crystal symmetry, this field needs to encode two strings: + The first string is for phase A. The second string is for phase B. + An example of this most complex case is the description of the + disorientation between crystals adjoining a hetero-phase boundary. + + + + + + + + Point group which defines an assumed symmetry imprinted upon processing + the material/sample which could give rise to or may justify to use a + simplified description of rotations, orientations, misorientations, + and disorientations via numerical procedures that are known as + symmetrization. + + If sample_symmetry is not provided, point group 1 is assumed. + + The traditionally used symmetrization operations within the texture + community in Materials Science, though, have become obsolete thanks + to improvements in methods, software, and available computing power. + + Therefore, users are encouraged to set the sample_symmetry to 1 (triclinic). + + In practice one often faces situations where indeed these assumed + symmetries are anyway not fully observed, and thus an accepting of + eventual inaccuracies just for the sake of reporting a simplified + symmetrized description should be avoided. + + + + + + + + The set of rotations expressed in quaternion parameterization considering + crystal_symmetry and sample_symmetry. Rotations which should be + interpreted as antipodal are not marked as such. + + + + + + + + + The set of rotations expressed in Euler angle parameterization considering + the same applied symmetries as detailed for the field rotation_quaternion. + To interpret Euler angles correctly, it is necessary to inspect the rotation + conventions behind reference_frame to resolve which of the many possible + Euler-angle conventions (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. + + + + + + + + + + + True for all those value tuples which have assumed antipodal symmetry. + False for all others. + + + + + + + + The set of orientations expressed in quaternion parameterization and + obeying symmetry for equivalent cases as detailed in crystal_symmetry + and sample_symmetry. The supplementary field is_antipodal can be used + to mark orientations with the antipodal property. + + + + + + + + + The set of orientations expressed in Euler angle parameterization following + the same assumptions like for orientation_quaternion. + To interpret Euler angles correctly, it is necessary to inspect the rotation + conventions behind reference_frame to resolve which of the many Euler-angle + conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. + + + + + + + + + + The set of misorientations expressed in quaternion parameterization + obeying symmetry operations for equivalent misorientations + as defined by crystal_symmetry and sample_symmetry. + + The misorientation should not be confused with the disorientation, + as for the latter the angular argument is expected to be the minimal + obeying symmetries. + + + + + + + + + Misorientation angular argument (eventually signed) following the same + symmetry assumptions as expressed for the field misorientation_quaternion. + + + + + + + + Misorientation axis (normalized) and signed following the same + symmetry assumptions as expressed for the field misorientation_angle. + + + + + + + + + + The set of disorientations expressed in quaternion parameterization + obeying symmetry operations for equivalent disorientations + as defined by crystal_symmetry and sample_symmetry. + + + + + + + + + Disorientations angular argument (should not be signed, see + `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) + following the same symmetry assumptions as expressed for the field + disorientation_quaternion. + + + + + + + + Disorientations axis (normalized) following the same symmetry assumptions + as expressed for the field disorientation_angle. + + + + + + + diff --git a/contributed_definitions/NXscanbox_em.nxdl.xml b/base_classes/NXscan_controller.nxdl.xml similarity index 76% rename from contributed_definitions/NXscanbox_em.nxdl.xml rename to base_classes/NXscan_controller.nxdl.xml index 3b930d8a80..b839a851b0 100644 --- a/contributed_definitions/NXscanbox_em.nxdl.xml +++ b/base_classes/NXscan_controller.nxdl.xml @@ -1,4 +1,4 @@ - + - + - Scan box and coils which deflect a beam of charged particles in a controlled manner. + The scan box or scan controller is a component that is used to deflect a + beam of charged particles in a controlled manner. The scan box is instructed by (an) instance(s) of :ref:`NXprogram`, some control software, - which is not necessarily the same program as for all components of an instrument. + which is not necessarily the same program as the one controlling other parts of the instrument. - The scanbox directs the probe of charged particles (electrons, ions) + The scan box directs the probe of charged particles (electrons, ions) to controlled locations according to a scan scheme and plan. Name of the typically tech-partner-specific term that specifies an - automated protocol which controls the details how the components - of the scan_box and instrument work together to achieve a controlled - scanning of the beam over the sample surface. + automated protocol which details how the components of the scan_box + and the instrument work together to achieve a controlled + scanning of the beam (over the sample surface). - In most cases users do not know, have to care, or are able to disentangle the - details of the spatiotemporal dynamics of the components of the instrument. - Instead, they often rely on the assumption that the microscope and control software + Oftentimes users do not need to or are not able to disentangle the intricate + details of the spatiotemporal dynamics of their instrument. Instead, often + they rely on the assumption that the instrument and its controlling programs work as expected. The field scan_schema can be used to add some constraints on how the beam was scanned over the surface. diff --git a/base_classes/NXsource.nxdl.xml b/base_classes/NXsource.nxdl.xml index 4af627bf88..a1d3c8a2d0 100644 --- a/base_classes/NXsource.nxdl.xml +++ b/base_classes/NXsource.nxdl.xml @@ -234,7 +234,7 @@ The size and position of an aperture inside the source. - + Individual electromagnetic lenses inside the source. diff --git a/contributed_definitions/NXspectrum.nxdl.xml b/base_classes/NXspectrum.nxdl.xml similarity index 97% rename from contributed_definitions/NXspectrum.nxdl.xml rename to base_classes/NXspectrum.nxdl.xml index dd1d91574a..ac42594101 100644 --- a/contributed_definitions/NXspectrum.nxdl.xml +++ b/base_classes/NXspectrum.nxdl.xml @@ -1,4 +1,4 @@ - + + + + Geometry of the unit cell quantified individually via parameter a. + + + + + Geometry of the unit cell quantified individually via parameter b. + + + + + Geometry of the unit cell quantified individually via parameter c. + + - Geometry of the unit cell quantified via parameters alpha, beta, and gamma. + Geometry of the unit cell quantified via parameters alpha, beta, and gamma. + + + Geometry of the unit cell quantified individually via parameter alpha. + + + + + Geometry of the unit cell quantified individually via parameter beta. + + + + + Geometry of the unit cell quantified individually via parameter gamma. + + - Crystal system. - - For a crystal system in 2D space monoclinic is an exact synonym for oblique. - For a crystal system in 2D space orthorhombic is an exact synonym for rectangular. - For a crystal system in 2D space tetragonal is an exact synonym for square. + Crystal system. + + For a crystal system in 2D space monoclinic is an exact synonym for oblique. + For a crystal system in 2D space orthorhombic is an exact synonym for rectangular. + For a crystal system in 2D space tetragonal is an exact synonym for square. @@ -89,45 +118,45 @@ - Laue group using International Table of Crystallography notation. + Laue group using International Table of Crystallography notation. - Point group using International Table of Crystallography notation. + Point group using International Table of Crystallography notation. - Space group from the International Table of Crystallography notation. + Space group from the International Table of Crystallography notation. - True if space group is considered a centrosymmetric one. - False if space group is considered a non-centrosymmetric one. - - Centrosymmetric has all types and combinations of symmetry elements - (translation, rotational axis, mirror planes, center of inversion) - Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). - Chiral compared to non-centrosymmetric is constrained (no mirror planes). + True if space group is considered a centrosymmetric one. + False if space group is considered a non-centrosymmetric one. + + Centrosymmetric has all types and combinations of symmetry elements + (translation, rotational axis, mirror planes, center of inversion) + Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). + Chiral compared to non-centrosymmetric is constrained (no mirror planes). - True if space group is considered a chiral one. - False if space group is consider a non-chiral one. + True if space group is considered a chiral one. + False if space group is consider a non-chiral one. - Area of the unit cell if dimensionality is 2. + Area of the unit cell if dimensionality is 2. - Volume of the unit cell if dimensionality is 3. + Volume of the unit cell if dimensionality is 3. diff --git a/contributed_definitions/nyaml/NXaberration.yaml b/base_classes/nyaml/NXaberration.yaml similarity index 58% rename from contributed_definitions/nyaml/NXaberration.yaml rename to base_classes/nyaml/NXaberration.yaml index 43792ab8d7..29b1343063 100644 --- a/contributed_definitions/nyaml/NXaberration.yaml +++ b/base_classes/nyaml/NXaberration.yaml @@ -1,6 +1,13 @@ category: base doc: | Quantified aberration coefficient in an aberration_model. + + For an introduction in the aberrations in electron microscopy + see `R. Dunin-Borkowski et al. `_ and + `S. J. Pennycock and P. D. Nellist `_ (page 44ff, and page 118ff) + for different definitions available and further details. + Table 7-2 of Ibid. publication (page 305ff) documents how to convert from the Nion to the CEOS definitions. + Conversion tables are also summarized by `Y. Liao `_ an introduction. type: group NXaberration(NXobject): magnitude(NX_NUMBER): @@ -33,11 +40,11 @@ NXaberration(NXobject): Given name to this aberration. alias(NX_CHAR): doc: | - Alias also used to name and refer to this specific type of aberration. + Alias to name or refer to this specific type of aberration. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0886da2916670a78790d1d643a4dcd05706da7f69d5605ad5456265640041c73 -# +# 56e233c76debb9af5eff7325e0624f51d50b71e6153718e5ecd01d30bae025b3 +# # # # # -# Quantified aberration coefficient in an aberration_model. +# Quantified aberration coefficient in an aberration_model. +# +# For an introduction in the aberrations in electron microscopy +# see `R. Dunin-Borkowski et al. <https://doi.org/10.1017/9781316337455.022>`_ and +# `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) +# for different definitions available and further details. +# Table 7-2 of Ibid. publication (page 305ff) documents how to convert from the Nion to the CEOS definitions. +# Conversion tables are also summarized by `Y. Liao <https://www.globalsino.com/EM/page3740.html>`_ an introduction. # # # -# Magnitude of the aberration +# Magnitude of the aberration # # # # -# Uncertainty of the magnitude of the aberration +# Uncertainty of the magnitude of the aberration # # # # -# Free-text description how magnitude_errors was quantified -# e.g. via the 95% confidence interval, variance, standard deviation, -# using which algorithm or statistical model. +# Free-text description how magnitude_errors was quantified +# e.g. via the 95% confidence interval, variance, standard deviation, +# using which algorithm or statistical model. # # # # -# Time elapsed since the last measurement. +# Time elapsed since the last measurement. # # # # -# For the CEOS definitions the C aberrations are radial-symmetric and have -# no angle entry, while the A, B, D, S, or R aberrations are n-fold -# symmetric and have an angle entry. -# For the NION definitions the coordinate system differs to the one -# used in CEOS and instead two aberration coefficients a and b are used. +# For the CEOS definitions the C aberrations are radial-symmetric and have +# no angle entry, while the A, B, D, S, or R aberrations are n-fold +# symmetric and have an angle entry. +# For the NION definitions the coordinate system differs to the one +# used in CEOS and instead two aberration coefficients a and b are used. # # # # -# Given name to this aberration. +# Given name to this aberration. # # # # -# Alias also used to name and refer to this specific type of aberration. +# Alias to name or refer to this specific type of aberration. # # # diff --git a/base_classes/nyaml/NXactuator.yaml b/base_classes/nyaml/NXactuator.yaml index bd9f95be57..e587584af8 100644 --- a/base_classes/nyaml/NXactuator.yaml +++ b/base_classes/nyaml/NXactuator.yaml @@ -45,7 +45,7 @@ NXactuator(NXcomponent): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # dd10bc8a1c83314427ae289d7c80bc4b53ecfb19d36fc046ef47927b5afa8098 -# +# # # +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# The number of ion candidates. +# +# +# +# +# Maximum number of allowed atoms per ion. +# +# +# +# +# Number of entries +# +# +# +# +# Base class to document the parameters, configuration, and results of a processing for recovering +# the charge state and nuclide composition of an ion from ranging definitions as used in the research +# field of atom probe microscopy. +# +# A ranging definition classically reports only the mass-to-charge-state-ratio interval plus the +# elemental composition, but not necessarily the nuclide that compose the ion. +# +# As the mass-resolving-power in an atom probe instrument is finite and typically lower +# than for cutting edge tandem mass spectrometry it is possible that different combinations of nuclides +# are indistinguishable and thus multiple ions in eventually even different charge states can be valid +# labels for a given mass-to-charge-state-ratio peak. Enumerating the possible combinations +# is a programmatic approach that can help with peak identification. +# +# +# +# Parameters for the algorithm used to recover which combinations of nuclides +# have a mass and charge that matches a set of constraints. +# +# Each parameter in this group is defines one constraint. +# +# +# +# Parameter that defines the elements considered in the combinatorial search. +# The array contains nuclides as many times as their multiplicity and must not be empty. +# Nuclides are encoded using the hashing rule that is defined in by nuclide_hash of :ref:`NXatom`. +# +# Constraining the elements or nuclides instead of providing all nuclides +# reduces the time to perform an exhaustive combinatorial search. +# +# +# +# +# +# +# +# Parameter that defines the interval :math:`[{\frac{m}{q}}_{min}, {\frac{m}{q}}_{max}]` within which +# ions with given mass-to-charge-state-ratio qualify as candidates. +# +# +# +# +# +# +# +# Parameter that defines the minimum half life for how long each nuclide of each +# ion needs to be stable such that the ion qualifies as a candidate. +# +# +# +# +# Parameter that defines the minimum natural abundance of each nuclide of each +# ion such that the ion qualifies as a candidate. +# +# +# +# +# If the value is false, it means that non-unique solutions are accepted. +# These are solutions where multiple candidates have been built from +# different nuclide instances but the charge_state of all the ions is the same. +# +# +# +# +# +# Signed charge, i.e. integer multiple of the elementary +# charge of each candidate. +# +# +# +# +# +# +# +# Table of nuclide instances of which each candidate is composed. +# Each row vector is sorted in descending order. +# Unused entries in the matrix should be set to 0. +# Use the hashing rule that is defined in nuclide_hash of :ref:`NXatom`. +# +# +# +# +# +# +# +# +# Accumulated mass of the nuclides in each candidate. +# Not corrected for quantum effects. +# +# +# +# +# +# +# +# The product of the natural abundances of the nuclides for each candidate. +# +# +# +# +# +# +# +# For each candidate the half life of the nuclide that has the +# shortest half life. +# +# +# +# +# +# diff --git a/base_classes/nyaml/NXapm_measurement.yaml b/base_classes/nyaml/NXapm_measurement.yaml new file mode 100644 index 0000000000..11f255a755 --- /dev/null +++ b/base_classes/nyaml/NXapm_measurement.yaml @@ -0,0 +1,113 @@ +category: base +doc: | + Base class for collecting a run with a real or a simulated atom probe or field-ion microscope. + + The term run is understood as an exact synonym for session, i.e. the usage of a real or simulated + tomograph or microscope for a certain amount of time during which one characterizes a single specimen. + + Research workflows for experiments and simulations of atom probe and related field-evaporation + evolve continuously and become increasingly connected with other methods used for material + characterization specifically electron microscopy. A few examples in this direction are: + + * `T. Kelly et al. `_ + * `C. Fleischmann et al. `_ + * `W. Windl et al. `_ + * `C. Freysoldt et al. `_ + * `G. da Costa et al. `_ + + The majority of atom probe research is performed using the so-called Local Electrode Atom Probe (LEAP) instruments + from AMETEK/Cameca. In addition, several research groups have built their own instruments and shared different + aspects of the technical specifications and approaches including how these groups apply data processing e.g.: + + * `M. Monajem et al. `_ + * `P. Stender et al. `_ + * `I. Dimkou et al. `_ + + to name but a few. +type: group +NXapm_measurement(NXobject): + status(NX_CHAR): + doc: | + A statement whether the measurement completed successfully, or was aborted. + enumeration: [success, aborted] + quality(NX_CHAR): + doc: | + Statement about the quality of the measurement. + + The value can be extracted from the CAnalysis.CResults.fQuality + field of a CamecaRoot ROOT file. + (NXinstrument_apm): + (NXevent_data_apm): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 85fa0cb41b085e4263ca6a0ddab3aff086d8648f508d16664b4ed50d3ac4c93e +# +# +# +# +# +# Base class for collecting a run with a real or a simulated atom probe or field-ion microscope. +# +# The term run is understood as an exact synonym for session, i.e. the usage of a real or simulated +# tomograph or microscope for a certain amount of time during which one characterizes a single specimen. +# +# Research workflows for experiments and simulations of atom probe and related field-evaporation +# evolve continuously and become increasingly connected with other methods used for material +# characterization specifically electron microscopy. A few examples in this direction are: +# +# * `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_ +# * `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_ +# * `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_ +# * `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_ +# * `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ +# +# The majority of atom probe research is performed using the so-called Local Electrode Atom Probe (LEAP) instruments +# from AMETEK/Cameca. In addition, several research groups have built their own instruments and shared different +# aspects of the technical specifications and approaches including how these groups apply data processing e.g.: +# +# * `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_ +# * `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ +# * `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ +# +# to name but a few. +# +# +# +# A statement whether the measurement completed successfully, or was aborted. +# +# +# +# +# +# +# +# +# Statement about the quality of the measurement. +# +# The value can be extracted from the CAnalysis.CResults.fQuality +# field of a CamecaRoot ROOT file. +# +# +# +# +# diff --git a/base_classes/nyaml/NXapm_ranging.yaml b/base_classes/nyaml/NXapm_ranging.yaml new file mode 100644 index 0000000000..18fd667eef --- /dev/null +++ b/base_classes/nyaml/NXapm_ranging.yaml @@ -0,0 +1,199 @@ +category: base +doc: | + Base class for the configuration and results of ranging definitions. + + Ranging is a data post-processing step used in the research field of + atom probe during which elemental, isotopic, and/or molecular identities + are assigned to mass-to-charge-state ratios within certain intervals. + The documentation of these steps is based on ideas that + have been described in the literature: + + * `M. K. Miller `_ + * `D. Haley et al. `_ + * `M. Kühbach et al. `_ +type: group +NXapm_ranging(NXprocess): + (NXprogram): + (NXnote): + mass_to_charge_distribution(NXprocess): + doc: | + Specifies the mass-to-charge-state ratio histogram. + (NXprogram): + min_mass_to_charge(NX_FLOAT): + unit: NX_ANY + doc: | + Smallest :math:`{\frac{m}{q}}_{min}` mass-to-charge-state ratio value. + + The lower (left-hand side) inclusive bound of the interval :math:`[{\frac{m}{q}}_{min}`, {\frac{m}{q}}_{max}]`. + max_mass_to_charge(NX_FLOAT): + unit: NX_ANY + doc: | + Largest :math:`{\frac{m}{q}}_{max}` mass-to-charge-state ratio value. + + The upper (right-hand side) inclusive bound of the interval :math:`[{\frac{m}{q}}_{min}`, {\frac{m}{q}}_{max}]`. + n_mass_to_charge(NX_POSINT): + unit: NX_UNITLESS + doc: | + The number of bins on the interval :math:`[{\frac{m}{q}}_{min}`, + {\frac{m}{q}}_{max}]`. + mass_spectrum(NXdata): + doc: | + A default histogram aka mass spectrum of + the mass-to-charge-state ratio values. + background_quantification(NXprocess): + doc: | + Details of the background model that was used to + correct the total counts per bin into counts. + (NXprogram): + description(NX_CHAR): + doc: | + Free-text field to describe how atom probers define a background model. + + Thereby, community feedback can be collected to inform an improved + version of this base class in the future. + peak_search_and_deconvolution(NXprocess): + doc: | + How were peaks in the mass-to-charge-state ratio histogram identified. + (NXprogram): + (NXpeak): + peak_identification(NXprocess): + doc: | + Details about how peaks, with taking into account + error models, were interpreted as ion types or not. + (NXprogram): + number_of_ion_types(NX_UINT): + unit: NX_UNITLESS + doc: | + How many ion types are distinguished. If no ranging was performed, each + ion is of the special unknown type. The iontype ID of this unknown type + is 0 representing a reserved value. + + Consequently, start counting iontypes from 1. + maximum_number_of_atoms_per_molecular_ion(NX_UINT): + unit: NX_UNITLESS + doc: | + Assumed maximum value that suffices to store all relevant molecular ions, + even the most complicated ones that one can typically observe and distinguish + typically. Currently, a value of 32 is used (see M. Kühbach et al. `_). + (NXatom): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# d4359bfc6a6c742eed6c496e3f87022335671b759f6947866bbcc9eda536b579 +# +# +# +# +# +# Base class for the configuration and results of ranging definitions. +# +# Ranging is a data post-processing step used in the research field of +# atom probe during which elemental, isotopic, and/or molecular identities +# are assigned to mass-to-charge-state ratios within certain intervals. +# The documentation of these steps is based on ideas that +# have been described in the literature: +# +# * `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ +# * `D. Haley et al. <https://doi.org/10.1017/S1431927620024290>`_ +# * `M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_ +# +# +# +# +# +# Specifies the mass-to-charge-state ratio histogram. +# +# +# +# +# Smallest :math:`{\frac{m}{q}}_{min}` mass-to-charge-state ratio value. +# +# The lower (left-hand side) inclusive bound of the interval :math:`[{\frac{m}{q}}_{min}`, {\frac{m}{q}}_{max}]`. +# +# +# +# +# Largest :math:`{\frac{m}{q}}_{max}` mass-to-charge-state ratio value. +# +# The upper (right-hand side) inclusive bound of the interval :math:`[{\frac{m}{q}}_{min}`, {\frac{m}{q}}_{max}]`. +# +# +# +# +# The number of bins on the interval :math:`[{\frac{m}{q}}_{min}`, +# {\frac{m}{q}}_{max}]`. +# +# +# +# +# A default histogram aka mass spectrum of +# the mass-to-charge-state ratio values. +# +# +# +# +# +# Details of the background model that was used to +# correct the total counts per bin into counts. +# +# +# +# +# Free-text field to describe how atom probers define a background model. +# +# Thereby, community feedback can be collected to inform an improved +# version of this base class in the future. +# +# +# +# +# +# How were peaks in the mass-to-charge-state ratio histogram identified. +# +# +# +# +# +# +# Details about how peaks, with taking into account +# error models, were interpreted as ion types or not. +# +# +# +# +# How many ion types are distinguished. If no ranging was performed, each +# ion is of the special unknown type. The iontype ID of this unknown type +# is 0 representing a reserved value. +# +# Consequently, start counting iontypes from 1. +# +# +# +# +# Assumed maximum value that suffices to store all relevant molecular ions, +# even the most complicated ones that one can typically observe and distinguish +# typically. Currently, a value of 32 is used (see M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_). +# +# +# +# +# diff --git a/base_classes/nyaml/NXapm_reconstruction.yaml b/base_classes/nyaml/NXapm_reconstruction.yaml new file mode 100644 index 0000000000..3472d6d12c --- /dev/null +++ b/base_classes/nyaml/NXapm_reconstruction.yaml @@ -0,0 +1,487 @@ +category: base +doc: | + Base class for the configuration and results of a reconstruction algorithm. + + Generating a tomographic reconstruction of the specimen uses selected and + calibrated ion hit positions, the evaporation sequence, and voltage curve data. + Very often scientists use own software scripts according to published procedures, + so-called reconstruction protocols. +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. + n: | + Number of ions spatially filtered from results of the hit_finding algorithm + from which an instance of a reconstructed volume has been generated. + These ions get new identifier assigned in the process - the so-called + evaporation_id, which must not be confused with the pulse_id! +type: group +NXapm_reconstruction(NXprocess): + (NXprogram): + (NXnote): + + # config + config(NXparameters): + doc: | + Parameters that configure a reconstruction algorithm which takes + hit data and mass-to-charge-state ratio values to construct a model + of the evaporated specimen. This model is called the reconstructed volume. + Researchers in the field of atom probe call these algorithms reconstruction + protocols. + + Different such protocols exist. Although these are qualitatively similar, + each protocol uses and interprets the parameters slightly differently. + + The majority of reconstructions is performed with the proprietary software + APSuite / IVAS, the source code for the reconstruction protocols that this + software implements in detail is not open but the parameters and their qualitative + effect on the reconstructed volume follows the protocols that are discussed in + the atom probe literature. This group allows to document these parameters in + a standardized manner. + voltage_filter_initial(NX_FLOAT): + unit: NX_VOLTAGE + doc: | + Lowest voltage at which an ion that is considered in the reconstructed + volume has been extracted from the specimen. + voltage_filter_final(NX_FLOAT): + unit: NX_VOLTAGE + doc: | + Highest voltage at which an ion that is considered in the reconstructed + volume has been extracted from the specimen. + protocol_name(NX_CHAR): + doc: | + Qualitative statement about which reconstruction protocol was used. + + For reconstructions performed with APSuite / IVAS the value "cameca" + should be used. + enumeration: + open_enum: true + items: [bas, geiser, gault, cameca] + primary_element(NX_CHAR): + doc: | + Assumed primary element based on which the reconstruction is calibrated. + + The value can be extracted from the CAnalysis.CSpatial.fPrimaryElement + field of a CamecaRoot ROOT file. + efficiency(NX_FLOAT): + unit: NX_DIMENSIONLESS + doc: | + Assumed detection efficiency + + The value can be extracted from the CAnalysis.CSpatial.fEfficiency + field of a CamecaRoot ROOT file. + flight_path(NX_FLOAT): + unit: NX_LENGTH + doc: | + Nominal flight path + + The value can be extracted from the CAnalysis.CSpatial.fFlightPath + field of a CamecaRoot ROOT file. + evaporation_field(NX_FLOAT): + unit: NX_ANY + doc: | + Assumed evaporation electric field + + The value can be extracted from the CAnalysis.CSpatial.fEvaporationField + field of a CamecaRoot ROOT file. + image_compression(NX_FLOAT): + unit: NX_UNITLESS + doc: | + Image compression factor (ICF) + + The value can be extracted from the CAnalysis.CSpatial.fImageCompression + field of a CamecaRoot ROOT file. + kfactor(NX_FLOAT): + unit: NX_VOLUME + doc: | + Sum of ion volumes + + The value can be extracted from the CAnalysis.CSpatial.fKfactor + field of a CamecaRoot ROOT file. + shank_angle(NX_FLOAT): + unit: NX_ANGLE + doc: | + Shank angle + + The value can be extracted from the CAnalysis.CSpatial.fShankAngle + field of a CamecaRoot ROOT file. + ion_volume(NX_FLOAT): + unit: NX_VOLUME + doc: | + Assumed atomic volume + tip_radius(NX_FLOAT): + unit: NX_LENGTH + doc: | + The value can be extracted from the CAnalysis.CSpatial.fTipRadius + field of a CamecaRoot ROOT file. + tip_radius_zero(NX_FLOAT): + unit: NX_LENGTH + doc: | + The value can be extracted from the CAnalysis.CSpatial.fTipRadius0 + field of a CamecaRoot ROOT file. + voltage_zero(NX_FLOAT): + unit: NX_VOLTAGE + doc: | + The value can be extracted from the CAnalysis.CSpatial.fVoltage0 + field of a CamecaRoot ROOT file. + crystallographic_calibration(NX_CHAR): + doc: | + Different strategies for crystallographic calibration of the + reconstruction are possible. Therefore, we collect first such + feedback before parametrizing this further. + + If no crystallographic calibration was performed, the field + should be filled with the n/a, meaning not applied. + comment(NX_CHAR): + doc: | + Possibility of a free text field that allows to report additional details related to + the reconstruction protocol. For LEAP systems and reconstructions that are + performed with APSuite / IVAS see also `B. Gault et al. _` + and `T. Blum et al. `_ (page 371). + for best practices on the reporting of metadata in atom probe tomography. + + # results + reconstructed_positions(NX_FLOAT): + unit: NX_LENGTH + doc: | + Three-dimensional positions of the ions in the reconstructed volume. + dimensions: + rank: 2 + dim: (n, 3) + \@depends_on(NX_CHAR): + doc: | + The instance of :ref:`NXcoordinate_system` in which the positions are defined. + + # plots and statistics about the reconstructed volume + naive_discretization(NXprocess): + (NXprogram): + (NXdata): + doc: | + Visual overview of the reconstructed dataset via a three-dimensional + histogram of ion counts. Ion counts are characterized using one nanometer + cubic bins without applying any smoothening of reconstructed positions + during the histogram computation. + + Such preview is useful to get an impression of the macroscopic shape of the + reconstructed volume. Visualizing by ion counts highlights density variations + the reconstructed volume that are signatures of features such as poles, + interfaces or irregularities of the specimen shape. + volume(NX_FLOAT): + unit: NX_VOLUME + doc: | + Sum of ion volumes + + The value can be extracted from the CAnalysis.CSpatial.fRecoVolume + field of a CamecaRoot ROOT file. + field_of_view(NX_FLOAT): + unit: NX_LENGTH + + # typically in nm reconstruction space not detector coordinates + doc: | + The nominal diameter of the specimen ROI which is measured in the + experiment. The physical specimen cannot be measured completely + because ions may launch but hit in locations other than the detector. + obb(NXcollection): + doc: | + Tight, axis-aligned bounding box about the point cloud of the reconstruction. + xmin(NX_FLOAT): + unit: NX_LENGTH + doc: | + Minimum coordinate value along the x-direction + xmax(NX_FLOAT): + unit: NX_LENGTH + doc: | + Maximum coordinate value along the x-direction + ymin(NX_FLOAT): + unit: NX_LENGTH + doc: | + Minimum coordinate value along the y-direction + ymax(NX_FLOAT): + unit: NX_LENGTH + doc: | + Maximum coordinate value along the y-direction + zmin(NX_FLOAT): + unit: NX_LENGTH + doc: | + Minimum coordinate value along the z-direction + zmax(NX_FLOAT): + unit: NX_LENGTH + doc: | + Maximum coordinate value along the z-direction + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# cb26300799d2708792b9a84040c6b2b80f994eaec0210976a888c5f141df38ff +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of ions spatially filtered from results of the hit_finding algorithm +# from which an instance of a reconstructed volume has been generated. +# These ions get new identifier assigned in the process - the so-called +# evaporation_id, which must not be confused with the pulse_id! +# +# +# +# +# Base class for the configuration and results of a reconstruction algorithm. +# +# Generating a tomographic reconstruction of the specimen uses selected and +# calibrated ion hit positions, the evaporation sequence, and voltage curve data. +# Very often scientists use own software scripts according to published procedures, +# so-called reconstruction protocols. +# +# +# +# +# +# +# Parameters that configure a reconstruction algorithm which takes +# hit data and mass-to-charge-state ratio values to construct a model +# of the evaporated specimen. This model is called the reconstructed volume. +# Researchers in the field of atom probe call these algorithms reconstruction +# protocols. +# +# Different such protocols exist. Although these are qualitatively similar, +# each protocol uses and interprets the parameters slightly differently. +# +# The majority of reconstructions is performed with the proprietary software +# APSuite / IVAS, the source code for the reconstruction protocols that this +# software implements in detail is not open but the parameters and their qualitative +# effect on the reconstructed volume follows the protocols that are discussed in +# the atom probe literature. This group allows to document these parameters in +# a standardized manner. +# +# +# +# Lowest voltage at which an ion that is considered in the reconstructed +# volume has been extracted from the specimen. +# +# +# +# +# Highest voltage at which an ion that is considered in the reconstructed +# volume has been extracted from the specimen. +# +# +# +# +# Qualitative statement about which reconstruction protocol was used. +# +# For reconstructions performed with APSuite / IVAS the value "cameca" +# should be used. +# +# +# +# +# +# +# +# +# +# +# Assumed primary element based on which the reconstruction is calibrated. +# +# The value can be extracted from the CAnalysis.CSpatial.fPrimaryElement +# field of a CamecaRoot ROOT file. +# +# +# +# +# Assumed detection efficiency +# +# The value can be extracted from the CAnalysis.CSpatial.fEfficiency +# field of a CamecaRoot ROOT file. +# +# +# +# +# Nominal flight path +# +# The value can be extracted from the CAnalysis.CSpatial.fFlightPath +# field of a CamecaRoot ROOT file. +# +# +# +# +# Assumed evaporation electric field +# +# The value can be extracted from the CAnalysis.CSpatial.fEvaporationField +# field of a CamecaRoot ROOT file. +# +# +# +# +# Image compression factor (ICF) +# +# The value can be extracted from the CAnalysis.CSpatial.fImageCompression +# field of a CamecaRoot ROOT file. +# +# +# +# +# Sum of ion volumes +# +# The value can be extracted from the CAnalysis.CSpatial.fKfactor +# field of a CamecaRoot ROOT file. +# +# +# +# +# Shank angle +# +# The value can be extracted from the CAnalysis.CSpatial.fShankAngle +# field of a CamecaRoot ROOT file. +# +# +# +# +# Assumed atomic volume +# +# +# +# +# The value can be extracted from the CAnalysis.CSpatial.fTipRadius +# field of a CamecaRoot ROOT file. +# +# +# +# +# The value can be extracted from the CAnalysis.CSpatial.fTipRadius0 +# field of a CamecaRoot ROOT file. +# +# +# +# +# The value can be extracted from the CAnalysis.CSpatial.fVoltage0 +# field of a CamecaRoot ROOT file. +# +# +# +# +# Different strategies for crystallographic calibration of the +# reconstruction are possible. Therefore, we collect first such +# feedback before parametrizing this further. +# +# If no crystallographic calibration was performed, the field +# should be filled with the n/a, meaning not applied. +# +# +# +# +# Possibility of a free text field that allows to report additional details related to +# the reconstruction protocol. For LEAP systems and reconstructions that are +# performed with APSuite / IVAS see also `B. Gault et al. <https://doi.org/10.1093/mam/ozae081>_` +# and `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). +# for best practices on the reporting of metadata in atom probe tomography. +# +# +# +# +# +# +# Three-dimensional positions of the ions in the reconstructed volume. +# +# +# +# +# +# +# +# The instance of :ref:`NXcoordinate_system` in which the positions are defined. +# +# +# +# +# +# +# +# +# Visual overview of the reconstructed dataset via a three-dimensional +# histogram of ion counts. Ion counts are characterized using one nanometer +# cubic bins without applying any smoothening of reconstructed positions +# during the histogram computation. +# +# Such preview is useful to get an impression of the macroscopic shape of the +# reconstructed volume. Visualizing by ion counts highlights density variations +# the reconstructed volume that are signatures of features such as poles, +# interfaces or irregularities of the specimen shape. +# +# +# +# +# +# Sum of ion volumes +# +# The value can be extracted from the CAnalysis.CSpatial.fRecoVolume +# field of a CamecaRoot ROOT file. +# +# +# +# +# +# The nominal diameter of the specimen ROI which is measured in the +# experiment. The physical specimen cannot be measured completely +# because ions may launch but hit in locations other than the detector. +# +# +# +# +# Tight, axis-aligned bounding box about the point cloud of the reconstruction. +# +# +# +# Minimum coordinate value along the x-direction +# +# +# +# +# Maximum coordinate value along the x-direction +# +# +# +# +# Minimum coordinate value along the y-direction +# +# +# +# +# Maximum coordinate value along the y-direction +# +# +# +# +# Minimum coordinate value along the z-direction +# +# +# +# +# Maximum coordinate value along the z-direction +# +# +# +# diff --git a/base_classes/nyaml/NXapm_simulation.yaml b/base_classes/nyaml/NXapm_simulation.yaml new file mode 100644 index 0000000000..946c069d7d --- /dev/null +++ b/base_classes/nyaml/NXapm_simulation.yaml @@ -0,0 +1,46 @@ +category: base +doc: | + Base class for simulation of ion extraction from matter via laser and/or voltage + pulsing. +type: group +NXapm_simulation(NXobject): + (NXprogram): + (NXparameters): + (NXprocess): + (NXdata): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 091fc2ed9cfe2e0bd98015b42569baa6d6db438f4fafa8fd81cae23cafcbe330 +# +# +# +# +# +# Base class for simulation of ion extraction from matter via laser and/or voltage +# pulsing. +# +# +# +# +# +# diff --git a/base_classes/nyaml/NXatom.yaml b/base_classes/nyaml/NXatom.yaml new file mode 100644 index 0000000000..712d05e432 --- /dev/null +++ b/base_classes/nyaml/NXatom.yaml @@ -0,0 +1,389 @@ +category: base +doc: | + Base class for documenting a set of atoms. + + Atoms in the set may be bonded. The set may have + a net charge to represent an ion. + An ion can be a molecular ion. +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. + n_pos: | + Number of atom positions. + d: | + Dimensionality + n_ivec_max: | + Maximum number of atoms/isotopes allowed per ion. + n_ranges: | + Number of mass-to-charge-state-ratio range intervals for ion type. +type: group +NXatom(NXobject): + name(NX_CHAR): + doc: | + Given name for the set. + + This field could for example be used in the research field + of atom probe tomography to store a standardized human-readable + name of the element or ion like such as Al +++ or 12C +. + id(NX_UINT): + unit: NX_UNITLESS + doc: | + Given numerical identifier for the set. + + The identifier zero is reserved for the special unknown ion type. + identifier_chemical(NX_CHAR): + doc: | + Identifier used to refer to if the set of atoms represents a substance. + enumeration: [inchi] + charge(NX_NUMBER): + unit: NX_CHARGE + doc: | + Signed net (partial) charge of the (molecular) ion. + + Different methods for computing charge are in use. + Care needs to be exercised with respect to the integration. + `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. + charge_state(NX_NUMBER): + unit: NX_UNITLESS + doc: | + Charge reported in multiples of the charge of an electron. + + For research using atom probe tomography the value should be set to + zero if the charge_state is unknown and irrecoverable. This can happen + when classical ranging definition files in formats like RNG, RRNG are used. + These file formats do not document the charge state explicitly but only + the number of atoms of each element per molecular ion surplus the + respective mass-to-charge-state-ratio interval. + + Details on ranging definition files in the literature are `M. K. Miller `_. + volume(NX_NUMBER): + unit: NX_VOLUME + doc: | + Assumed volume affected by the set of atoms. + + Neither individual atoms nor a set of cluster of these have a volume + that is unique as a some cut-off criterion is required. + indices(NX_CHAR): + doc: | + Index for each atom at locations as detailed by position. + Indices can be used as identifier and thus names for individual atoms. + dimensions: + rank: 1 + dim: (n_pos,) + type(NX_UINT): + unit: NX_UNITLESS + doc: | + Nuclide information for each atom at locations as detailed by position. + + One `approach `_ for storing nuclide information + efficiently is via individual hash values. + Consult the docstring of ``nuclide_hash`` for further details. + dimensions: + rank: 1 + dim: (n_pos,) + position(NX_NUMBER): + unit: NX_ANY + doc: | + Position of each atom. + dimensions: + rank: 2 + dim: (n_pos, d) + \@depends_on(NX_CHAR): + doc: | + Path to an instance of :ref:`NXcoordinate_system` to document + the reference frame in which the positions are defined. + + This resolves ambiguity when the reference frame is different + to the NeXus default reference frame (McStas). + occupancy(NX_NUMBER): + unit: NX_DIMENSIONLESS + doc: | + Relative occupancy of the atom position. + + This field is useful for specifying the atomic motif in + instances of :ref:`NXunit_cell`. + dimensions: + rank: 1 + dim: (n_pos,) + nuclide_hash(NX_UINT): + unit: NX_UNITLESS + doc: | + Vector of nuclide hash values. The vector is sorted in decreasing order. + + Individual hash values :math:`H` `encode `_ + for each nuclide or element the number of protons :math:`Z` and a constant :math:`c` + via the following hashing rule :math:`H = Z + c \cdot 256`. :math:`Z` and :math:`c` must be 8-bit unsigned integers. + + The constant :math:`c` is either set to number of neutrons :math:`N` or to the special value 255. + The special value 255 is used to refer to all isotopes of an element from the IUPAC periodic table. + + Some examples: + + * The element hydrogen (meaning irrespective which isotope), its hash value is :math:`H = 1 + 255 \cdot 256 = 65281`. + * The :math:`^{1}H` hydrogen isotope (:math:`Z = 1, N = 0`), its hash value is :math:`H = 1 + 0 \cdot 256 = 1`. + * The :math:`^{2}H` deuterium isotope (:math:`Z = 1, N = 1`), its hash value is :math:`H = 1 + 1 \cdot 256 = 257`. + * The :math:`^{3}H` tritium isotope (:math:`Z = 1, N = 2`), its hash value is :math:`H = 1 + 2 \cdot 256 = 513`. + * The :math:`^{99}Tc` technetium isotope (:math:`Z = 43, N = 56`), its hash value is :math:`H = 43 + 56 \cdot 256 = 14379`. + + The special hash value :math:`0` is a placeholder. + + This hashing rule implements a bitshift operation. The benefit is that this enables encoding of all + currently known nuclides and elements efficiently into an 16-bit unsigned integer. Sufficient + unused indices remain to case situations when new elements will be discovered. + dimensions: + rank: 1 + dim: (n_ivec_max,) + nuclide_list(NX_UINT): + unit: NX_UNITLESS + doc: | + Table which decodes the entries in nuclide_hash into a human-readable matrix + instances for either nuclids or elements. Specifically, the first row specifies the + nuclide mass number. When the nuclide_hash values are used this means + the row should report the sum :math:`Z + N` or 0. The value 0 documents that + an element from the IUPAC periodic table is meant. + The second row specifies the number of protons :math:`Z`. + The value 0 in this case documents a placeholder or that no element-specific + information is relevant. + + Taking a carbon-14 nuclide as an example the mass number is 14. + That is encoded as a column vector (14, 6). + The array is stored matching the order of nuclide_hash. + dimensions: + rank: 2 + dim: (n_ivec_max, 2) + mass_to_charge_range(NX_NUMBER): + unit: NX_ANY + doc: | + Associated lower :math:`{\frac{m}{q}}_{min}` and upper :math:`{\frac{m}{q}}_{max}` bounds of the + mass-to-charge-state ratio interval(s) :math:`[{\frac{m}{q}}_{min}, {\frac{m}{q}}_{max}]`. + (boundaries inclusive). This field is primarily of interest for documenting :ref:`NXprocess` + steps of indexing a ToF/mass-to-charge-state ratio histogram. + dimensions: + rank: 2 + dim: (n_ranges, 2) + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 4206980cd0848593553abf0f86e1635d60421cdb4907604abdf41526bbe3632a +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of atom positions. +# +# +# +# +# Dimensionality +# +# +# +# +# Maximum number of atoms/isotopes allowed per ion. +# +# +# +# +# Number of mass-to-charge-state-ratio range intervals for ion type. +# +# +# +# +# Base class for documenting a set of atoms. +# +# Atoms in the set may be bonded. The set may have +# a net charge to represent an ion. +# An ion can be a molecular ion. +# +# +# +# Given name for the set. +# +# This field could for example be used in the research field +# of atom probe tomography to store a standardized human-readable +# name of the element or ion like such as Al +++ or 12C +. +# +# +# +# +# Given numerical identifier for the set. +# +# The identifier zero is reserved for the special unknown ion type. +# +# +# +# +# Identifier used to refer to if the set of atoms represents a substance. +# +# +# +# +# +# +# +# Signed net (partial) charge of the (molecular) ion. +# +# Different methods for computing charge are in use. +# Care needs to be exercised with respect to the integration. +# `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. +# +# +# +# +# Charge reported in multiples of the charge of an electron. +# +# For research using atom probe tomography the value should be set to +# zero if the charge_state is unknown and irrecoverable. This can happen +# when classical ranging definition files in formats like RNG, RRNG are used. +# These file formats do not document the charge state explicitly but only +# the number of atoms of each element per molecular ion surplus the +# respective mass-to-charge-state-ratio interval. +# +# Details on ranging definition files in the literature are `M. K. Miller <https://doi.org/10.1002/sia.1719>`_. +# +# +# +# +# Assumed volume affected by the set of atoms. +# +# Neither individual atoms nor a set of cluster of these have a volume +# that is unique as a some cut-off criterion is required. +# +# +# +# +# Index for each atom at locations as detailed by position. +# Indices can be used as identifier and thus names for individual atoms. +# +# +# +# +# +# +# +# Nuclide information for each atom at locations as detailed by position. +# +# One `approach <https://doi.org/10.1017/S1431927621012241>`_ for storing nuclide information +# efficiently is via individual hash values. +# Consult the docstring of ``nuclide_hash`` for further details. +# +# +# +# +# +# +# +# Position of each atom. +# +# +# +# +# +# +# +# Path to an instance of :ref:`NXcoordinate_system` to document +# the reference frame in which the positions are defined. +# +# This resolves ambiguity when the reference frame is different +# to the NeXus default reference frame (McStas). +# +# +# +# +# +# Relative occupancy of the atom position. +# +# This field is useful for specifying the atomic motif in +# instances of :ref:`NXunit_cell`. +# +# +# +# +# +# +# +# Vector of nuclide hash values. The vector is sorted in decreasing order. +# +# Individual hash values :math:`H` `encode <https://doi.org/10.1017/S1431927621012241>`_ +# for each nuclide or element the number of protons :math:`Z` and a constant :math:`c` +# via the following hashing rule :math:`H = Z + c \cdot 256`. :math:`Z` and :math:`c` must be 8-bit unsigned integers. +# +# The constant :math:`c` is either set to number of neutrons :math:`N` or to the special value 255. +# The special value 255 is used to refer to all isotopes of an element from the IUPAC periodic table. +# +# Some examples: +# +# * The element hydrogen (meaning irrespective which isotope), its hash value is :math:`H = 1 + 255 \cdot 256 = 65281`. +# * The :math:`^{1}H` hydrogen isotope (:math:`Z = 1, N = 0`), its hash value is :math:`H = 1 + 0 \cdot 256 = 1`. +# * The :math:`^{2}H` deuterium isotope (:math:`Z = 1, N = 1`), its hash value is :math:`H = 1 + 1 \cdot 256 = 257`. +# * The :math:`^{3}H` tritium isotope (:math:`Z = 1, N = 2`), its hash value is :math:`H = 1 + 2 \cdot 256 = 513`. +# * The :math:`^{99}Tc` technetium isotope (:math:`Z = 43, N = 56`), its hash value is :math:`H = 43 + 56 \cdot 256 = 14379`. +# +# The special hash value :math:`0` is a placeholder. +# +# This hashing rule implements a bitshift operation. The benefit is that this enables encoding of all +# currently known nuclides and elements efficiently into an 16-bit unsigned integer. Sufficient +# unused indices remain to case situations when new elements will be discovered. +# +# +# +# +# +# +# +# Table which decodes the entries in nuclide_hash into a human-readable matrix +# instances for either nuclids or elements. Specifically, the first row specifies the +# nuclide mass number. When the nuclide_hash values are used this means +# the row should report the sum :math:`Z + N` or 0. The value 0 documents that +# an element from the IUPAC periodic table is meant. +# The second row specifies the number of protons :math:`Z`. +# The value 0 in this case documents a placeholder or that no element-specific +# information is relevant. +# +# Taking a carbon-14 nuclide as an example the mass number is 14. +# That is encoded as a column vector (14, 6). +# The array is stored matching the order of nuclide_hash. +# +# +# +# +# +# +# +# +# Associated lower :math:`{\frac{m}{q}}_{min}` and upper :math:`{\frac{m}{q}}_{max}` bounds of the +# mass-to-charge-state ratio interval(s) :math:`[{\frac{m}{q}}_{min}, {\frac{m}{q}}_{max}]`. +# (boundaries inclusive). This field is primarily of interest for documenting :ref:`NXprocess` +# steps of indexing a ToF/mass-to-charge-state ratio histogram. +# +# +# +# +# +# +# diff --git a/base_classes/nyaml/NXcalibration.yaml b/base_classes/nyaml/NXcalibration.yaml index 76a4ad6476..e4975512b9 100644 --- a/base_classes/nyaml/NXcalibration.yaml +++ b/base_classes/nyaml/NXcalibration.yaml @@ -145,7 +145,7 @@ NXcalibration(NXprocess): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # f5654f5bdbdb2bd6e822f6157450547dba893407062dec07456dcbbf707b59ab -# +# # # -# +# # # Number of vertices for each face. # @@ -249,7 +253,7 @@ NXcg_face_list_data_structure(NXcg_primitive): # # # -# +# # # Number of edges for each face. # @@ -260,12 +264,12 @@ NXcg_face_list_data_structure(NXcg_primitive): # # # -# +# # # Number of faces of the primitives. # # -# +# # # Integer offset whereby the identifier of the first member # of the vertices differs from zero. @@ -274,7 +278,7 @@ NXcg_face_list_data_structure(NXcg_primitive): # Inspect the definition of NXcg_primitive for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the edges differs from zero. @@ -283,7 +287,7 @@ NXcg_face_list_data_structure(NXcg_primitive): # Inspect the definition of NXcg_primitive for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the faces differs from zero. @@ -292,7 +296,7 @@ NXcg_face_list_data_structure(NXcg_primitive): # Inspect the definition of NXcg_primitive for further details. # # -# +# # # Integer identifier to distinguish all vertices explicitly. # @@ -300,7 +304,7 @@ NXcg_face_list_data_structure(NXcg_primitive): # # # -# +# # # Integer used to distinguish all edges explicitly. # @@ -308,7 +312,7 @@ NXcg_face_list_data_structure(NXcg_primitive): # # # -# +# # # Integer used to distinguish all faces explicitly. # @@ -384,6 +388,7 @@ NXcg_face_list_data_structure(NXcg_primitive): # * 0 - undefined # * 1 - counter-clockwise (CCW) # * 2 - clock-wise (CW) +# # # # diff --git a/contributed_definitions/nyaml/NXcg_grid.yaml b/base_classes/nyaml/NXcg_grid.yaml similarity index 98% rename from contributed_definitions/nyaml/NXcg_grid.yaml rename to base_classes/nyaml/NXcg_grid.yaml index 86ee02e448..9a971cae8e 100644 --- a/contributed_definitions/nyaml/NXcg_grid.yaml +++ b/base_classes/nyaml/NXcg_grid.yaml @@ -78,7 +78,7 @@ NXcg_grid(NXcg_primitive): # does it have to be a tight bounding box? # a good example for a general bounding box description for such a grids of triclinic cells # https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallelepiped - number_of_boundaries(NX_INT): + number_of_boundaries(NX_UINT): unit: NX_UNITLESS doc: | Number of boundaries distinguished @@ -127,8 +127,8 @@ NXcg_grid(NXcg_primitive): description can be used instead. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 9ae5f6a385db0e8c9c49989e03d512f279fbf61becb69b11c8fa012dbdb01893 -# +# c5bee596e67c2209b40728d8aef705108736ff7e8edce3781bd661d458bfbe13 +# # # -# +# # # Number of boundaries distinguished # diff --git a/contributed_definitions/nyaml/NXcg_half_edge_data_structure.yaml b/base_classes/nyaml/NXcg_half_edge_data_structure.yaml similarity index 92% rename from contributed_definitions/nyaml/NXcg_half_edge_data_structure.yaml rename to base_classes/nyaml/NXcg_half_edge_data_structure.yaml index d80a8a6dd6..db5d3a300f 100644 --- a/contributed_definitions/nyaml/NXcg_half_edge_data_structure.yaml +++ b/base_classes/nyaml/NXcg_half_edge_data_structure.yaml @@ -5,6 +5,8 @@ doc: | Such a data structure can be used to efficiently circulate around faces and iterate over vertices of a planar graph. The data structure is also known as a doubly connected edge list. + + Indices can be used as identifier and thus names for individual instances. # holes in the polygon mesh can be handled symbols: @@ -26,7 +28,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): Dimensionality of the primitives described. # resulting in a design similar to that of NXoff_geometry and the XDMF mixed primitive topology - number_of_vertices(NX_INT): + number_of_vertices(NX_UINT): unit: NX_UNITLESS doc: | Number of vertices for each face. @@ -36,7 +38,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): dimensions: rank: 1 dim: (n_f,) - number_of_edges(NX_INT): + number_of_edges(NX_UINT): unit: NX_UNITLESS doc: | Number of edges for each face. @@ -46,7 +48,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): dimensions: rank: 1 dim: (n_he,) - identifier_vertex_offset(NX_INT): + index_offset_vertex(NX_INT): unit: NX_UNITLESS doc: | Integer offset whereby the identifier of the first member @@ -54,7 +56,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): Identifier can be defined explicitly or implicitly. Inspect the definition of :ref:`NXcg_primitive` for further details. - identifier_edge_offset(NX_INT): + index_offset_edge(NX_INT): unit: NX_UNITLESS doc: | Integer offset whereby the identifier of the first member @@ -62,7 +64,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): Identifier can be defined explicitly or implicitly. Inspect the definition of :ref:`NXcg_primitive` for further details. - identifier_face_offset(NX_INT): + index_offset_face(NX_INT): doc: | Integer offset whereby the identifier of the first member of the faces differs from zero. @@ -70,7 +72,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): Identifier can be defined explicitly or implicitly. Inspect the definition of :ref:`NXcg_primitive` for further details. - # therefore, identifier_ -vertex, -face, -half_edge are implicit + # therefore, indices_ -vertex, -face, -half_edge are implicit position(NX_NUMBER): unit: NX_ANY doc: | @@ -141,8 +143,8 @@ NXcg_half_edge_data_structure(NXcg_primitive): of microstructural objects like crystals/grains. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6984d4a73236b8d8843788fecf74cd41114a16880a4a9a2f14e78f667a075d41 -# +# b10ac48eea45ef41a87c498cb5948f0214ae0b644dac489dba9373b8f3afcff6 +# # # -# +# # # Number of vertices for each face. # @@ -216,7 +220,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): # # # -# +# # # Number of edges for each face. # @@ -227,7 +231,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): # # # -# +# # # Integer offset whereby the identifier of the first member # of the vertices differs from zero. @@ -236,7 +240,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): # Inspect the definition of :ref:`NXcg_primitive` for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the edges differs from zero. @@ -245,7 +249,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): # Inspect the definition of :ref:`NXcg_primitive` for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the faces differs from zero. @@ -254,7 +258,7 @@ NXcg_half_edge_data_structure(NXcg_primitive): # Inspect the definition of :ref:`NXcg_primitive` for further details. # # -# +# # # # The position of the vertices. diff --git a/contributed_definitions/nyaml/NXcg_hexahedron.yaml b/base_classes/nyaml/NXcg_hexahedron.yaml similarity index 95% rename from contributed_definitions/nyaml/NXcg_hexahedron.yaml rename to base_classes/nyaml/NXcg_hexahedron.yaml index 55f55a8198..f2af5f16d8 100644 --- a/contributed_definitions/nyaml/NXcg_hexahedron.yaml +++ b/base_classes/nyaml/NXcg_hexahedron.yaml @@ -138,22 +138,18 @@ NXcg_hexahedron(NXcg_primitive): hexahedra(NXcg_face_list_data_structure): doc: | Combined storage of all primitives of all hexahedra. - HEXAHEDRON(NXcg_face_list_data_structure): - nameType: any + hexahedronID(NXcg_face_list_data_structure): + nameType: partial doc: | Individual storage of each hexahedron. - - Instances should use hexahedron as a name prefix. - HEXAHEDRON_HALF_EDGE(NXcg_half_edge_data_structure): - nameType: any + hexahedron_half_edgeID(NXcg_half_edge_data_structure): + nameType: partial doc: | Individual storage of each hexahedron as a graph. - - Instances should use hexahedron_half_edge as a name prefix. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# e2ccf5cb709c2a56bbf5ccaa145046d39aab23421ade9e81860e5fa6e7fa81a5 -# +# 9a91e731a011f357acdd1310cdece4aa43a4ec09ec35774d98505a570d5e986d +# # # # # -# To specify which parallelogram is a rectangle. +# To specify which parallelogram is a rectangle. # # # @@ -152,9 +150,9 @@ NXcg_parallelogram(NXcg_primitive): # # # -# Only to be used if is_rectangle is present. In this case, this field -# describes whether parallelograms are rectangles whose primary edges -# are parallel to the axes of the coordinate system. +# Only to be used if is_rectangle is present. In this case, this field +# describes whether parallelograms are rectangles whose primary edges +# are parallel to the axes of the coordinate system. # # # @@ -163,14 +161,12 @@ NXcg_parallelogram(NXcg_primitive): # # # -# Combined storage of all parallelograms. +# Combined storage of all parallelograms. # # -# +# # -# Individual storage of each parallelogram. -# -# Instances should use parallelogram as a name prefix. +# Individual storage of each parallelogram. # # # diff --git a/contributed_definitions/nyaml/NXcg_point.yaml b/base_classes/nyaml/NXcg_point.yaml similarity index 99% rename from contributed_definitions/nyaml/NXcg_point.yaml rename to base_classes/nyaml/NXcg_point.yaml index f121fa2c3e..33db7ec47b 100644 --- a/contributed_definitions/nyaml/NXcg_point.yaml +++ b/base_classes/nyaml/NXcg_point.yaml @@ -50,7 +50,7 @@ NXcg_point(NXcg_primitive): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # 14c313890564590cf516821eca33c4e26bed72d15a8078e0dc52a5bff904ad30 -# +# # # # # -# The total number of vertices when visiting every polygon. +# The total number of vertices when visiting every polygon. # # # # # -# Computational geometry description of a set of polygons in Euclidean space. -# -# Polygons are specialized polylines: -# -# * A polygon is a geometric primitive that is bounded by a closed polyline -# * All vertices of this polyline lay in the d-1 dimensional plane. -# whereas vertices of a polyline do not necessarily lay on a plane. -# * A polygon has at least three vertices. -# -# Each polygon is built from a sequence of vertices (points with identifiers). -# The members of a set of polygons may have a different number of vertices. -# Sometimes a collection/set of polygons is referred to as a soup of polygons. -# -# As three-dimensional objects, a set of polygons can be used to define the -# hull of what is effectively a polyhedron; however users are advised to use -# the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed -# polyhedra. Even more general complexes can be thought of. An example are the -# so-called piecewise-linear complexes used in the TetGen library. -# -# As these complexes can have holes though, polyhedra without holes are one -# subclass of such complexes, users should rather design an own base class -# e.g. NXcg_polytope to describe such even more complex primitives instead -# of abusing this base class for such purposes. +# Computational geometry description of a set of polygons in Euclidean space. +# +# Polygons are specialized polylines: +# +# * A polygon is a geometric primitive that is bounded by a closed polyline +# * All vertices of this polyline lay in the d-1 dimensional plane. +# whereas vertices of a polyline do not necessarily lay on a plane. +# * A polygon has at least three vertices. +# +# Each polygon is built from a sequence of vertices (points with identifiers). +# The members of a set of polygons may have a different number of vertices. +# Sometimes a collection/set of polygons is referred to as a soup of polygons. +# +# As three-dimensional objects, a set of polygons can be used to define the +# hull of what is effectively a polyhedron; however users are advised to use +# the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed +# polyhedra. Even more general complexes can be thought of. An example are the +# so-called piecewise-linear complexes used in the TetGen library. +# +# As these complexes can have holes though, polyhedra without holes are one +# subclass of such complexes, users should rather design their own base class +# e.g. NXcg_polytope to describe such even more complex primitives instead +# of abusing this base class for such purposes. # -# +# # -# The total number of vertices in the set. +# The total number of vertices in the set. # # # # # -# Combined storage of all primitives of all polygons. +# Combined storage of all primitives of all polygons. # # -# +# # -# Individual storage of the mesh of each polygon. -# -# Instances should use polygon as a name prefix. +# Individual storage of the mesh of each polygon. # # -# +# # -# Individual storage of each polygon as a graph. -# -# Instances should use polygon_half_edge as a name prefix. +# Individual storage of each polygon as a graph. # # # # # -# For each polygon its accumulated length along its edges. +# For each polygon its accumulated length along its edges. # # # @@ -200,11 +192,11 @@ NXcg_polygon(NXcg_primitive): # # # -# Interior angles for each polygon. There are as many values per polygon -# as the are number_of_vertices. -# The angle is the angle at the specific vertex, i.e. between the adjoining -# edges of the vertex according to the sequence in the polygons array. -# Usually, the winding_order field is required to interpret the value. +# Interior angles for each polygon. There are as many values per polygon +# as there are number_of_vertices. +# The angle is the angle at the specific vertex, i.e. between the adjoining +# edges of the vertex according to the sequence in the polygons array. +# Usually, the winding_order field is required to interpret the value. # # # @@ -212,11 +204,11 @@ NXcg_polygon(NXcg_primitive): # # # -# Curvature type: -# -# * 0 - unspecified, -# * 1 - convex, -# * 2 - concave +# Curvature type: +# +# * 0 - unspecified, +# * 1 - convex, +# * 2 - concave # # # diff --git a/contributed_definitions/nyaml/NXcg_polyhedron.yaml b/base_classes/nyaml/NXcg_polyhedron.yaml similarity index 73% rename from contributed_definitions/nyaml/NXcg_polyhedron.yaml rename to base_classes/nyaml/NXcg_polyhedron.yaml index 44ec1d3ddd..c591e07215 100644 --- a/contributed_definitions/nyaml/NXcg_polyhedron.yaml +++ b/base_classes/nyaml/NXcg_polyhedron.yaml @@ -18,21 +18,11 @@ symbols: The total number of edges for all polyhedra. n_f_total: | The total number of faces for all polyhedra. - -# it is useful to define own base classes for frequently used classes -# a polyhedron is a specific polytope in 3d, do we need -# higher-dimensional polytopes? that could be useful for simplices though -# as they are used in numerics etc. maybe reach out here to our friends -# from MarDI, for now let's assume we do not need polytopes for d > 3 -# NeXus already supports polyhedra via NXoff_geometry -# the here proposed base class extends the capabilities to qualifiers of -# polyhedra and also half_edge_data_structures that can be useful -# for clean graph-based descriptions of polyhedra. type: group NXcg_polyhedron(NXcg_primitive): # qualifiers and properties of polyhedra - number_of_faces(NX_INT): + number_of_faces(NX_UINT): unit: NX_UNITLESS doc: | The number of faces for each polyhedron. Faces of adjoining polyhedra @@ -47,7 +37,7 @@ NXcg_polyhedron(NXcg_primitive): dimensions: rank: 1 dim: (n_f_total,) - number_of_edges(NX_INT): + number_of_edges(NX_UINT): doc: | The number of edges for each polyhedron. Edges of adjoining polyhedra are counted for each polyhedron. @@ -63,22 +53,18 @@ NXcg_polyhedron(NXcg_primitive): polyhedra(NXcg_face_list_data_structure): doc: | Combined storage of all primitives of all polyhedra. - POLYHEDRON(NXcg_face_list_data_structure): - nameType: any + polyhedronID(NXcg_face_list_data_structure): + nameType: partial doc: | Individual storage of each polyhedron. - - Instances should use polyhedron as a name prefix. - POLYHEDRON_HALF_EDGE(NXcg_half_edge_data_structure): - nameType: any + polyhedron_half_edgeID(NXcg_half_edge_data_structure): + nameType: partial doc: | Individual storage of each polygon as a graph. - - Instances should use cluster_analysis as a name prefix. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 59836c499259273600f4e8e9ecf9eb5f6810c21501fbe79a284e17e8ad8e9f90 -# +# d7fb29aff4740eed151d11ee4c352507406b734ab3e56f56c58b9079918ad461 +# # # -# # # # @@ -144,7 +120,7 @@ NXcg_polyhedron(NXcg_primitive): # by creating customized instances of an :ref:`NXcg_polygon`. # # -# +# # # The number of faces for each polyhedron. Faces of adjoining polyhedra # are counted for each polyhedron. @@ -161,7 +137,7 @@ NXcg_polyhedron(NXcg_primitive): # # # -# +# # # The number of edges for each polyhedron. Edges of adjoining polyhedra # are counted for each polyhedron. @@ -181,18 +157,14 @@ NXcg_polyhedron(NXcg_primitive): # Combined storage of all primitives of all polyhedra. # # -# +# # # Individual storage of each polyhedron. -# -# Instances should use polyhedron as a name prefix. # # -# +# # # Individual storage of each polygon as a graph. -# -# Instances should use cluster_analysis as a name prefix. # # # diff --git a/contributed_definitions/nyaml/NXcg_polyline.yaml b/base_classes/nyaml/NXcg_polyline.yaml similarity index 95% rename from contributed_definitions/nyaml/NXcg_polyline.yaml rename to base_classes/nyaml/NXcg_polyline.yaml index cc720cf7b7..26e3a753e1 100644 --- a/contributed_definitions/nyaml/NXcg_polyline.yaml +++ b/base_classes/nyaml/NXcg_polyline.yaml @@ -27,15 +27,15 @@ NXcg_polyline(NXcg_primitive): Reference to an instance of :ref:`NXcg_point` which defines the location of the vertices that are referred to in this NXcg_polyline instance. - number_of_unique_vertices(NX_POSINT): + number_of_unique_vertices(NX_UINT): unit: NX_UNITLESS doc: | The total number of vertices that have different positions. - number_of_total_vertices(NX_INT): + number_of_total_vertices(NX_UINT): unit: NX_UNITLESS doc: | The total number of vertices, irrespective of their eventual uniqueness. - number_of_vertices(NX_INT): + number_of_vertices(NX_UINT): unit: NX_UNITLESS doc: | The total number of vertices of each polyline, irrespectively @@ -95,8 +95,8 @@ NXcg_polyline(NXcg_primitive): dim: (n_total,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f838ec9411d9e75d720c6e986fbaa571e08927458a68c6e48d9272421b5742b9 -# +# b14cc08d68ff1d70e5adca4bb17904235e53d9c9d2fd6c3aa5438efa188a2fed +# # # # -# -# -# Constant to be used in the definition: the number of channels of the -# circuit board. -# -# -# -# number of channels of the circuit board. -# -# -# # -# Application definition for circuit devices. +# Base class for documenting circuit devices. # -# Electronic circuits are hardware components connecting several electronic components to achieve +# Electronic circuits are hardware components that connect several electronic components to achieve # specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. # # # -# Hardware where the circuit is implanted; includes information about the hardware manufacturers and -# type (e.g. part number) +# Hardware where the circuit is implanted; includes information about the +# hardware manufacturers and type (e.g. part number) # All the elements below may be single numbers of an array of values with length N_channel # describing multiple input and output channels. # # -# +# # # List of components used in the circuit, e.g., resistors, capacitors, transistors or any # other complex components. # # -# +# # # Description of how components are interconnected, including connection points # and wiring. # # -# +# # # Details of the power source for the circuit, including voltage and current # ratings. # # -# +# # # Type of signal (input signal) the circuit is designed to handle, e.g., analog, # digital, mixed-signal. @@ -182,9 +166,14 @@ NXcircuit(NXcomponent): # # # -# The operating frequency of the circuit, see also bandwidth below, which is possibly -# centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth -# amplifier at low, audio frequencies 1 - 20,000 Hz) +# The operating frequency of the circuit, see also bandwidth, which is possibly +# but not necessarily centered around this frequency (e.g. running a 100 kHz bandwidth +# amplifier at low, audio frequencies 1 - 20,000 Hz). +# +# +# +# +# The bandwidth of the frequency response of the circuit. # # # @@ -200,18 +189,14 @@ NXcircuit(NXcomponent): # # # -# Gain of the circuit, if applicable, usually all instruments have a gain which might be -# important or not. +# Gain of the circuit, if applicable, usually all instruments have a gain +# which might be important or not. # # # # -# RMS noise level (in current or voltage) in the circuit in voltage or current. -# -# -# -# -# The bandwidth of the frequency response of the circuit. +# Root-mean-square (RMS) noise level (in current or voltage) +# in the circuit in voltage or current. # # # @@ -231,7 +216,7 @@ NXcircuit(NXcomponent): # # # -# Number of output channels collected to this circuit. Most probably N_channel. +# Number of output channels connected to this circuit. Most probably N_channel. # # # @@ -244,7 +229,7 @@ NXcircuit(NXcomponent): # Power consumption of the circuit per unit time. # # -# +# # # Status indicators for the circuit, e.g., LEDs, display readouts. # diff --git a/base_classes/nyaml/NXcollectioncolumn.yaml b/base_classes/nyaml/NXcollectioncolumn.yaml index 842d5b94e0..942ff618ec 100644 --- a/base_classes/nyaml/NXcollectioncolumn.yaml +++ b/base_classes/nyaml/NXcollectioncolumn.yaml @@ -52,12 +52,12 @@ NXcollectioncolumn(NXcomponent): (NXdeflector): doc: | Deflectors in the collection column section - (NXlens_em): + (NXelectromagnetic_lens): doc: | Individual lenses in the collection column section # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# c65d66fb60eaea70870271e535ad711dd3d16981558679ee97a089bdbe2fdeec +# 413fd15abd46105afd849c327cd57fb1a37701d7fcd8a985c9afb1c707e94b6b # # # -# # # # @@ -212,12 +172,14 @@ NXcorrector_cs(NXcomponent): # Different technology partners use different conventions and # models for quantifying the aberration coefficients. # -# The corrector in an electron microscope is composed of multiple lenses -# and multipole stigmators with details that are specific for the technology partner -# and microscope. Most technical details are proprietary knowledge. +# Correctors in an electron microscope are composed of multiple lenses +# and multipole stigmators. Their technical details are specific for the +# technology partner as well as microscope. Most technical details are +# proprietary knowledge. # -# If one component corrects for multiple types of aberrations (like it is the case reported -# here `CEOS <https://www.ceos-gmbh.de/en/research/electrostat>`_) follow this design: +# If one component corrects for multiple types of aberrations (like it is the case +# reported here `CEOS <https://www.ceos-gmbh.de/en/research/electrostat>`_) follow this +# design when using corrector and monochromator in an application definition: # # * Use :ref:`NXcorrector_cs` for spherical aberration # * Use :ref:`NXmonochromator` for energy filtering or chromatic aberration @@ -229,9 +191,9 @@ NXcorrector_cs(NXcomponent): # Was the corrector used? # # -# +# # -# Specific information about the alignment procedure that is a process during which +# Specific information about the alignment procedure. This is a process during which # the corrector is configured to enable calibrated usage of the instrument. # # This :ref:`NXprocess` group should also be used when one describes in a computer @@ -248,7 +210,8 @@ NXcorrector_cs(NXcomponent): # The outer tilt angle of the beam in tableau acquisition. # # TODO: The relevant axes which span the tilt_angle need a -# cleaner description. +# cleaner description. Suggestions from the community are +# welcome here for guiding an improvement of this base class. # # # @@ -271,14 +234,14 @@ NXcorrector_cs(NXcomponent): # # # -# +# # # Image(s) taken during the alignment procedure # # # # -# Convention used for storing measured or estimated aberrations (for each image or final) +# Convention used for storing measured or estimated aberrations (for each or the final image) # via fields c_1, a_1, c_1_0, c_1_2_a, and so on and so forth. # # See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) @@ -334,46 +297,7 @@ NXcorrector_cs(NXcomponent): # # # -# -# +# # # # diff --git a/base_classes/nyaml/NXcs_computer.yaml b/base_classes/nyaml/NXcs_computer.yaml new file mode 100644 index 0000000000..38e22e57a5 --- /dev/null +++ b/base_classes/nyaml/NXcs_computer.yaml @@ -0,0 +1,108 @@ +category: base +doc: | + Base class for reporting the description of a computer +type: group +NXcs_computer(NXobject): + name(NX_CHAR): + doc: | + Given name/alias to the computing system, e.g. MyDesktop. + operating_system(NX_CHAR): + doc: | + Name of the operating system, e.g. Windows, Linux, Mac, Android. + \@version(NX_CHAR): + doc: | + Version plus build number, commit hash, or description of an ever + persistent resource where the source code of the program and build + instructions can be found so that the program can be configured in + such a manner that the result file is ideally recreatable yielding + the same results. + + # difference e.g. in Win11 between hardware ID, UUID, and device ID + uuid(NX_CHAR): + doc: | + A globally unique persistent identifier of the computer, i.e. + the Universally Unique Identifier (UUID) of the computing node. + processorID(NXcs_processor): + nameType: partial + doc: | + Multiple instances should be named processor1, processor2, etc. + memoryID(NXcs_memory): + nameType: partial + doc: | + Multiple instances should be named memory1, memory2, etc. + storageID(NXcs_storage): + nameType: partial + doc: | + Multiple instances should be named storage1, storage2, etc. + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 770ae9844db4717757cb4c6e56bb4f34a6a859d225df9a95cc46f022dcbdf9f5 +# +# +# +# +# +# Base class for reporting the description of a computer +# +# +# +# Given name/alias to the computing system, e.g. MyDesktop. +# +# +# +# +# Name of the operating system, e.g. Windows, Linux, Mac, Android. +# +# +# +# Version plus build number, commit hash, or description of an ever +# persistent resource where the source code of the program and build +# instructions can be found so that the program can be configured in +# such a manner that the result file is ideally recreatable yielding +# the same results. +# +# +# +# +# +# +# A globally unique persistent identifier of the computer, i.e. +# the Universally Unique Identifier (UUID) of the computing node. +# +# +# +# +# Multiple instances should be named processor1, processor2, etc. +# +# +# +# +# Multiple instances should be named memory1, memory2, etc. +# +# +# +# +# Multiple instances should be named storage1, storage2, etc. +# +# +# diff --git a/base_classes/nyaml/NXcs_filter_boolean_mask.yaml b/base_classes/nyaml/NXcs_filter_boolean_mask.yaml new file mode 100644 index 0000000000..873e3a6f33 --- /dev/null +++ b/base_classes/nyaml/NXcs_filter_boolean_mask.yaml @@ -0,0 +1,136 @@ +category: base +doc: | + Base class for packing and unpacking booleans. + + The field mask should be constructed from packing a vector of booleans + (a bitfield) into unsigned integers with bytesize bitdepth. Padding to + an integer number of such integers is assumed. + + Thereby, this base class can be used to inform software about necessary modulo + operations to decode the mask to recover e.g. set membership of objects in sets + whose membership has been encoded as a vector of booleans. + + This is useful e.g. when processing object sets such as point cloud data. + If e.g. a spatial filter has been applied to a set of points, we may wish to document + memory-space efficiently which points were analyzed. An array of boolean values + is one option to achieve this. A value is true if the point is included and false otherwise. +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. + n_objs: | + Number of entries (e.g. number of points or objects). + bitdepth: | + Number of bits assumed for the container datatype used. + n_total: | + Length of mask considering the eventual need for padding. +type: group +NXcs_filter_boolean_mask(NXobject): + depends_on(NX_CHAR): + doc: | + Possibility to refer to which set this mask applies. + + If depends_on is not provided, it is assumed that the mask + applies to its direct parent. + number_of_objects(NX_UINT): + unit: NX_UNITLESS + doc: | + Number of objects represented by the mask. + bitdepth(NX_UINT): + unit: NX_UNITLESS + doc: | + Number of bits assumed matching on a default datatype. + (e.g. 8 bits for a C-style uint8). + mask(NX_UINT): + unit: NX_UNITLESS + doc: | + The content of the mask. If padding is used, + padding bits have to be set to 0. + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 3995cd8327636f3badc570bb6935642361b70139dac5f3c16b883e21538a5bc8 +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of entries (e.g. number of points or objects). +# +# +# +# +# Number of bits assumed for the container datatype used. +# +# +# +# +# Length of mask considering the eventual need for padding. +# +# +# +# +# Base class for packing and unpacking booleans. +# +# The field mask should be constructed from packing a vector of booleans +# (a bitfield) into unsigned integers with bytesize bitdepth. Padding to +# an integer number of such integers is assumed. +# +# Thereby, this base class can be used to inform software about necessary modulo +# operations to decode the mask to recover e.g. set membership of objects in sets +# whose membership has been encoded as a vector of booleans. +# +# This is useful e.g. when processing object sets such as point cloud data. +# If e.g. a spatial filter has been applied to a set of points, we may wish to document +# memory-space efficiently which points were analyzed. An array of boolean values +# is one option to achieve this. A value is true if the point is included and false otherwise. +# +# +# +# Possibility to refer to which set this mask applies. +# +# If depends_on is not provided, it is assumed that the mask +# applies to its direct parent. +# +# +# +# +# Number of objects represented by the mask. +# +# +# +# +# Number of bits assumed matching on a default datatype. +# (e.g. 8 bits for a C-style uint8). +# +# +# +# +# The content of the mask. If padding is used, +# padding bits have to be set to 0. +# +# +# diff --git a/base_classes/nyaml/NXcs_memory.yaml b/base_classes/nyaml/NXcs_memory.yaml new file mode 100644 index 0000000000..f4ed105c75 --- /dev/null +++ b/base_classes/nyaml/NXcs_memory.yaml @@ -0,0 +1,68 @@ +category: base +doc: | + Base class for reporting the description of the memory system of a computer. +type: group +NXcs_memory(NXcomponent): + (NXcircuit): + doc: | + Typically, computers have multiple instances of memory. + type(NX_CHAR): + doc: | + Qualifier for the type of random access memory. + enumeration: + open_enum: true + items: [ddr4, ddr5] + max_physical_capacity(NX_POSINT): + unit: NX_ANY + doc: | + Total amount of data which the medium can hold. + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 02c8be65151092e9de874ee9a8bc407b53c0f3925f193755b7694d4b3e9934a6 +# +# +# +# +# +# Base class for reporting the description of the memory system of a computer. +# +# +# +# Typically, computers have multiple instances of memory. +# +# +# +# Qualifier for the type of random access memory. +# +# +# +# +# +# +# +# +# Total amount of data which the medium can hold. +# +# +# +# diff --git a/contributed_definitions/nyaml/NXcs_prng.yaml b/base_classes/nyaml/NXcs_prng.yaml similarity index 63% rename from contributed_definitions/nyaml/NXcs_prng.yaml rename to base_classes/nyaml/NXcs_prng.yaml index 7050d56074..dd10ad12f4 100644 --- a/contributed_definitions/nyaml/NXcs_prng.yaml +++ b/base_classes/nyaml/NXcs_prng.yaml @@ -2,8 +2,8 @@ category: base doc: | Computer science description of pseudo-random number generator. - The purpose of this base class is to identify if exactly the same sequence - can be reproduced, like for a PRNG or not (for a true physically random source). + The purpose of this base class is to identify if exactly the same sequence can be + reproduced, like for a PRNG or not, like for a true physically random source. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -15,14 +15,14 @@ NXcs_prng(NXobject): Different approaches for generating random numbers with a computer exists. Some use a dedicated physical device whose the state is unpredictable - (physically). Some use a strategy of mangling information from the system + physically. Some use a strategy of mangling information from the system clock. Also in this case the sequence is not reproducible without having additional pieces of information. In most cases though so-called pseudo-random number generator (PRNG) algorithms are used. These yield a deterministic sequence of practically randomly appearing numbers. These algorithms differ in their quality in - how close the resulting sequences are random, i.e. sequentially + how random the resulting sequences actually are, i.e. sequentially uncorrelated. Nowadays one of the most commonly used algorithm is the MersenneTwister (mt19937). enumeration: [physical, system_clock, mt19937, other] @@ -48,13 +48,13 @@ NXcs_prng(NXobject): # one could also think about making reference to the NIST PRNG test suite to qualify the PRNG # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 7cab5bbba4affc39c86fe740226d4ce392527678c47a47e1c18f37157aaba203 -# +# 71bcdf7b83514e93216b0edf195944e7a8766346d2d65aac4edd7823439aa944 +# # # +# +# +# Base class for reporting the description of processing units of a computer. +# +# Examples are e.g. classical so-called central processing units (CPUs), +# coprocessors, graphic cards, accelerator processing units or a system of these. +# +# +# +# Typical examples for the granularization of processing units are: +# +# * A desktop computer with a single CPU; describe using one instance of NXcircuit. +# * A dual-socket server; describe using two instances of NXcircuit. +# * A server with two dual-socket server nodes; describe with four +# instances of NXcircuit surplus a field that defines their level +# in the hierarchy. +# +# +# +# General type of the processing unit e.g. +# +# * pu, processing core or hyper-threading core +# * cpu, (multi-)core central processing unit +# * gpu, (multi-)core general purpose processing unit +# * fpga, field programmable gate array +# +# +# +# +# +# +# +# +# +# +# Clock speed of the circuit +# +# +# +# diff --git a/base_classes/nyaml/NXcs_profiling.yaml b/base_classes/nyaml/NXcs_profiling.yaml new file mode 100644 index 0000000000..259c107801 --- /dev/null +++ b/base_classes/nyaml/NXcs_profiling.yaml @@ -0,0 +1,252 @@ +category: base +doc: | + Computer science description for performance and profiling data of an application. + + Performance monitoring and benchmarking of software is a task where questions + can be asked at various levels of detail. In general, there are three main + contributions to performance: + + * Hardware capabilities and configuration + * Software configuration and capabilities + * Dynamic effects of the system in operation and the system working together + with eventually multiple computers, especially when these have to exchange + information across a network and these are used usually by multiple users. + + At the most basic level users may wish to document how long e.g. a data + analysis with a scientific software, i.e. an app took. + A frequent idea is here to answer practical questions like how critical is the + effect on the workflow of the scientists, i.e. is the analysis possible in + a few seconds or would it take days if I were to run this analysis on a + comparable machine? + For this more qualitative performance monitoring, mainly the order of + magnitude is relevant, as well as how this was achieved using parallelization + (i.e. reporting the number of CPU and GPU resources used, the number of + processes and threads configured, and providing basic details about the computer). + + At more advanced levels benchmarks may go as deep as detailed temporal tracking + of individual processor instructions, their relation to other instructions, the + state of call stacks; in short eventually the entire app execution history + and hardware state history. Such analyses are mainly used for performance + optimization, i.e. by software and hardware developers as well as for + tracking bugs. Specialized software exists which documents such performance + data in specifically-formatted event log files or databases. + + This base class cannot and should not replace these specific solutions for now. + Instead, the intention of the base class is to serve scientists at the + basic level to enable simple monitoring of performance data and log profiling + data of key algorithmic steps or parts of computational workflows, so that + these pieces of information can guide users which order of magnitude differences + should be expected or not. + + Developers of application definitions should add additional fields and + references to e.g. more detailed performance data to which they wish to link + the metadata in this base class. +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. +type: group +NXcs_profiling(NXobject): + + # details about queuing systems etc + current_working_directory(NX_CHAR): + doc: | + Path to the directory from which the tool was called. + command_line_call(NX_CHAR): + doc: | + Command line call with arguments if applicable. + start_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information + included when the app was started. + end_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information + included when the app terminated or crashed. + total_elapsed_time(NX_NUMBER): + unit: NX_TIME + doc: | + Wall-clock time how long the app execution took. This may be in principle + end_time minus start_time; however usage of eventually more precise timers + may warrant to use a finer temporal discretization, + and thus demands a more precise record of the wall-clock time. + max_processes(NX_UINT): + unit: NX_UNITLESS + doc: | + The number of nominal processes that the app invoked at runtime. + + The main idea behind this field e.g. for apps which use e.g. MPI + (Message Passing Interface) parallelization is to communicate + how many processes were used. + + For sequentially running apps number_of_processes and number_of_threads + is one. If the app exclusively uses GPU parallelization, number_of_gpus + can be larger than one. If no GPU is used, number_of_gpus is zero, + even though the hardware may have GPUs installed. + max_threads(NX_UINT): + unit: NX_UNITLESS + doc: | + The number of nominal threads that the app invoked at runtime. + Specifically here the maximum number of threads used for the + high-level threading library used (e.g. OMP_NUM_THREADS), posix. + max_gpus(NX_UINT): + unit: NX_UNITLESS + doc: | + The number of nominal GPUs that the app invoked at runtime. + (NXcs_computer): + doc: | + A collection with one or more computing nodes each with own resources. + This can be as simple as a laptop or the nodes of a cluster computer. + eventID(NXcs_profiling_event): + nameType: partial + doc: | + A collection of individual profiling event data which detail e.g. how + much time the app took for certain computational steps and/or how much + memory was consumed during these operations. + ID is an increasing unsigned integer starting at 1. + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 1a4fa6f0dbd2fe7ab1feecd16624bba61f1641ec076e4173c9df3147a38b6967 +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Computer science description for performance and profiling data of an application. +# +# Performance monitoring and benchmarking of software is a task where questions +# can be asked at various levels of detail. In general, there are three main +# contributions to performance: +# +# * Hardware capabilities and configuration +# * Software configuration and capabilities +# * Dynamic effects of the system in operation and the system working together +# with eventually multiple computers, especially when these have to exchange +# information across a network and these are used usually by multiple users. +# +# At the most basic level users may wish to document how long e.g. a data +# analysis with a scientific software, i.e. an app took. +# A frequent idea is here to answer practical questions like how critical is the +# effect on the workflow of the scientists, i.e. is the analysis possible in +# a few seconds or would it take days if I were to run this analysis on a +# comparable machine? +# For this more qualitative performance monitoring, mainly the order of +# magnitude is relevant, as well as how this was achieved using parallelization +# (i.e. reporting the number of CPU and GPU resources used, the number of +# processes and threads configured, and providing basic details about the computer). +# +# At more advanced levels benchmarks may go as deep as detailed temporal tracking +# of individual processor instructions, their relation to other instructions, the +# state of call stacks; in short eventually the entire app execution history +# and hardware state history. Such analyses are mainly used for performance +# optimization, i.e. by software and hardware developers as well as for +# tracking bugs. Specialized software exists which documents such performance +# data in specifically-formatted event log files or databases. +# +# This base class cannot and should not replace these specific solutions for now. +# Instead, the intention of the base class is to serve scientists at the +# basic level to enable simple monitoring of performance data and log profiling +# data of key algorithmic steps or parts of computational workflows, so that +# these pieces of information can guide users which order of magnitude differences +# should be expected or not. +# +# Developers of application definitions should add additional fields and +# references to e.g. more detailed performance data to which they wish to link +# the metadata in this base class. +# +# +# +# +# Path to the directory from which the tool was called. +# +# +# +# +# Command line call with arguments if applicable. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# included when the app was started. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# included when the app terminated or crashed. +# +# +# +# +# Wall-clock time how long the app execution took. This may be in principle +# end_time minus start_time; however usage of eventually more precise timers +# may warrant to use a finer temporal discretization, +# and thus demands a more precise record of the wall-clock time. +# +# +# +# +# The number of nominal processes that the app invoked at runtime. +# +# The main idea behind this field e.g. for apps which use e.g. MPI +# (Message Passing Interface) parallelization is to communicate +# how many processes were used. +# +# For sequentially running apps number_of_processes and number_of_threads +# is one. If the app exclusively uses GPU parallelization, number_of_gpus +# can be larger than one. If no GPU is used, number_of_gpus is zero, +# even though the hardware may have GPUs installed. +# +# +# +# +# The number of nominal threads that the app invoked at runtime. +# Specifically here the maximum number of threads used for the +# high-level threading library used (e.g. OMP_NUM_THREADS), posix. +# +# +# +# +# The number of nominal GPUs that the app invoked at runtime. +# +# +# +# +# A collection with one or more computing nodes each with own resources. +# This can be as simple as a laptop or the nodes of a cluster computer. +# +# +# +# +# A collection of individual profiling event data which detail e.g. how +# much time the app took for certain computational steps and/or how much +# memory was consumed during these operations. +# ID is an increasing unsigned integer starting at 1. +# +# +# diff --git a/contributed_definitions/nyaml/NXcs_profiling_event.yaml b/base_classes/nyaml/NXcs_profiling_event.yaml similarity index 55% rename from contributed_definitions/nyaml/NXcs_profiling_event.yaml rename to base_classes/nyaml/NXcs_profiling_event.yaml index 1d3a66efcf..33fce1541b 100644 --- a/contributed_definitions/nyaml/NXcs_profiling_event.yaml +++ b/base_classes/nyaml/NXcs_profiling_event.yaml @@ -30,18 +30,30 @@ NXcs_profiling_event(NXobject): wall-clock time. Elapsed time may contain time portions where resources were idling. - number_of_processes(NX_UINT): + max_processes(NX_UINT): unit: NX_UNITLESS doc: | - Number of processes used (max) during the execution of this event. - number_of_threads(NX_UINT): + The number of nominal processes that the app invoked during the execution of this event. + + The main idea behind this field e.g. for apps which use e.g. MPI + (Message Passing Interface) parallelization is to communicate + how many processes were used. + + For sequentially running apps number_of_processes and number_of_threads + is one. If the app exclusively uses GPU parallelization, number_of_gpus + can be larger than one. If no GPU is used, number_of_gpus is zero, + even though the hardware may have GPUs installed. + max_threads(NX_UINT): unit: NX_UNITLESS doc: | - Number of threads used (max) during the execution of this event. - number_of_gpus(NX_UINT): + The number of nominal threads that the app invoked at during the execution of this event. + Specifically here the maximum number of threads used for the + high-level threading library used (e.g. OMP_NUM_THREADS), posix. + max_gpus(NX_UINT): unit: NX_UNITLESS doc: | - Number of GPUs used (max) during the execution of this event. + The number of nominal GPUs that the app invoked during the execution of this + event. max_virtual_memory_snapshot(NX_NUMBER): unit: NX_ANY doc: | @@ -58,8 +70,8 @@ NXcs_profiling_event(NXobject): dim: (n_processes,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# d783e6ceae7d0db339dd1ef0edea44e0faf6443c8b665d23c7a06ea9ad055c73 -# +# 03c76ab650460ab324d251eefa4dfadec0492caba590035735913dfdee451936 +# # # +# +# +# Base class for reporting the description of the I/O of a computer. +# +# +# +# +# Qualifier for the type of storage medium used. +# +# +# +# +# +# +# +# +# +# +# Total amount of data which the medium can hold. +# +# +# +# +# Maximum read rate of the storage medium. +# +# +# +# +# Maximum write rate of the storage medium. +# +# +# +# diff --git a/base_classes/nyaml/NXdata.yaml b/base_classes/nyaml/NXdata.yaml index 0af712aa56..e7517d724d 100644 --- a/base_classes/nyaml/NXdata.yaml +++ b/base_classes/nyaml/NXdata.yaml @@ -515,7 +515,7 @@ NXdata(NXobject): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # 2aaac78a2fa54b76ecb740cfd6efc667d9c57e9f29428dfb751d195629973972 -# +# # # -# -# -# +# # # Base class for an electro-magnetic lens or a compound lens. -# +# # For :ref:`NXtransformations` the origin of the coordinate system is placed -# in the center of the lens (its polepiece, pinhole, or another -# point of reference). The origin should be specified in the :ref:`NXtransformations`. -# -# For details of electro-magnetic lenses in the literature see e.g. +# in the center of the lens its polepiece, pinhole, or another point of reference. +# The origin should be specified in the :ref:`NXtransformations`. +# +# For details of electro-magnetic lenses in the literature see e.g. # # * `L. Reimer: Scanning Electron Microscopy <https://doi.org/10.1007/978-3-540-38967-5>`_ # * `P. Hawkes: Magnetic Electron Lenses <https://link.springer.com/book/10.1007/978-3-642-81516-4>`_ # * `Y. Liao: Practical Electron Microscopy and Database <https://www.globalsino.com/EM/>`_ -# # # # @@ -129,7 +122,7 @@ NXlens_em(NXcomponent): # # Ideally, use instances of ``identifierNAME`` to point to a resource # that provides further details. -# +# # If such a resource does not exist or should not be used, use this free text, # although it is not recommended. # @@ -139,8 +132,8 @@ NXlens_em(NXcomponent): # Descriptor for the lens excitation when the exact technical details # are unknown or not directly controllable as the control software of # the microscope does not enable or was not configured to display these -# values (for end users). -# +# values for users. +# # Although this value does not document the exact physical voltage or # excitation, it can still give useful context to reproduce the lens # setting, provided a properly working instrument and software sets the lens @@ -153,7 +146,7 @@ NXlens_em(NXcomponent): # Descriptor for the operation mode of the lens when other details are not # directly controllable as the control software of the microscope # does not enable or is not configured to display these values. -# +# # Like value, the mode can only be interpreted for a specific microscope # but can still be useful to guide users as to how to repeat the measurement. # @@ -162,7 +155,7 @@ NXlens_em(NXcomponent): # # # Excitation voltage of the lens. -# +# # For dipoles it is a single number. # For higher order multipoles, it is an array. # @@ -170,7 +163,7 @@ NXlens_em(NXcomponent): # # # Excitation current of the lens. -# +# # For dipoles it is a single number. # For higher-order multipoles, it is an array. # @@ -189,4 +182,9 @@ NXlens_em(NXcomponent): # # # +# +# +# Qualitative description of the lens based on the number of pole pieces. +# +# # diff --git a/base_classes/nyaml/NXelectronanalyzer.yaml b/base_classes/nyaml/NXelectronanalyzer.yaml index 1900f3c7ab..cbdf791174 100644 --- a/base_classes/nyaml/NXelectronanalyzer.yaml +++ b/base_classes/nyaml/NXelectronanalyzer.yaml @@ -201,7 +201,7 @@ NXelectronanalyzer(NXcomponent): (NXdeflector): doc: | Deflectors outside the main optics ensembles described by the subclasses - (NXlens_em): + (NXelectromagnetic_lens): doc: | Individual lenses outside the main optics ensembles described by the subclasses (NXfabrication): @@ -210,7 +210,7 @@ NXelectronanalyzer(NXcomponent): Any other resolution not explicitly named in this base class. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 967c4216aca6f2de37207ac0165fb3688087b402c00d8c72ab6a763a145fb53f +# 19c74dca6181b11be20cda210181fbcb56f50081bbf46e9454cce8ff2ccb28ac # # # +# # # # An overview of the entire ROI. diff --git a/contributed_definitions/nyaml/NXem_eds.yaml b/base_classes/nyaml/NXem_eds.yaml similarity index 94% rename from contributed_definitions/nyaml/NXem_eds.yaml rename to base_classes/nyaml/NXem_eds.yaml index 4283acc634..45c47c50d2 100644 --- a/contributed_definitions/nyaml/NXem_eds.yaml +++ b/base_classes/nyaml/NXem_eds.yaml @@ -10,10 +10,6 @@ doc: | In effect, the resulting three-dimensional elemental information mappings are truly the result of a correlation and post-processing of several measurements which is the field of correlative tomographic usage of electron microscopy. - -# NEW ISSUE: use computational geometry to offer arbitrary scan pattern -# NEW ISSUE: make the binning flexible per scan point -# energy typically the fastest direction symbols: n_photon_energy: | Number of X-ray photon energy (bins) @@ -62,9 +58,6 @@ NXem_eds(NXprocess): This field can be used when creating instances of :ref:`NXpeak` is not desired. However, a collection of instances of NXpeak with individual NXatom can be used to add isotopic information and other relevant context. - dimensions: - rank: 1 - dim: (n_elements,) (NXpeak): doc: | Details about individual indexed peaks. @@ -90,7 +83,8 @@ NXem_eds(NXprocess): dimensions: rank: 1 dim: (n_iupac_line_names,) - (NXimage): + ELEMENT_SPECIFIC_MAP(NXimage): + nameType: any doc: | Individual element-specific EDS/EDX/EDXS/SXES mapping @@ -110,7 +104,7 @@ NXem_eds(NXprocess): description(NX_CHAR): doc: | Discouraged free-text field to add additional information. - iupac_line_candidate(NX_CHAR): + iupac_line_candidates(NX_CHAR): doc: | Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that documents which elements and their specific lines are theoretically located within @@ -139,8 +133,8 @@ NXem_eds(NXprocess): contributes to the intensity of the EDS map. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f4ee4e51409c8bc28b5bb4947e2034139a37f4b7eba4473bf6aa3bd086fd61fa -# +# 3903897979b6ea01fe3d2ffbcfc0642fe9593e9419111b1d5de3f419609f3505 +# # # # -# # # # @@ -250,9 +241,6 @@ NXem_eds(NXprocess): # However, a collection of instances of NXpeak with individual NXatom # can be used to add isotopic information and other relevant context. # -# -# -# # # # @@ -286,7 +274,7 @@ NXem_eds(NXprocess): # # # -# +# # # Individual element-specific EDS/EDX/EDXS/SXES mapping # @@ -309,7 +297,7 @@ NXem_eds(NXprocess): # Discouraged free-text field to add additional information. # # -# +# # # Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that # documents which elements and their specific lines are theoretically located within diff --git a/contributed_definitions/nyaml/NXem_eels.yaml b/base_classes/nyaml/NXem_eels.yaml similarity index 98% rename from contributed_definitions/nyaml/NXem_eels.yaml rename to base_classes/nyaml/NXem_eels.yaml index 35784eb1fa..85c1f2aa24 100644 --- a/contributed_definitions/nyaml/NXem_eels.yaml +++ b/base_classes/nyaml/NXem_eels.yaml @@ -24,7 +24,7 @@ NXem_eels(NXprocess): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # e7654e681ca515cfec03ae8d5052c572a7f40c2770c5e0537e34df4897b2cfbd -# +# # # # diff --git a/base_classes/nyaml/NXem_interaction_volume.yaml b/base_classes/nyaml/NXem_interaction_volume.yaml new file mode 100644 index 0000000000..d0089402ce --- /dev/null +++ b/base_classes/nyaml/NXem_interaction_volume.yaml @@ -0,0 +1,92 @@ +category: base +doc: | + Base class to describe the volume of interaction for particle-matter interaction. + + Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam + interaction simulations can be used to qualify and (or) quantify the shape of + the interaction volume. Results of such simulations can be summary statistics + or single-particle-resolved sets of trajectories. + + Explicit or implicit descriptions of the geometry of this + interaction volume are possible: + + * An implicit description is via a set of electron/specimen interactions + represented ideally as trajectory data from the computer simulation. + * An explicit description is via iso-contour surface using either + a simulation grid or a triangulated surface mesh of the approximated + iso-contour surface evaluated at specific threshold values. + Iso-contours could be computed from electron or particle flux through + an imaginary control surface (the iso-surface) or energy-levels + (e.g. the case of X-rays). Details depend on the model. + * Another explicit description is via theoretical models which may + be relevant e.g. for X-ray spectroscopy + + Further details on how the interaction volume can be quantified + is available in the literature for example: + + * `S. Richter et al. `_ + * `J. Bünger et al. `_ + * `J. F. Ziegler et al. `_ +type: group +NXem_interaction_volume(NXobject): + (NXdata): + (NXprocess): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# cb86a024070ad98fc7ab27376818569c2bd9043b3e28c2019d4e6b2a88ddd019 +# +# +# +# +# +# Base class to describe the volume of interaction for particle-matter interaction. +# +# Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam +# interaction simulations can be used to qualify and (or) quantify the shape of +# the interaction volume. Results of such simulations can be summary statistics +# or single-particle-resolved sets of trajectories. +# +# Explicit or implicit descriptions of the geometry of this +# interaction volume are possible: +# +# * An implicit description is via a set of electron/specimen interactions +# represented ideally as trajectory data from the computer simulation. +# * An explicit description is via iso-contour surface using either +# a simulation grid or a triangulated surface mesh of the approximated +# iso-contour surface evaluated at specific threshold values. +# Iso-contours could be computed from electron or particle flux through +# an imaginary control surface (the iso-surface) or energy-levels +# (e.g. the case of X-rays). Details depend on the model. +# * Another explicit description is via theoretical models which may +# be relevant e.g. for X-ray spectroscopy +# +# Further details on how the interaction volume can be quantified +# is available in the literature for example: +# +# * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ +# * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ +# * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ +# +# +# +# diff --git a/base_classes/nyaml/NXem_measurement.yaml b/base_classes/nyaml/NXem_measurement.yaml new file mode 100644 index 0000000000..48e4dc84a0 --- /dev/null +++ b/base_classes/nyaml/NXem_measurement.yaml @@ -0,0 +1,41 @@ +category: base +doc: | + Base class for documenting a measurement with an electron microscope. +type: group +NXem_measurement(NXobject): + instrument(NXinstrument_em): + eventID(NXevent_data_em): + nameType: partial + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# b316172f1da3439b7e2e8914311c4473c77b211748924007325b78d22ab4bfa2 +# +# +# +# +# +# Base class for documenting a measurement with an electron microscope. +# +# +# +# diff --git a/contributed_definitions/nyaml/NXoptical_system_em.yaml b/base_classes/nyaml/NXem_optical_system.yaml similarity index 91% rename from contributed_definitions/nyaml/NXoptical_system_em.yaml rename to base_classes/nyaml/NXem_optical_system.yaml index 705757deb0..6ae78a0f85 100644 --- a/contributed_definitions/nyaml/NXoptical_system_em.yaml +++ b/base_classes/nyaml/NXem_optical_system.yaml @@ -2,7 +2,7 @@ category: base doc: | Base class for qualifying an electron optical system. type: group -NXoptical_system_em(NXobject): +NXem_optical_system(NXobject): camera_length(NX_NUMBER): unit: NX_LENGTH doc: @@ -51,10 +51,16 @@ NXoptical_system_em(NXobject): spec: EMglossary term: Working Distance url: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 - probe(NXcg_ellipsoid): + + # use NXcg_ellipsoid in the future for probe + probe(NX_NUMBER): doc: | Geometry of the cross-section formed when the primary beam shines onto the - specimen surface. + specimen surface. Reported as length of the semiaxes of the ellipsoidal + cross-section with semiaxes values sorted by decreasing length. + dimensions: + rank: 1 + dim: (2,) # dimensions: # rank: 2 @@ -84,7 +90,7 @@ NXoptical_system_em(NXobject): rotation(NX_NUMBER): unit: NX_ANGLE doc: | - In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated + In the process of passing through an :ref:`NXelectromagnetic_lens` electrons are typically accelerated on a helical path about the optical axis. This causes an image rotation whose strength is affected by the magnification. @@ -133,8 +139,8 @@ NXoptical_system_em(NXobject): url: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f70f9651e027dbd19d14b17716bb0bbf83cf667b9b9361f8989be079ec7cc317 -# +# fef9bdec79829f836cd6aabb31794918ca4edbd347af278401b81beda14f9f1a +# # # -# +# # # Base class for qualifying an electron optical system. # @@ -209,12 +215,17 @@ NXoptical_system_em(NXobject): # .. _Working Distance: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 # # -# +# +# # # Geometry of the cross-section formed when the primary beam shines onto the -# specimen surface. +# specimen surface. Reported as length of the semiaxes of the ellipsoidal +# cross-section with semiaxes values sorted by decreasing length. # -# +# +# +# +# # # @@ -244,7 +255,7 @@ NXoptical_system_em(NXobject): # # # -# In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated +# In the process of passing through an :ref:`NXelectromagnetic_lens` electrons are typically accelerated # on a helical path about the optical axis. This causes an image rotation whose strength # is affected by the magnification. # diff --git a/base_classes/nyaml/NXem_simulation.yaml b/base_classes/nyaml/NXem_simulation.yaml new file mode 100644 index 0000000000..68eba8b949 --- /dev/null +++ b/base_classes/nyaml/NXem_simulation.yaml @@ -0,0 +1,44 @@ +category: base +doc: | + Base class for documenting a simulation of electron beam-matter interaction. +type: group +NXem_simulation(NXobject): + (NXprogram): + (NXparameters): + (NXprocess): + (NXdata): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# c481ee0c18dbbeebd612e013186b8f69866a0cdbc59610bd02a1d819a1af7af0 +# +# +# +# +# +# Base class for documenting a simulation of electron beam-matter interaction. +# +# +# +# +# +# diff --git a/base_classes/nyaml/NXenergydispersion.yaml b/base_classes/nyaml/NXenergydispersion.yaml index 94f6d96ef9..880ed56044 100644 --- a/base_classes/nyaml/NXenergydispersion.yaml +++ b/base_classes/nyaml/NXenergydispersion.yaml @@ -126,13 +126,13 @@ NXenergydispersion(NXcomponent): (NXdeflector): doc: | Deflectors in the energy dispersive section - (NXlens_em): + (NXelectromagnetic_lens): doc: | Individual lenses in the energy dispersive section (NXfabrication): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# e2f13c1f4aa880371c13322f9461fe624e2c7a325bf12149166edd8f72b5a644 +# 0217b29a2b3843f36c81b4410357b0a531b5f5bdb14fe7e625dacdd00818c381 # # # +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of pulses collected in between start_time and end_time. +# +# +# +# +# Base class to store state and (meta)data of events over the course of an atom probe experiment. +# +# Having at least one instance for an instance of NXapm is recommended. +# +# This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs +# of atom probe research. Again static and dynamic quantities are split to avoid a duplication +# of information. Specifically, the time interval considered is the entire time +# starting at start_time until end_time during which we assume the pulser triggered pulses. +# These pulses are identified via the pulse_id field. The point in time when each pulse was +# fired can be recovered from analyzing start_time and delta_time. +# +# Which temporal granularity is adequate depends on the situation and research question. +# Using a model which enables a collection of events offers the most flexible way to cater for +# both atom probe experiments or simulation. To monitor the course of an ion extraction experiment +# (or simulation) it makes sense to track time explicitly via time stamps or implicitly +# via e.g. a clock inside the instrument, such as the clock of the pulser and respective pulse_id. +# +# +# +# ISO 8601 time code with local time zone offset to UTC information included +# when the snapshot time interval started. +# +# If users wish to specify an interval of time that the snapshot should represent +# during which the instrument was stable and configured using specific settings and +# calibrations, the start_time is the start, the left bound of the time interval, while +# the end_time specifies the end, the right bound of the time interval. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information included +# when the snapshot time interval ended. +# +# +# +# +# Delta time array which resolves for each pulse_id the time difference +# between when that pulse was fired and start_time. +# +# In summary, using start_time, end_time, delta_time, pulse_id_offset, +# and pulse_id provides temporal context information when a pulse was +# fired relative to start_time and when it is relevant to translate this into +# coordinated world time UTC. +# +# Note that pulses in reality have a shape and thus additional documentation +# is required to assure that the entries in delta_time are always taken at +# at points in time that, relative to the triggering of the pulse, represent an +# as close as possible state of the pulse. +# +# +# +# +# +# +# +# Integer which defines the first pulse_id. +# Typically, this is either zero or one. +# +# +# +# +# An integer to identify a specific pulse in a sequence. +# +# There are two possibilities to report pulse_id values: +# If pulse_id_offset is provided, the pulse_id values are defined +# by the sequence :math:`[pulse\_id\_offset, pulse\_id\_offset + p]` +# with :math:`p` the number of pulses collected in between +# start_time and end_time. +# +# Alternatively, pulse_id_offset is not provided but instead +# a sequence of :math:`p` values is defined. +# These integer values do not need to be sorted. +# +# +# +# +# +# +# +# Place to store dynamic metadata of the instrument to document as close as possible +# the state of the instrument during the event, i.e. in between start_time and end_time. +# +# +# diff --git a/contributed_definitions/nyaml/NXevent_data_em.yaml b/base_classes/nyaml/NXevent_data_em.yaml similarity index 76% rename from contributed_definitions/nyaml/NXevent_data_em.yaml rename to base_classes/nyaml/NXevent_data_em.yaml index edbd9c5e3c..b423b02492 100644 --- a/contributed_definitions/nyaml/NXevent_data_em.yaml +++ b/base_classes/nyaml/NXevent_data_em.yaml @@ -2,6 +2,17 @@ category: base doc: | Base class to store state and (meta)data of events for electron microscopy. + Event-related (meta)data, typically measured datasets like images and spectra. + To avoid repetitively storing static instrument-related metadata, + the dynamic (meta)data that typically changes for each image and spectrum + is split from the static (meta)data. + + Which temporal granularity is adequate to log events depends on the situation and + research question. Using a model which enables a collection of events offers + the most flexible way to cater for both experiments with controlled electron + beams in a real microscope or the simulation of such experiments or + individual aspects of such experiments. + Electron microscopes are dynamic. Scientists often report that microscopes *perform differently* across sessions. That *they* perform differently from one day or another. In some cases, root causes for performance differences @@ -10,23 +21,17 @@ doc: | bring the microscope into a state where conditions are considered better or of whatever high enough quality for starting or continuing the measurement. - Which temporal granularity is adequate to log events depends on the situation and - research question. Using a model which enables a collection of events offers - the most flexible way to cater for both experiments with controlled electron - beams in a real microscope or the simulation of such experiments or - individual aspects of such experiments. - In all these use cases it is useful to have a mechanism whereby time-dependent data of the instrument state can be stored and documented in an representation - that facilitates interoperability. + that facilitates interoperability. This is the idea behind this base class. :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly whatever is considered a time interval during which the instrument is - considered stable enough for allowing any working on tasks with the microscope. + considered stable enough for allowing any working on tasks with it. Examples of such tasks are the collecting of data (images and spectra) or the calibrating the instrument or individual of its components. Users may wish to take - only a single scan or image and complete their microscope session thereafter. - Alternatively, users are working for much longer time at the microscope, + only a single scan or image and complete their session thereafter. + Alternatively, users are working for much longer time at the instrument, perform recalibrations in between and take several scans (of different ROIs on the specimen), or they explore the state of the microscope for service or maintenance tasks. @@ -36,14 +41,7 @@ doc: | * Firstly, via a header section whose purpose is to contextualize and identify the event instance in time. * Secondly, via a data and metadata section where individual data - collections can be stored in a standardized representation. - - The idea of the first section, the event-based em_lab, is to document the - state of the microscope as it was found during the event. The idea of the other, - the :ref:`NXem` application-definition-based em_lab(NXinstrument) section is to - keep all those data that are static in the sense that they remain the same - across multiple :ref:`NXevent_data_em` instances. - This reduces the need for having many copies of the same metadata. + collections can be stored in a standardized representation. We are aware of the fact that given the variety how an electron microscope is used, there is a need for a flexible and adaptive documentation system. @@ -62,29 +60,28 @@ doc: | or a stack of spectra. Having to deal with instabilities is a common theme in electron microscopy practice. Numerical protocols can be used during data post-processing to correct for some of the instabilities. - A few exemplar references to provide an overview on the subject is - available in the literature: + A few exemplar references provide an overview on the subject: * `C. Ophus et al. `_ * `B. Berkels et al. `_ * `L. Jones et al. `_ For specific simulation purposes, mainly in an effort to digitally repeat or simulate - the experiment, it is tempting to consider dynamics of the instrument, + the experiment (digital twin), it is tempting to consider dynamics of the instrument, implemented as time-dependent functional descriptions of e.g. lens excitations, - beam shape functions, trajectories of groups of electrons and ions, - or detector noise models. This warrants to document the time-dependent - details of individual components of the microscope - as is implemented in :ref:`NXevent_data_em`. + beam shape functions, trajectories of groups of electrons and ions, or detector noise models. + This also warrants to document the time-dependent details of individual components + of the microscope via the here implemented class :ref:`NXevent_data_em`. type: group NXevent_data_em(NXobject): start_time(NX_DATE_TIME): doc: | ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval started. If the user wishes to specify an - interval of time that the snapshot should represent during which the instrument - was stable and configured using specific settings and calibrations, - the start_time is the start (left bound of the time interval) while + when the snapshot time interval started. + + If users wish to specify an interval of time that the snapshot should represent + during which the instrument was stable and configured using specific settings and + calibrations, the start_time is the start (left bound of the time interval) while the end_time specifies the end (right bound) of the time interval. end_time(NX_DATE_TIME): doc: | @@ -97,8 +94,7 @@ NXevent_data_em(NXobject): identifier_sample(NX_CHAR): unit: NX_UNITLESS doc: | - The name of the sample instance under NXem/ENTRY/SAMPLE to resolve - ambiguities that are explained in the docstring of NXem/ENTRY/SAMPLE. + The name of the sample to resolve ambiguities. type(NX_CHAR): doc: | Which specific event/measurement type. Examples are: @@ -122,19 +118,16 @@ NXevent_data_em(NXobject): about the event for which there is at the moment no other place. In the long run such free-text field description should be avoided as - they are difficult to machine-interpret. Instead, reference should be given - to refactoring these descriptions into structured metadata. - The reason why in this base class the field event_type is nonetheless kept - is to offer a place whereby practically users may enter data for - follow-up modifications to support arriving at an improved :ref:`NXevent_data_em` base class. + it is difficult to machine-interpret. Instead, an enumeration should + be used. (NXuser): (NXinstrument_em): (NXimage): (NXspectrum): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# d0890b27942320dbf4382853e519c0130d7c43493192ffaebedf553294adf939 -# +# 9ab7fcd4482d84b1a491b17d7985199287f979dd3f253d941dd6318c428e09db +# # # +# +# +# Base class for a set of components equipping an instrument with FIB capabilities. +# +# Focused-ion-beam (FIB) capabilities turn especially scanning electron microscopes +# into specimen preparation labs. FIB is a material preparation technique whereby +# portions of the sample are illuminated with a focused ion beam with controlled +# intensity. The beam is controlled such that it is intense, focused, and equipped +# with sufficient ion having sufficient momentum to remove material in a controlled +# manner. +# +# The fact that an electron microscope with FIB capabilities achieves these functionalities +# via a second component (aka the ion gun) that has its own relevant control circuits, +# focusing lenses, and other components, warrants the definition of an own base class +# to group these components and distinguish them from the lenses and components for creating +# and shaping the electron beam. +# +# For more details about the relevant physics and application examples +# consult the literature, for example: +# +# * `L. A. Giannuzzi et al. <https://doi.org/10.1007/b101190>`_ +# * `E. I. Preiß et al. <https://link.springer.com/content/pdf/10.1557/s43578-020-00045-w.pdf>`_ +# * `J. F. Ziegler et al. <https://www.sciencedirect.com/science/article/pii/S0168583X10001862>`_ +# * `J. Lili <https://www.osti.gov/servlets/purl/924801>`_ +# * `N. Yao <https://doi.org/10.1017/CBO9780511600302>`_ +# +# +# +# Tech-partner, microscope-, and control-software-specific name of the +# specific operation mode how the ibeam_column and its components are +# controlled to achieve specific illumination conditions. +# +# In many cases the users of an instrument do not or can not be expected to know +# all intricate spatiotemporal dynamics of their hardware. Instead, they rely on +# assumptions that the instrument, its control software, and components work as +# expected to focus on their research questions. +# +# For these cases, having a place for documenting the operation_mode is useful +# in as much as at least some constraints on how the illumination conditions were +# is documented. +# +# +# +# +# The source which creates the ion beam. +# +# +# +# Given name/alias for the ion gun. +# +# +# +# +# Emitter type used to create the ion beam. +# +# If the emitter type is other, give further +# details in the description field. +# +# +# +# +# +# +# +# +# +# +# Ideally, a (globally) unique persistent identifier, link, +# or text to a resource which gives further details. +# +# +# +# +# Which elements, ions, or molecular ions form the beam. +# Examples are gallium, helium, neon, argon, krypton, +# or xenon, O2+. +# +# +# +# +# Average/nominal flux +# +# +# +# +# Average/nominal brightness +# +# +# +# +# +# Charge current +# +# +# +# +# Ion acceleration voltage upon source exit and +# entering the vacuum flight path. +# +# +# +# +# To be defined more specifically. Community suggestions are welcome. +# +# +# +# +# +# +# +# +# A component for blanking the ion beam or generating pulsed ion beams. +# +# +# +# +# +# +# +# Individual characterization results for the position, shape, +# and characteristics of the ion beam. +# +# :ref:`NXtransformations` should be used to specify the location or position +# at which details about the ion beam are probed. +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXimage.yaml b/base_classes/nyaml/NXimage.yaml similarity index 66% rename from contributed_definitions/nyaml/NXimage.yaml rename to base_classes/nyaml/NXimage.yaml index 72dcd0441d..9aa76e2047 100644 --- a/contributed_definitions/nyaml/NXimage.yaml +++ b/base_classes/nyaml/NXimage.yaml @@ -1,6 +1,6 @@ category: base doc: | - Base class for reporting a set of images. + Base class for reporting a set of images representing specializations of NXdata. The most commonly used scanning methods are supported. That is one-, two-, three-dimensional ROIs discretized using regular Euclidean tilings. @@ -10,19 +10,18 @@ doc: | pixel and voxel identify the smallest discretization unit. In this case, pixel and voxel are polygonal or polyhedral unit cells respectively of the underlying tiling of the ROI within the reference space. For all other tilings e.g. non-equispaced, the shape and size of pixel and voxel differs. Using the term - (image) point is eventually more appropriate when working with such tilings. + image point is eventually more appropriate when working with such tilings. - Therefore, all docstrings in this base class refer to points (including pixel and voxel i.e. regular tilings). + Therefore, all docstrings in this base class refer to points. Points are considered + exact synonyms for pixel and voxel, which are terms used for regular tilings. Point coordinates identify the location of the barycenter. For images in reciprocal space in practice, complex numbers are encoded via some formatted pair of real values. - Typically, fast algorithms for computing Fourier transformations (FFT) are used to encode - images in reciprocal (frequency) space. FFT libraries are used for implementing the key functionalities of - these mathematical operations. - + Typically, fast algorithms for computing Fourier transformations (FFT) are used to encode images in reciprocal + (frequency) space. FFT libraries are used for implementing the key functionalities of these mathematical operations. Different libraries use different representations and encoding of the images. - Details can be found in the respective sections of the typical FFT libraries documentations + Details can be found in the respective sections of the typical FFT libraries documentations: * `FFTW by M. Frigo and S. G. Johnson `_ * `Intel MKL by the Intel Co. `_ @@ -36,15 +35,28 @@ doc: | It is often the case that several images are combined using processing. In this case, the number of images which are combined into collections is not necessarily the same for each collection. The NXimage base class addresses this logical distinction - through the notation of identifier_image and identifier_group concepts. - That is identifier_image are always counting from offset in increments of one. + through the notation of indices_image and indices_group concepts. + That is indices_image are always counting from offset in increments of one as each image is its own entity. By contrast, a group may contain no, or several images. - Consequently, identifier_group are not required to be contiguous. + Consequently, indices_group are not required to be contiguous. + + Classically, images depict objects in real space. Such usage of NXimage essentially is equivalent to + storing pictures. For this purpose the image_1d, image_2d, or image_3d NXdata instances respectively + should be used such that all their axes axis_i, axis_j, axis_k are constrained to NeXus Unit Category NX_LENGTH. + + Imaging modes in electron microscopy are typically more versatile, specifically for use cases + in scanning transmission electron microscopy, so-called 4DSTEM. In this case, one two-dimensional + diffraction image is taken for each point that gets scanned in real space. Consequently, + image_3d and image_4d NXdata instances should be used for these cases with axis_k and axis_m + respectively of NeXus Unit Category NX_LENGTH and axis_i and axis_j respectively of + NeXus Unit Category NX_WAVENUMBER or NX_UNITLESS. # set of frequently made specializations of NXdata instances for images symbols: n_img: | Number of images in the stack, for stacks the slowest dimension. + n_m: | + Number of image points along the slowest dimension. n_k: | Number of image points along the slow dimension (k equivalent to z). n_j: | @@ -71,7 +83,7 @@ NXimage(NXobject): Reference to a location inside the artifact that points to the specific group of values that were processed if the artifacts contains several groups of values and thus further resolving of ambiguities is required. - identifier_detector(NX_CHAR): + detector_identifier(NX_CHAR): doc: | Link or name of an :ref:`NXdetector` instance with which the data were collected. @@ -112,9 +124,15 @@ NXimage(NXobject): rank: 1 dim: (n_i,) axis_i(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_i,) @@ -155,9 +173,15 @@ NXimage(NXobject): rank: 2 dim: (n_j, n_i) axis_j(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_j,) @@ -165,9 +189,15 @@ NXimage(NXobject): doc: | Point coordinate along the fast dimension. axis_i(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_i,) @@ -208,9 +238,15 @@ NXimage(NXobject): rank: 3 dim: (n_k, n_j, n_i) axis_k(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the slow dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_k,) @@ -218,9 +254,15 @@ NXimage(NXobject): doc: | Point coordinate along the slow dimension. axis_j(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_j,) @@ -228,9 +270,112 @@ NXimage(NXobject): doc: | Point coordinate along the fast dimension. axis_i(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + dimensions: + rank: 1 + dim: (n_i,) + \@long_name(NX_CHAR): + doc: | + Point coordinate along the fastest dimension. + image_4d(NXdata): + doc: | + Four-dimensional image. + intensity(NX_NUMBER): + unit: NX_UNITLESS + doc: | + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + dimensions: + rank: 4 + dim: (n_m, n_k, n_j, n_i) + real(NX_NUMBER): + unit: NX_UNITLESS + doc: | + Real part of the image intensity per point. + dimensions: + rank: 4 + dim: (n_m, n_k, n_j, n_i) + imag(NX_NUMBER): + unit: NX_UNITLESS + doc: | + Imaginary part of the image intensity per point. + dimensions: + rank: 4 + dim: (n_m, n_k, n_j, n_i) + complex(NX_COMPLEX): + unit: NX_UNITLESS + doc: | + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + dimensions: + rank: 4 + dim: (n_m, n_k, n_j, n_i) + axis_m(NX_NUMBER): + unit: NX_ANY + doc: | + Point coordinate along the slowest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + dimensions: + rank: 1 + dim: (n_m,) + \@long_name(NX_CHAR): + doc: | + Point coordinate along the slowest dimension. + axis_k(NX_NUMBER): + unit: NX_ANY + doc: | + Point coordinate along the slow dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + dimensions: + rank: 1 + dim: (n_k,) + \@long_name(NX_CHAR): + doc: | + Point coordinate along the slow dimension. + axis_j(NX_NUMBER): + unit: NX_ANY + doc: | + Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + dimensions: + rank: 1 + dim: (n_j,) + \@long_name(NX_CHAR): + doc: | + Point coordinate along the fast dimension. + axis_i(NX_NUMBER): + unit: NX_ANY + doc: | + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_i,) @@ -270,7 +415,7 @@ NXimage(NXobject): dimensions: rank: 2 dim: (n_img, n_i) - identifier_group(NX_INT): + indices_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -280,7 +425,7 @@ NXimage(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - identifier_image(NX_INT): + indices_image(NX_INT): unit: NX_UNITLESS doc: | Image identifier @@ -291,9 +436,15 @@ NXimage(NXobject): doc: | Image identifier axis_i(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_i,) @@ -333,7 +484,7 @@ NXimage(NXobject): dimensions: rank: 3 dim: (n_img, n_j, n_i) - identifier_group(NX_INT): + indices_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -343,7 +494,7 @@ NXimage(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - identifier_image(NX_INT): + indices_image(NX_INT): unit: NX_UNITLESS doc: | Image identifier @@ -354,9 +505,15 @@ NXimage(NXobject): doc: | Image identifier. axis_j(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_j,) @@ -364,9 +521,15 @@ NXimage(NXobject): doc: | Point coordinate along the fast dimension. axis_i(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_i,) @@ -406,7 +569,7 @@ NXimage(NXobject): dimensions: rank: 4 dim: (n_img, n_k, n_j, n_i) - identifier_group(NX_INT): + indices_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -416,7 +579,7 @@ NXimage(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - identifier_image(NX_INT): + indices_image(NX_INT): unit: NX_UNITLESS doc: | Image identifier @@ -427,9 +590,15 @@ NXimage(NXobject): doc: | Image identifier axis_k(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the slow dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_k,) @@ -437,9 +606,15 @@ NXimage(NXobject): doc: | Point coordinate along the slow dimension. axis_j(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_j,) @@ -447,9 +622,15 @@ NXimage(NXobject): doc: | Point coordinate along the fast dimension. axis_i(NX_NUMBER): - unit: NX_LENGTH + unit: NX_ANY doc: | Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. dimensions: rank: 1 dim: (n_i,) @@ -458,8 +639,8 @@ NXimage(NXobject): Point coordinate along the fastest dimension. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 14849fc3750b85080e14a17ec7018488675ce01287a9974a11eedc0a7979050c -# +# c4a38af030f63e92da6ee3d6d9e71c432dfcd4751cc14df5ce7d3d7b66860165 +# # # # +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of pulses collected in between start_time and end_time +# inside a parent instance of :ref:`NXevent_data_apm`. +# +# +# # -# Base class to document an instrument used for atom probe microscopy. +# Base class for instrument-related details of a real or simulated +# atom probe tomograph or field-ion microscope. # -# Inheriting from NXinstrument, this base class is designed to offer the same concepts about -# instrument-centric metadata to be used in two places inside NXapm without demanding that -# the application definition needs to define the concepts in two places as maintaining this is -# prone to errors. This base class implements the key design idea behind the NXapm application -# definition in that we would like to offer a design where all (meta)data which over the course -# of a measurement remain static can be stored only once and without polluting the application -# definition with another group with concepts that should be used for storing (meta)data about -# the instrument during events that happen during the course of the measurement. +# For collecting data and experiments which are simulations of an atom probe +# microscope or a session with such instrument use the :ref:`NXapm` application definition +# and the :ref:`NXevent_data_apm` groups it provides. # -# This design was inspired by NXem and electron microscopy where typically the instrument is -# used in sessions and dozens of logical sets of data are collected under not necessarily always -# the same instrument conditions. We do not want to repeat therefore the static (meta)data, as -# this is redundant storage by virtue of design. The typical example is an electron microscope -# where hundreds of images are taken and all static instrument data stored with each image. -# This makes sense in cases when the image is used as a digital artifact that is exchanged across -# different software applications or research data management systems but as in NeXus there -# is either all information bundled into one artifact or there is a coordinating master artifact -# that references related artifacts there is no point to store hundreds of times that always the -# same microscope with the same lens setup was used to collect these images. +# This base class implements the concept of :ref:`NXapm` whereby (meta)data are distinguished +# whether these typically change during a session, so-called dynamic, or not, so-called static metadata. +# This design allows to store e.g. hardware related concepts only once instead of demanding +# that each image or spectrum from the session needs to be stored also with the static metadata. # # # @@ -362,21 +361,27 @@ NXinstrument_apm(NXinstrument): # # # -# +# # # # Location of the lab or place where the instrument is installed. Using GEOREF is # preferred. # # +# +# +# Nominal flight path +# +# The value can be extracted from the CAnalysis.CSpatial.fFlightPath +# field of a CamecaRoot ROOT file. +# +# # # # Device which reduces ToF differences of ions in ToF experiments. # # For atom probe the reflectron can be considered an energy compensation device. -# Such a device can be realized technically for example with a Poschenrieder lens. +# Such a device can be realized technically e.g. with a Poschenrieder lens. # # Consult the following U.S. patents for further details: # @@ -394,15 +399,13 @@ NXinstrument_apm(NXinstrument): # # # -# +# # # A counter electrode of the LEAP 6000 series atom probes. # # -# -# +# +# # # A local electrode guiding the ion flight path. # Also called counter or extraction electrode. @@ -412,13 +415,27 @@ NXinstrument_apm(NXinstrument): # Acceleration voltage # # +# +# +# The type of aperture used when the local_electrode has an aperture or acts as an aperture +# in addition to acting as an extraction electrode. +# +# The local electrode is a component which combines functionalities +# of :ref:`NXelectromagnetic_lens`, :ref:`NXaperture`, if not even :ref:`NXdeflector`: +# +# * "n/a", use when no aperture is present in the experiment +# * "conical", conical aperture with a circular hole +# * "feedthrough", an aperture where the specimen protrudes through a circular hole +# * "custom", a user modified aperture, which is otherwise non-standard +# +# +# +# +# +# +# +# # -# # # # Detector for taking raw time-of-flight and ion/hit impact positions data. @@ -428,8 +445,10 @@ NXinstrument_apm(NXinstrument): # Amplitude of the signal detected on the multi-channel plate (MCP). # # This field should be used for storing the signal amplitude quantity -# within ATO files. The ATO file format is used primarily by the -# atom probe groups of the GPM in Rouen, France. +# within ATO files when the detector was an MCP. +# +# The ATO file format is used primarily by the atom probe group of the +# GPM in Rouen, France. # # # @@ -437,12 +456,14 @@ NXinstrument_apm(NXinstrument): # # # -# CRunHeader.fMcpEfficiency +# The value can be extracted from the CRunHeader.fMcpEfficiency +# field of a CamecaRoot RHIT file. # # # # -# CRunHeader.fMeshEfficiency +# The value can be extracted from the CRunHeader.fMeshEfficiency +# field of a CamecaRoot RHIT file. # # # @@ -450,6 +471,22 @@ NXinstrument_apm(NXinstrument): # # # Laser- and/or voltage-pulsing device to trigger ion removal. +# +# When the base class NXinstrument_apm is used in the NXapm +# application definition, the values for the following fields: +# +# * pulse_frequency +# * pulse_fraction +# * pulse_voltage +# * pulse_number +# * standing_voltage +# * pulse_energy +# * incidence_vector +# * pinhole_position +# * spot_position +# +# should be recorded in the order of, and assumed associated, +# with the pulse_id in an instance of :ref:`NXevent_data_apm`. # # # @@ -463,23 +500,10 @@ NXinstrument_apm(NXinstrument): # # # -# # # # Frequency with which the pulser fire(s). # -# -# -# Path to identifier_pulse -# -# # # # @@ -490,11 +514,6 @@ NXinstrument_apm(NXinstrument): # (as a function of standing voltage). Otherwise, this field should # not be present. # -# -# -# Path to identifier_pulse -# -# # # # # # Direct current voltage between the specimen and the (local electrode) in # the case of local electrode atom probe (LEAP) instrument. Otherwise, the # standing voltage applied to the sample, relative to system ground. # -# -# -# Path to identifier_pulse -# -# # -# +# # -# Atom probe microscopes use controlled laser, voltage, or a combination of -# pulsing strategies to trigger ion extraction via exciting and eventual field evaporation +# Group to store details about components that enable laser pulsing strategies. +# +# When multiple sources are available, these should be named source1, source2; +# the LEAP 6000 series instruments have two sources. The majority of instruments +# still has one source. In this case the variable part "ID" can be omitted. +# Consequently the group should be named "source" when writing instance data. +# +# Atom probe microscopes use controlled laser, voltage, or a combination of pulsing +# strategies to trigger ion extraction via exciting and eventual field evaporation # field emission of ion at the specimen surface. # # @@ -554,11 +564,11 @@ NXinstrument_apm(NXinstrument): # # # -# Path to identifier_pulse +# Path to pulse_id # # # -# +# # # Details about specific positions along the laser beam # which illuminates the (atom probe) specimen. @@ -569,33 +579,18 @@ NXinstrument_apm(NXinstrument): # how the laser beam shines on the specimen, i.e. the mean vector # is parallel to the laser propagation direction. # -# -# -# Path to identifier_pulse -# -# # # # # Track time-dependent settings over the course of the measurement # where the laser beam exits the focusing optics. # -# -# -# Path to identifier_pulse -# -# # # # # Track time-dependent settings over the course of the # measurement where the laser hits the specimen. # -# -# -# Path to identifier_pulse in an instance of :ref:`NXevent_data_apm`. -# -# # # # @@ -612,7 +607,8 @@ NXinstrument_apm(NXinstrument): # # # -# CRunHeader.CAnalysis.fSpecimenTemperature +# The value can be extracted from the CRunHeader.CAnalysis.fSpecimenTemperature +# field of a CamecaRoot RHIT file. # # # @@ -633,7 +629,8 @@ NXinstrument_apm(NXinstrument): # # # -# CRunHeader.CLasHeader.fAnalysisPressure +# The value can be extracted from the CRunHeader.CLasHeader.fAnalysisPressure +# field of a CamecaRoot RHIT file. # # # @@ -648,24 +645,21 @@ NXinstrument_apm(NXinstrument): # Free-text field for additional comments. # # -# +# # # Relevant quantities during a measurement with a LEAP system as were # suggested by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_. # # # -# Parameter set typically in the GUI of the control software which -# defines the rules and control loops whereby the pulser and other -# components of the instrument are controlled during evaporation. +# Parameter that defines the rules and control loops whereby the pulser and +# other components of the instrument are controlled during evaporation. # # # # -# Control parameter set typically in the GUI relevant to assure that -# the instrument internally controls its settings such to assure a -# significant yet not too high ion influx on the detector to avoid -# detection losses. +# Parameter that assure maintenance of a significant yet not too high +# ion influx on the detector to avoid detection losses. # # # diff --git a/contributed_definitions/nyaml/NXinstrument_em.yaml b/base_classes/nyaml/NXinstrument_em.yaml similarity index 92% rename from contributed_definitions/nyaml/NXinstrument_em.yaml rename to base_classes/nyaml/NXinstrument_em.yaml index 96f85e5599..823df9f1dc 100644 --- a/contributed_definitions/nyaml/NXinstrument_em.yaml +++ b/base_classes/nyaml/NXinstrument_em.yaml @@ -47,7 +47,7 @@ NXinstrument_em(NXinstrument): (NXibeam_column): # (NXpbeam_column) for adding laser pulsing capabilities (NXsource + x) - (NXoptical_system_em): + (NXem_optical_system): (NXdetector): doc: | Description of the type of the detector. @@ -55,8 +55,8 @@ NXinstrument_em(NXinstrument): Electron microscopes have typically multiple detectors. Different technologies are in use like CCD, scintillator, direct electron, CMOS, or image plate to name but a few. - (NXscanbox_em): - stage(NXmanipulator): + stageID(NXmanipulator): + nameType: partial doc: | Stages in an electron microscope are multi-functional devices. @@ -64,8 +64,8 @@ NXinstrument_em(NXinstrument): on the specimen. Modern stages realize a hierarchy of components. A multi-axial tilt rotation holder is a good example where the control of each degree of freedom is technically implemented via providing instances - of either :ref:`NXpositioner`, :ref:`NXactuator`, or specialized :ref:`NXobject` - that achieve the rotating and positioning of the specimen. + of e.g. :ref:`NXpositioner` or :ref:`NXactuator` that achieve the rotating + and positioning of the specimen. The physical process of mounting a specimen on a stage in practice often comes with an own hierarchy of fixtures to bridge e.g. length scales technically. @@ -102,7 +102,6 @@ NXinstrument_em(NXinstrument): # see for complicated positioning tools like an eucentric five-axis table stage in an SEM # https://www.nanotechnik.com/e5as.html - (NXfabrication): design(NX_CHAR): doc: | Principal design of the stage. @@ -167,27 +166,30 @@ NXinstrument_em(NXinstrument): dimensions: rank: 1 dim: (3,) - nanoprobe(NXmanipulator): + nanoprobeID(NXmanipulator): + nameType: partial doc: | - In contrast to the stage, the nanoprobe is an additional manipulator that is specifically + In contrast to the stage, the nanoprobe is an additional manipulator that is a specifically frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and - relocated portions of the specimen that have been cut free to realize specialized - geometries locally and enable site-specific measurements. - - # https://nano.oxinst.com/nanomanipulators. - (NXfabrication): + relocated portions of the specimen that have been cut off during site-specific lift-outs + and specimen preparation. + gas_injector(NXcomponent): + doc: | + Gas injection systems (GIS) are components of microscopes that are equipped with focused-ion beam + capabilities. The component is used to introduce reactive neutral gases to the sample surface for + enhanced etching, preferential etching, or material deposition. (NXpump): (NXsensor): (NXactuator): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0c0b9673eb5204cb0e015c407d3d938792a099d8bce4af50862e6b27c7062e81 -# +# 4b56a758c2ec8bb62faf19ecb426b97d7b99d1d87f6fa9df5741c32e857b3cf9 +# # # -# +# # # # Description of the type of the detector. @@ -271,8 +273,7 @@ NXinstrument_em(NXinstrument): # direct electron, CMOS, or image plate to name but a few. # # -# -# +# # # Stages in an electron microscope are multi-functional devices. # @@ -280,8 +281,8 @@ NXinstrument_em(NXinstrument): # on the specimen. Modern stages realize a hierarchy of components. # A multi-axial tilt rotation holder is a good example where the control of # each degree of freedom is technically implemented via providing instances -# of either :ref:`NXpositioner`, :ref:`NXactuator`, or specialized :ref:`NXobject` -# that achieve the rotating and positioning of the specimen. +# of e.g. :ref:`NXpositioner` or :ref:`NXactuator` that achieve the rotating +# and positioning of the specimen. # # The physical process of mounting a specimen on a stage in practice often # comes with an own hierarchy of fixtures to bridge e.g. length scales technically. @@ -318,7 +319,6 @@ NXinstrument_em(NXinstrument): # # -# # # # Principal design of the stage. @@ -397,15 +397,20 @@ NXinstrument_em(NXinstrument): # # # -# +# # -# In contrast to the stage, the nanoprobe is an additional manipulator that is specifically +# In contrast to the stage, the nanoprobe is an additional manipulator that is a specifically # frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and -# relocated portions of the specimen that have been cut free to realize specialized -# geometries locally and enable site-specific measurements. +# relocated portions of the specimen that have been cut off during site-specific lift-outs +# and specimen preparation. +# +# +# +# +# Gas injection systems (GIS) are components of microscopes that are equipped with focused-ion beam +# capabilities. The component is used to introduce reactive neutral gases to the sample surface for +# enhanced etching, preferential etching, or material deposition. # -# -# # # # diff --git a/base_classes/nyaml/NXpeak.yaml b/base_classes/nyaml/NXpeak.yaml index 8d012dc4e1..1c0a23a98b 100644 --- a/base_classes/nyaml/NXpeak.yaml +++ b/base_classes/nyaml/NXpeak.yaml @@ -1,13 +1,13 @@ category: base doc: | Base class for describing a peak, its functional form, and support values - (i.e., the discretization (points) at which the function has been evaluated). + i.e., the discretization points at which the function has been evaluated. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. dimRank: | - Rank of the dependent and independent data arrays (for - multivariate scalar-valued fit.) + Rank of the dependent and independent data arrays + (for multivariate scalar-valued fit). type: group NXpeak(NXobject): label(NX_CHAR): @@ -23,7 +23,7 @@ NXpeak(NXobject): dimensions: rank: dimRank doc: | - The ``position`` field must have the same rank (``dimRank``) + The ``position`` field must have the same rank ``dimRank`` as the ``intensity`` field. Each individual dimension of ``position`` must have the same number of points as the corresponding dimension in the ``intensity`` field. @@ -34,21 +34,21 @@ NXpeak(NXobject): dimensions: rank: dimRank doc: | - The ``intensity`` field must have the same rank (``dimRank``) + The ``intensity`` field must have the same rank ``dimRank`` as the ``intensity`` field. Each individual dimension of ``position`` must have the same number of points as the corresponding dimension in the ``position`` field. function(NXfit_function): doc: | - The functional form of the peak. This could be a Gaussian, Lorentzian, - Voigt, etc. + The functional form of the peak. This could be a Gaussian, Lorentzian, Voigt, + etc. total_area(NX_NUMBER): unit: NX_ANY doc: | Total area under the curve. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# c1ef8c595d09a93e7ad66155a94c084d37deeebf8267fa50809bdefe8f041dbe +# d031e893b82d7cea452fefe22659749f2800907294468a589e45c74bf75d8519 # # # # # -# +# +# +# +# # diff --git a/base_classes/nyaml/NXprocess.yaml b/base_classes/nyaml/NXprocess.yaml index 6806037c7c..1cc93036b5 100644 --- a/base_classes/nyaml/NXprocess.yaml +++ b/base_classes/nyaml/NXprocess.yaml @@ -1,6 +1,9 @@ category: base doc: | - Document an event of data processing, reconstruction, or analysis for this data. + The :ref:`NXprocess` class describes an operation used to + process data as part of an analysis workflow, providing + information such as the software used, the date of the + operation, the input parameters, and the resulting data. type: group NXprocess(NXobject): program(NX_CHAR): @@ -8,9 +11,8 @@ NXprocess(NXobject): Name of the program used sequence_index(NX_POSINT): doc: | - Sequence index of processing, - for determining the order of multiple **NXprocess** steps. - Starts with 1. + Sequence index of processing, for determining the order of + multiple **NXprocess** steps. Starts with 1. version(NX_CHAR): doc: | Version of the program used @@ -19,21 +21,27 @@ NXprocess(NXobject): Date and time of processing. (NXnote): doc: | - The note will contain information about how the data was processed - or anything about the data provenance. - The contents of the note can be anything that the processing code - can understand, or simple text. + The note will contain information about how the data was + processed or anything about the data provenance. The + contents of the note can be anything that the processing + code can understand, or simple text. The name will be numbered to allow for ordering of steps. + (NXparameters): + doc: | + Parameters used in performing the data analysis. + (NXdata): + doc: | + The data resulting from the operation. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6c22762a03d66eb4d983bfd65020e29612873eb4310fd9ce15a7baf5e70887a0 +# 9679057768d7997c800021bbdf0c06f8205cdabfd8254eafd4106a102b314240 # -# +# # # # -# Device to reduce an atmosphere (real or simulated) to a controlled pressure. +# Device to reduce an atmosphere to a controlled pressure. # # # # Principle type of the pump. # -# +# # # # # +# +# +# +# +# +# +# +# +# The minimum pressure achievable in a chamber after +# it has been pumped down for an extended period. +# +# +# +# +# The material being moved by the pump. +# +# Pumps intending to create a vacuum should state "vacuum" as the medium, +# while pumps having the primary purpose of creating a flow or pressure +# of gas should state "gas" as the medium. +# +# +# +# +# +# +# # # # +# +# +# Base class to report on the characterization of an area or volume of material. +# +# This area or volume of material is considered a region-of-interest (ROI). +# +# This base class should be used when the characterization was achieved by +# processing data from experiment or computer simulations into models of +# the microstructure of the material and the properties of the material or its +# crystal defects within this ROI. Microstructural features is a narrow synonym +# for these crystal defects. +# +# This base class can also be used to store data and metadata of the +# representation of the ROI, i.e. its discretization and shape. +# +# Methods from computational geometry are typically used for +# defining a discretization of the area and volume. +# +# Do not confuse this base class with :ref:`NXregion`. The purpose +# of the :ref:`NXregion` base class is to document data access i.e. +# I/O pattern on arrays. Therefore, concepts from :ref:`NXregion` operate +# in data space rather than in real or simulated real space. +# +# +# diff --git a/base_classes/nyaml/NXroot.yaml b/base_classes/nyaml/NXroot.yaml index 0dc93b3044..a554d1857b 100644 --- a/base_classes/nyaml/NXroot.yaml +++ b/base_classes/nyaml/NXroot.yaml @@ -205,7 +205,7 @@ NXroot: # A list of concepts in an application definition this file describes. # This is for partially filling an application definition. # If this attribute is not present the application definition is assumed -# to be valid, if not only the specified concepts/paths are assumed to be valid. +# to be valid, if not only the specified concepts/paths are assumed to be valid. # # # diff --git a/contributed_definitions/nyaml/NXrotations.yaml b/base_classes/nyaml/NXrotations.yaml similarity index 66% rename from contributed_definitions/nyaml/NXrotations.yaml rename to base_classes/nyaml/NXrotations.yaml index 5149ba6425..d9e2bbfbd8 100644 --- a/contributed_definitions/nyaml/NXrotations.yaml +++ b/base_classes/nyaml/NXrotations.yaml @@ -18,6 +18,9 @@ doc: | (like crystal lattice) into a crystallographic equivalent orientation: * `R. Bonnet `_ + + The concepts of mis- and disorientation are relevant when analyzing the + crystallography of interfaces. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -189,8 +192,8 @@ NXrotations(NXobject): dim: (c, 3) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 8c767a10ea4d5024333d74f4bb13db55b7f8a6ad9e390653b8b512dac30f4d22 -# +# 239aa437e4fe8b7fac66e7536590b07dbedff1e73a6f5361bff263fae970c716 +# # # # -# Base class to detail a set of rotations, orientations, and disorientations. -# -# For getting a more detailed insight into the discussion of the -# parameterized description of orientations in materials science see: -# -# * `H.-J. Bunge <https://doi.org/10.1016/C2013-0-11769-2>`_ -# * `T. B. Britton et al. <https://doi.org/10.1016/j.matchar.2016.04.008>`_ -# * `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_ -# * `A. Morawiec <https://doi.org/10.1007/978-3-662-09156-2>`_ -# -# Once orientations are defined, one can continue to characterize the -# misorientation and specifically the disorientation. The misorientation describes -# the rotation that is required to register the lattices of two oriented objects -# (like crystal lattice) into a crystallographic equivalent orientation: -# -# * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ +# Base class to detail a set of rotations, orientations, and disorientations. +# +# For getting a more detailed insight into the discussion of the +# parameterized description of orientations in materials science see: +# +# * `H.-J. Bunge <https://doi.org/10.1016/C2013-0-11769-2>`_ +# * `T. B. Britton et al. <https://doi.org/10.1016/j.matchar.2016.04.008>`_ +# * `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_ +# * `A. Morawiec <https://doi.org/10.1007/978-3-662-09156-2>`_ +# +# Once orientations are defined, one can continue to characterize the +# misorientation and specifically the disorientation. The misorientation describes +# the rotation that is required to register the lattices of two oriented objects +# (like crystal lattice) into a crystallographic equivalent orientation: +# +# * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ +# +# The concepts of mis- and disorientation are relevant when analyzing the +# crystallography of interfaces. # # # -# Reference to an instance of :ref:`NXcoordinate_system` which contextualizes -# how the here reported parameterized quantities can be interpreted. +# Reference to an instance of :ref:`NXcoordinate_system` which contextualizes +# how the here reported parameterized quantities can be interpreted. # # # # -# Point group which defines the symmetry of the crystal. -# -# This has to be at least a single string. If crystal_symmetry is not -# provided, point group 1 is assumed. -# -# In the case that misorientation or disorientation fields are used -# and the two crystal sets resolve for phases with a different -# crystal symmetry, this field needs to encode two strings: -# The first string is for phase A. The second string is for phase B. -# An example of this most complex case is the description of the -# disorientation between crystals adjoining a hetero-phase boundary. +# Point group which defines the symmetry of the crystal. +# +# This has to be at least a single string. If crystal_symmetry is not +# provided, point group 1 is assumed. +# +# In the case that misorientation or disorientation fields are used +# and the two crystal sets resolve for phases with a different +# crystal symmetry, this field needs to encode two strings: +# The first string is for phase A. The second string is for phase B. +# An example of this most complex case is the description of the +# disorientation between crystals adjoining a hetero-phase boundary. # # # @@ -274,24 +280,24 @@ NXrotations(NXobject): # # # -# Point group which defines an assumed symmetry imprinted upon processing -# the material/sample which could give rise to or may justify to use a -# simplified description of rotations, orientations, misorientations, -# and disorientations via numerical procedures that are known as -# symmetrization. -# -# If sample_symmetry is not provided, point group 1 is assumed. -# -# The traditionally used symmetrization operations within the texture -# community in Materials Science, though, have become obsolete thanks -# to improvements in methods, software, and available computing power. +# Point group which defines an assumed symmetry imprinted upon processing +# the material/sample which could give rise to or may justify to use a +# simplified description of rotations, orientations, misorientations, +# and disorientations via numerical procedures that are known as +# symmetrization. +# +# If sample_symmetry is not provided, point group 1 is assumed. +# +# The traditionally used symmetrization operations within the texture +# community in Materials Science, though, have become obsolete thanks +# to improvements in methods, software, and available computing power. +# +# Therefore, users are encouraged to set the sample_symmetry to 1 (triclinic). # -# Therefore, users are encouraged to set the sample_symmetry to 1 (triclinic). -# -# In practice one often faces situations where indeed these assumed -# symmetries are anyway not fully observed, and thus an accepting of -# eventual inaccuracies just for the sake of reporting a simplified -# symmetrized description should be avoided. +# In practice one often faces situations where indeed these assumed +# symmetries are anyway not fully observed, and thus an accepting of +# eventual inaccuracies just for the sake of reporting a simplified +# symmetrized description should be avoided. # # # @@ -299,9 +305,9 @@ NXrotations(NXobject): # # # -# The set of rotations expressed in quaternion parameterization considering -# crystal_symmetry and sample_symmetry. Rotations which should be -# interpreted as antipodal are not marked as such. +# The set of rotations expressed in quaternion parameterization considering +# crystal_symmetry and sample_symmetry. Rotations which should be +# interpreted as antipodal are not marked as such. # # # @@ -310,11 +316,11 @@ NXrotations(NXobject): # # # -# The set of rotations expressed in Euler angle parameterization considering -# the same applied symmetries as detailed for the field rotation_quaternion. -# To interpret Euler angles correctly, it is necessary to inspect the rotation -# conventions behind reference_frame to resolve which of the many possible -# Euler-angle conventions (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. +# The set of rotations expressed in Euler angle parameterization considering +# the same applied symmetries as detailed for the field rotation_quaternion. +# To interpret Euler angles correctly, it is necessary to inspect the rotation +# conventions behind reference_frame to resolve which of the many possible +# Euler-angle conventions (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. # # # @@ -327,8 +333,8 @@ NXrotations(NXobject): # # # -# True for all those value tuples which have assumed antipodal symmetry. -# False for all others. +# True for all those value tuples which have assumed antipodal symmetry. +# False for all others. # # # @@ -336,10 +342,10 @@ NXrotations(NXobject): # # # -# The set of orientations expressed in quaternion parameterization and -# obeying symmetry for equivalent cases as detailed in crystal_symmetry -# and sample_symmetry. The supplementary field is_antipodal can be used -# to mark orientations with the antipodal property. +# The set of orientations expressed in quaternion parameterization and +# obeying symmetry for equivalent cases as detailed in crystal_symmetry +# and sample_symmetry. The supplementary field is_antipodal can be used +# to mark orientations with the antipodal property. # # # @@ -348,11 +354,11 @@ NXrotations(NXobject): # # # -# The set of orientations expressed in Euler angle parameterization following -# the same assumptions like for orientation_quaternion. -# To interpret Euler angles correctly, it is necessary to inspect the rotation -# conventions behind reference_frame to resolve which of the many Euler-angle -# conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. +# The set of orientations expressed in Euler angle parameterization following +# the same assumptions like for orientation_quaternion. +# To interpret Euler angles correctly, it is necessary to inspect the rotation +# conventions behind reference_frame to resolve which of the many Euler-angle +# conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. # # # @@ -364,13 +370,13 @@ NXrotations(NXobject): # orientation_axis_angle(NX_NUMBER):--> # # -# The set of misorientations expressed in quaternion parameterization -# obeying symmetry operations for equivalent misorientations -# as defined by crystal_symmetry and sample_symmetry. +# The set of misorientations expressed in quaternion parameterization +# obeying symmetry operations for equivalent misorientations +# as defined by crystal_symmetry and sample_symmetry. # -# The misorientation should not be confused with the disorientation, -# as for the latter the angular argument is expected to be the minimal -# obeying symmetries. +# The misorientation should not be confused with the disorientation, +# as for the latter the angular argument is expected to be the minimal +# obeying symmetries. # # # @@ -379,8 +385,8 @@ NXrotations(NXobject): # # # -# Misorientation angular argument (eventually signed) following the same -# symmetry assumptions as expressed for the field misorientation_quaternion. +# Misorientation angular argument (eventually signed) following the same +# symmetry assumptions as expressed for the field misorientation_quaternion. # # # @@ -388,8 +394,8 @@ NXrotations(NXobject): # # # -# Misorientation axis (normalized) and signed following the same -# symmetry assumptions as expressed for the field misorientation_angle. +# Misorientation axis (normalized) and signed following the same +# symmetry assumptions as expressed for the field misorientation_angle. # # # @@ -400,9 +406,9 @@ NXrotations(NXobject): # fundamental zone of SO3 for given crystal and sample symmetry--> # # -# The set of disorientations expressed in quaternion parameterization -# obeying symmetry operations for equivalent disorientations -# as defined by crystal_symmetry and sample_symmetry. +# The set of disorientations expressed in quaternion parameterization +# obeying symmetry operations for equivalent disorientations +# as defined by crystal_symmetry and sample_symmetry. # # # @@ -411,10 +417,10 @@ NXrotations(NXobject): # # # -# Disorientations angular argument (should not be signed, see -# `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) -# following the same symmetry assumptions as expressed for the field -# disorientation_quaternion. +# Disorientations angular argument (should not be signed, see +# `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) +# following the same symmetry assumptions as expressed for the field +# disorientation_quaternion. # # # @@ -422,8 +428,8 @@ NXrotations(NXobject): # # # -# Disorientations axis (normalized) following the same symmetry assumptions -# as expressed for the field disorientation_angle. +# Disorientations axis (normalized) following the same symmetry assumptions +# as expressed for the field disorientation_angle. # # # diff --git a/contributed_definitions/nyaml/NXscanbox_em.yaml b/base_classes/nyaml/NXscan_controller.yaml similarity index 72% rename from contributed_definitions/nyaml/NXscanbox_em.yaml rename to base_classes/nyaml/NXscan_controller.yaml index 350d84e3cc..c80180add4 100644 --- a/contributed_definitions/nyaml/NXscanbox_em.yaml +++ b/base_classes/nyaml/NXscan_controller.yaml @@ -1,26 +1,27 @@ category: base doc: | - Scan box and coils which deflect a beam of charged particles in a controlled manner. + The scan box or scan controller is a component that is used to deflect a + beam of charged particles in a controlled manner. The scan box is instructed by (an) instance(s) of :ref:`NXprogram`, some control software, - which is not necessarily the same program as for all components of an instrument. + which is not necessarily the same program as the one controlling other parts of the instrument. - The scanbox directs the probe of charged particles (electrons, ions) + The scan box directs the probe of charged particles (electrons, ions) to controlled locations according to a scan scheme and plan. type: group -NXscanbox_em(NXcomponent): +NXscan_controller(NXcomponent): # user perspective scan_schema(NX_CHAR): doc: | Name of the typically tech-partner-specific term that specifies an - automated protocol which controls the details how the components - of the scan_box and instrument work together to achieve a controlled - scanning of the beam over the sample surface. + automated protocol which details how the components of the scan_box + and the instrument work together to achieve a controlled + scanning of the beam (over the sample surface). - In most cases users do not know, have to care, or are able to disentangle the - details of the spatiotemporal dynamics of the components of the instrument. - Instead, they often rely on the assumption that the microscope and control software + Oftentimes users do not need to or are not able to disentangle the intricate + details of the spatiotemporal dynamics of their instrument. Instead, often + they rely on the assumption that the instrument and its controlling programs work as expected. The field scan_schema can be used to add some constraints on how the beam was scanned over the surface. @@ -58,8 +59,8 @@ NXscanbox_em(NXcomponent): (NXcircuit): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 3f374a059a0aa9d3a7e9cbf324b64fb43c925313c54d9bf84e3bc7561100d1ba -# +# 255bda2d8a7c0e6ef138a62d20cd276e93691ad987938eb0f44b82e5f8ae9aec +# # # -# +# # -# Scan box and coils which deflect a beam of charged particles in a controlled manner. +# The scan box or scan controller is a component that is used to deflect a +# beam of charged particles in a controlled manner. # # The scan box is instructed by (an) instance(s) of :ref:`NXprogram`, some control software, -# which is not necessarily the same program as for all components of an instrument. +# which is not necessarily the same program as the one controlling other parts of the instrument. # -# The scanbox directs the probe of charged particles (electrons, ions) +# The scan box directs the probe of charged particles (electrons, ions) # to controlled locations according to a scan scheme and plan. # # # # # Name of the typically tech-partner-specific term that specifies an -# automated protocol which controls the details how the components -# of the scan_box and instrument work together to achieve a controlled -# scanning of the beam over the sample surface. +# automated protocol which details how the components of the scan_box +# and the instrument work together to achieve a controlled +# scanning of the beam (over the sample surface). # -# In most cases users do not know, have to care, or are able to disentangle the -# details of the spatiotemporal dynamics of the components of the instrument. -# Instead, they often rely on the assumption that the microscope and control software +# Oftentimes users do not need to or are not able to disentangle the intricate +# details of the spatiotemporal dynamics of their instrument. Instead, often +# they rely on the assumption that the instrument and its controlling programs # work as expected. The field scan_schema can be used to add some constraints # on how the beam was scanned over the surface. # diff --git a/base_classes/nyaml/NXsource.yaml b/base_classes/nyaml/NXsource.yaml index 2b9a6e7454..de1a157e89 100644 --- a/base_classes/nyaml/NXsource.yaml +++ b/base_classes/nyaml/NXsource.yaml @@ -177,7 +177,7 @@ NXsource(NXcomponent): (NXaperture): doc: | The size and position of an aperture inside the source. - (NXlens_em): + (NXelectromagnetic_lens): doc: | Individual electromagnetic lenses inside the source. (NXdeflector): @@ -200,7 +200,7 @@ NXsource(NXcomponent): :width: 40% # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# de3d584448407bafe8e2c9d26aefbbcf2554c055f77b0d24b4c384efa3fd407d +# a85fe87f55e843178bfcbad58a624e22d12f62d8e164a496d68e129e7b5e7d0c # # # +# +# +# Geometry of the unit cell quantified individually via parameter a. +# +# +# +# +# Geometry of the unit cell quantified individually via parameter b. +# +# +# +# +# Geometry of the unit cell quantified individually via parameter c. +# +# # # -# Geometry of the unit cell quantified via parameters alpha, beta, and gamma. +# Geometry of the unit cell quantified via parameters alpha, beta, and gamma. # # # # # +# +# +# Geometry of the unit cell quantified individually via parameter alpha. +# +# +# +# +# Geometry of the unit cell quantified individually via parameter beta. +# +# +# +# +# Geometry of the unit cell quantified individually via parameter gamma. +# +# # # -# Crystal system. -# -# For a crystal system in 2D space monoclinic is an exact synonym for oblique. -# For a crystal system in 2D space orthorhombic is an exact synonym for rectangular. -# For a crystal system in 2D space tetragonal is an exact synonym for square. +# Crystal system. +# +# For a crystal system in 2D space monoclinic is an exact synonym for oblique. +# For a crystal system in 2D space orthorhombic is an exact synonym for rectangular. +# For a crystal system in 2D space tetragonal is an exact synonym for square. # # # @@ -169,45 +220,45 @@ NXunit_cell(NXobject): # # # -# Laue group using International Table of Crystallography notation. +# Laue group using International Table of Crystallography notation. # # # # # -# Point group using International Table of Crystallography notation. +# Point group using International Table of Crystallography notation. # # # # -# Space group from the International Table of Crystallography notation. +# Space group from the International Table of Crystallography notation. # # # # -# True if space group is considered a centrosymmetric one. -# False if space group is considered a non-centrosymmetric one. -# -# Centrosymmetric has all types and combinations of symmetry elements -# (translation, rotational axis, mirror planes, center of inversion) -# Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). -# Chiral compared to non-centrosymmetric is constrained (no mirror planes). +# True if space group is considered a centrosymmetric one. +# False if space group is considered a non-centrosymmetric one. +# +# Centrosymmetric has all types and combinations of symmetry elements +# (translation, rotational axis, mirror planes, center of inversion) +# Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). +# Chiral compared to non-centrosymmetric is constrained (no mirror planes). # # # # -# True if space group is considered a chiral one. -# False if space group is consider a non-chiral one. +# True if space group is considered a chiral one. +# False if space group is consider a non-chiral one. # # # # -# Area of the unit cell if dimensionality is 2. +# Area of the unit cell if dimensionality is 2. # # # # -# Volume of the unit cell if dimensionality is 3. +# Volume of the unit cell if dimensionality is 3. # # # diff --git a/contributed_definitions/NXafm.nxdl.xml b/contributed_definitions/NXafm.nxdl.xml index a8ecf2a76a..30ea5c02c1 100644 --- a/contributed_definitions/NXafm.nxdl.xml +++ b/contributed_definitions/NXafm.nxdl.xml @@ -1,4 +1,4 @@ - + - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of hit qualities (hit types) distinguished. - - - - - Number of delay-line wires of the detector. - - - - - Number of bins used in the mass-to-charge-state-ratio spectrum. - - - - - Number of pulses collected in between start_time and end_time resolved by an - instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of - ions included in the reconstructed volume if the application definition is used - to store results of an already reconstructed datasets. - - - - - Number of pulses returned by the hit finding algorithm. - Neither necessarily equal to p nor to n. - - - - - Number of ions spatially filtered from results of the hit_finding algorithm - from which an instance of a reconstructed volume has been generated. - These ions get new identifier assigned in the process (the so-called - identifier_evaporation). This identifier must not be confused with - the identifier_pulse. Typically smaller than both p_out and p_out. - - - - - Application definition for atom probe and field ion microscopy experiments. - - - - - - - - - - - The configuration of the I/O writer software (e.g. `pynxtools <https://github.com/FAIRmat-NFDI/pynxtools>`_ or its plugins) - which was used to generate this NeXus file instance. - - - - - A collection of all programs and libraries which are considered relevant - to understand with which software tools this NeXus file instance was - generated. Ideally, to enable a binary recreation from the input data. - - Examples include the name and version of the libraries used to write the - instance. Ideally, the software which writes these NXprogram instances - also includes the version of the set of NeXus classes i.e. the specific - set of base classes, application definitions, and contributed definitions - with which the here described concepts can be resolved. - - For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ - which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ - research data management system, it makes sense to store e.g. the GitHub - repository commit and respective submodule references used. - - - - - - - - - - - The identifier whereby the experiment is referred to in the control software. - This is neither the specimen_name nor the experiment_identifier. For - Local Electrode Atom Probe (LEAP) instruments, it is recommended to use the - run_number from the proprietary software IVAS/APSuite of AMETEK/Cameca. - For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, - or the instruments at GPM in Rouen, use the identifier which matches - best conceptually to the LEAP run number. - The field does not have to be required if the information is recoverable - in the dataset which for LEAP instruments is the case (provided these - RHIT or HITS files respectively are stored alongside a data artifact). - With NXapm the RHIT or HITS can be stored via NXnote in the - hit_finding algorithm section. - - As a destructive microscopy technique, a run can be performed only once. - It is possible, however, to interrupt a run and restart data acquisition - while still using the same specimen. In this case, each evaporation run - needs to be distinguished with different run numbers. - We follow this habit of most atom probe groups. Such interrupted runs - should be stored as individual :ref:`NXentry` instances in one NeXus file. - - - - - Either an identifier or an alias that is human-friendly so that scientists find that experiment again. - For experiments usually this is the run_number but for simulation typically no run_numbers are issued. - - - - - Free-text description about the experiment. - - Users are strongly advised to parameterize the description of their experiment - by using respective groups and fields and base classes instead of writing prose - into this field. - - The reason is that such free-text field is difficult to machine-interpret. - The motivation behind keeping this field for now is to learn in how far the - current base classes need extension based on user feedback. - - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the atom probe session started. If the exact duration of - the measurement is not relevant start_time only should be used. - - Often though it is useful to specify both start_time and end_time to - capture more detailed bookkeeping of the experiment. The user should - be aware that even with having both dates specified, it may not be - possible to infer how long the experiment took or for how long data - were collected. - - More detailed timing data over the course of the experiment have to be - collected to compute this event chain during the experiment. For this - purpose the :ref:`NXevent_data_apm` instance should be used. - - - - - ISO 8601 time code with local time zone offset to UTC included - when the atom probe session ended. - - - - - How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime - - - - - - - - - - - - - - What type of atom probe experiment is performed? This field is meant to - inform research data management systems to allow filtering: - - * apt are experiments where the analysis_chamber has no imaging gas. - experiment with LEAP instruments are typically performed such. - * fim are experiments where the analysis_chamber has an imaging gas, - which should be specified with the atmosphere in the analysis_chamber group. - * apt_fim should be used for combinations of the two imaging modes. - few experiments of this type have been performed as this can be detrimental - to LEAP systems (see `S. Katnagallu et al. <https://doi.org/10.1017/S1431927621012381>`_). - * other should be used in combination with the user specifying details - in the experiment_documentation field. - - If NXapm is used for storing details about a simulation use other for now. - - - - - - - - - - - - - - - - Description of the sample from which the specimen was prepared or - site-specifically cut out using e.g. a focused-ion beam instrument. - - The sample group is currently a place for storing suggestions from - atom probers about knowledge they have gained about the sample. - There are cases where the specimen is machined further or exposed to - external stimuli during the experiment. In this case, these details should - not be stored under sample but suggestions should be made - how this application definition can be improved. - - In the future also details like how the grain_diameter was characterized, - how the sample was prepared, how the material was heat-treated etc., - should be stored. For this specific application definitions/schemas can be - used which are then arranged and documented with a description of the - workflow so that actionable graphs become instantiatable. - - - - - Qualifier whether the sample is a real (in which case is_simulation should be set to false) - or a virtual one (in which case is_simulation should be set to true). - - - - - Given name/alias for the sample. - - - - - Qualitative information about the grain size, here specifically - described as the equivalent spherical diameter of an assumed - average grain size for the crystal ensemble. - Users of this information should be aware that although the grain - diameter or radius is often referred to as grain size. - - In atom probe it is possible that the specimen may contain a few - crystals only. In this case the grain_diameter is not a reliable - descriptor. Reporting a grain size may be useful though as it allows - judging if specific features are expected to be found in the - detector hit map. - - - - - Magnitude of the standard deviation of the grain_diameter. - - - - - - The temperature of the last heat treatment step before quenching. - Knowledge about this value can give an idea how the sample - was heat treated. However, if a documentation of the annealing - treatment as a function of time is available one should better - rely on this information and have it stored alongside the NeXus file. - - - - - Magnitude of the standard deviation of the heat_treatment_temperature. - - - - - Rate of the last quenching step. Knowledge about this value can give - an idea how the sample was heat treated. However, there are many - situations where one can imagine that the scalar value for just the - quenching rate is insufficient. - - An example is when the sample was left in the furnace after the - furnace was switched off. In this case the sample cools down with - a specific rate of how this furnace cools down in the lab. - Processes which in practice are often not documented. - - This can be problematic though because when the furnace door was left open - or the ambient temperature in the lab changed, i.e. for a series of - experiments where one is conducted on a hot summer day and the next - during winter this can have an effect on the evolution of the microstructure. - There are many cases where this has been reported to be an QA issue in industry, - e.g. think about aging aluminum samples left on the factory - parking lot on a hot summer day. - - - - - Magnitude of the standard deviation of the heat_treatment_quenching_rate. - - - - - - The chemical composition of the sample. Typically, it is assumed that - this more macroscopic composition is representative for the material - so that the composition of the typically substantially less voluminous - specimen probes from the more voluminous sample. - - - - - - - - - - - - - - Qualifier whether the specimen is a real (in which case is_simulation should be set to false) - or a virtual one (in which case is_simulation should be set to true). - - - - - Given name an alias. Better use identifierNAME and identifier_parent instead. - A single NXentry should be used only for the characterization of a single specimen. - - - - - Identifier of the sample from which the specimen was cut or the string - n/a. The purpose of this field is to support functionalities for - tracking sample provenance via a research data management system. - - - - - ISO 8601 time code with local time zone offset to UTC information - when the specimen was prepared. - - Ideally, report the end of the preparation, i.e. the last known time - the measured specimen surface was actively prepared. Ideally, this - matches the last timestamp that is mentioned in the digital resource - pointed to by identifier_parent. - - Knowing when the specimen was exposed to e.g. specific atmosphere is - especially required for environmentally sensitive material such as - hydrogen charged specimens or experiments including tracers with a - short half time. Additional time stamps prior to preparation_date - should better be placed in resources which describe but which do not - pollute the description here with prose. Resolving these connected - pieces of information is considered within the responsibility of the - research data management system. - - - - - List of comma-separated elements from the periodic table that are - contained in the specimen. If the specimen substance has multiple - components, all elements from each component must be included in - `atom_types`. - - The purpose of the field is to offer research data management systems an - opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by identifier_parent or walk through - eventually deeply nested groups in data instances. - - - - - Discouraged free-text field. - - - - - Report if the specimen is polycrystalline, in which case it - contains a grain or phase boundary, or if the specimen is a - single crystal. - - - - - Report if the specimen is amorphous. - - - - - Ideally measured otherwise best elaborated guess of the initial radius of the - specimen. - - - - - Ideally measured otherwise best elaborated guess of the (initial) shank angle. - This is a measure of the specimen taper. Define it in such a way that the base of the specimen - is modelled as a conical frustrum so that the shank angle is the (shortest) angle between - the specimen space z-axis and a vector on the lateral surface of the cone. - - - - - - The conventions used when reporting crystal orientations. - We follow the best practices of the Material Science community - that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - Convention how a positive rotation angle is defined when viewing - from the end of the rotation unit vector towards its origin. - This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - Counter_clockwise is equivalent to a right-handed choice. - Clockwise is equivalent to a left-handed choice. - - - - - - - - - How are rotations interpreted into an orientation according to convention 3 - of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - - How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) - according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - The most frequently used convention is zxz, which is based on the work of H.-J. Bunge - but other conventions are possible. Apart from undefined, proper Euler angles - are distinguished from (improper) Tait-Bryan angles. - - - - - - - - - - - - - - - - - - - To which angular range is the rotation angle argument of an - axis-angle pair parameterization constrained according to - convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - Which sign convention is followed when converting orientations - between different parametrizations/representations according - to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - - - A collection of coordinate systems. Several Euclidean - coordinate systems (CS) are used in the field of atom probe: - - * World space; - a CS specifying a local coordinate system of the planet earth which - identifies into which direction gravity is pointing such that - the laboratory space CS can be rotated into this world CS. - * The laboratory space; - a CS specifying the room where the instrument is located in or - a physical landmark on the instrument, e.g. the direction of the - transfer rod where positive is the direction how the rod - has to be pushed during loading a specimen into the instrument. - In summary, this CS is defined by the chassis of the instrument. - * The specimen space; - a CS affixed to either the base or the initial apex of the specimen, - whose z axis points towards the detector. - * The detector space; - a CS affixed to the detector plane whose xy plane is usually in the - detector and whose z axis points towards the specimen. - This is a distorted space with respect to the reconstructed ion - positions. - * The reconstruction space; - a CS in which the reconstructed ion positions are defined. - The orientation depends on the analysis software used. - * Eventually further coordinate systems attached to the - flight path of individual ions might be defined. - - In atom probe microscopy a frequently used choice for the detector - space (CS) is discussed with the so-called detector space image - (stack). This is a stack of two-dimensional histograms of detected ions - within a predefined evaporation identifier interval. Typically, the set of - ion evaporation sequence identifiers is grouped into chunks. - - For each chunk a histogram of the ion hit positions on the detector - is computed. This leaves the possibility for inconsistency between - the so-called detector space and the e.g. specimen space. - - To avoid these ambiguities, instances of :ref:`NXtransformations` should be used. - - - - - - - - - - - - Base class for collecting a session with a real atom probe or field-ion microscope. - - Workflows used during experiments or simulations of atom probe and related field-evaporation - research should be documented in more detail and be better contextualized not only because of - ongoing developments and the tighter becoming connection between atom probe and other - methods for material characterization foremost electron microscopy see e.g.: - - * `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_ - * `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_ - * `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_ - * `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_ - * `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ - - to mention but a few. - - To arrive at a design of base classes and an application definition that can be used - for both real and simulated atom probe experiments it is worthwhile to recall concepts that are - related to events and (molecular) ions: - - * Pulsing events which are used to trigger ion extraction events. - * Physical events and corresponding signal triggered by an ion hitting the detector. - Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. - * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input - and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are - worthwhile to be considered further and eventually included in the reconstructed volume. - * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually - selected (molecular) ions based on which an instance of a reconstruction is created. - * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values - and charge states of the (molecular) ions to substantiate that some of these ions can be considered - as rangeable ions and hence an iontype can be assigned to these via running peak finding algorithms - and subsequent peak labeling. In the field of atom probe this these peak identification methods - are known as ranging definitions. - - Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts - are well distinguished. However, the algorithms used to transform correlations between pulses and physical events - into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. - - Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme - where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier - i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. - That is identifier_evaporation values take the role of an implicit time and course of the experiment given that - ion extraction physically is a sequential process. - - There is a number of research groups who build own instruments and share different aspects of their technical - specifications and approaches how they apply data processing e.g.: - - * `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_ - * `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ - * `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ - - to name but a few. - - Despite some of these activities embrace practices of open-source development, they use essentially the same - workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface - software is used to explore and thus analyze reconstructed atom probe datasets. - - Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. - Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which - scientific conclusions about the characterized material volume are made. Also here a reconstruction is - point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. - - By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all - the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. - Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. - We argue that this divide can be bridged with realizing the above-mentioned context and the realization that - similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. - - A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed - datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment - and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting - a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as - (spatial) filtering and reconstruction algorithms. - - Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation - simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. - Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. - Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. - Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require - simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps - in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. - Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) - than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path - such as local electrodes or physical obstacles and electric fields (controlled or stray fields). - - - - A statement whether the measurement was successful or failed prematurely. - - - - - - - - - CAnalysis.CResults.fQuality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free text field for additional comments. - - - - - - - Group to hold instances of :ref:`NXevent_data_apm`. - - Which temporal granularity is adequate depends on the situation and research - question. Using a model which enables a collection of events offers the most - flexible way to cater for both atom probe experiments or simulation. - - To monitor the course of an ion extraction experiment (or simulation) - it makes sense to track time explicitly via time stamps or implicitly - via e.g. a clock inside the instrument, such as the clock of the pulser - and respective pulsing event identifier. - - As set and measured quantities typically change over time and we do not - yet know during the measurement which of the events have associated - (molecular) ions that will end up in the reconstructed volume, we must not - document quantities as a function of the identifier_evaporation but as a - function of the (pulsing) identifier_event. - - - - - Instances should use event as a name prefix. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Simulation of ion extraction from matter via laser and/or voltage pulsing. - - - - - - A region-of-interest analyzed either during or after the session for which - specific processed data of the measured or simulated data are available. - - - - - SEM or TEM image of the initial specimen (ideally taken prior data acquisition). - - - - - - - - - - - - - - - - - - - - - - - - For almost atom probe instruments (meta)data about raw data follow proprietary semantics. - Therefore, this group can currently be used only to point to these digital artifacts - in an effort to document all step of an analysis workflow. - - The physical quantities measured in an atom probe experiment are time-of-flight and - tuples of arrival_time_pairs as a function of the event chain on the pulser. - From these tuples hits are computed in a process called hit_finding. - - - - - - - - - - - - - - - - - - The number of wires in the detector. - - - - - - - - - - Alias tuple (begin, end) of each DLD wire of the detector. - Order follows arrival_time_pairs. - - - - - - - - - Raw readings from the analog-to-digital-converter - timing circuits of the detector wires. - - - - - - - - - - - Configuration of and results obtained from a hit finding algorithm. - - - - - - - - - - - - - - - - - - - Evaluated ion impact coordinates on the detector. - Use the depends_on field to specify which reference - frame the positions are defined. - - - - - - - - Defines in which reference frame the positions are defined. - - - - - - CRunHeader.fTotalEventGolden - - - - - CRunHeader.fTotalEventIncomplete - - - - - CRunHeader.fTotalEventMultiple - - - - - CRunHeader.fTotalEventPartials - - - - - CRunHeader.fTotalEventRecords - - - - - Identifier used for each hit_quality type. - Following the order of hit_quality_types. - - - - - - - - Hit quality identifier for each pulse. - Identifier have to be within identifier_hit_quality. - - - - - - - - This processing yields for each ion with how many others it evaporated - if these were collected on the same pulse. Extraction of multiple ions - on one pulse on different or even the same pixel of the detector are possible. - - Multiplicity must not be confused with how many atoms of the same element - a molecular ion contains. - - - - - - - - - - - - - - - - - - - - - - - Integer used to name the first pulse to know if there is an - offset of the identifier_evaporation to zero. - - Identifiers can be defined either implicitly or explicitly. - For implicit indexing identifiers are defined on the interval - :math:`[identifier\_offset, identifier\_offset + c - 1]`. - - Therefore, implicit identifier are completely defined by the value of - identifier_offset and cardinality. For example if identifier run from - -2 to 3 the value for identifier_offset is -2. - - For explicit indexing the field identifier has to be used. - Fortran-/Matlab- and C-/Python-style indexing have specific implicit - identifier conventions where identifier_offset is 1 and 0 respectively. - - - - - (Molecular) ion identifier which resolves the sequence in which - the ions were evaporated but taking into account that a hit_finding - and spatial_filtering was applied. - - - - - - - - - - - - - - - - - Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. - - The voltage-and-bowl correction is a data post-processing step to correct ion impact - positions for flight path differences, detector bias, and nonlinearities. - - - - - - - - - - - - - - - - - Raw time-of-flight data without corrections. - - - - - - - - - The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate - - - - - Calibrated time-of-flight. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - For LEAP and IVAS/APSuite-based analyses root file which stores - the settings whereby an RHIT/HITS file can be used to regenerate the - reconstruction that is here referred to. - - The respective RHIT/HITS file should ideally be specified in the serialized - group of the hit_finding section of this application definition. - - - - - - - - - For LEAP and IVAS/APSuite-based analyses the resulting typically - file with the reconstructed positions and (calibrated) mass-to-charge - state ratio values. - - For other data collection/analysis software the data artifact which comes - closest conceptually to AMETEK/Cameca's typical file formats. - - These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, - which should be stored alongside this record in the research data - management system. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The respective ranging definitions file RNG/RRNG/ENV/HDF5. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (Out-of-sync) background levels in ppm/ns - reported by e.g. IVAS/APSuite for LEAP systems. - - - - - MRP, mass-resolving power, `D. Larson et al. - <https://doi.org/10.1007/978-1-4614-8721-0>`_ (p282, Eqs. D.7 and D.8). - - - - - MRP, at which mrp_value was specified. - - - - - - - - - - - - - - - - - Category for the peak offering a qualitative statement of the location of the peak - in light of limited mass-resolving power that is relevant for - composition quantification. See `D. Larson et al. (p172) <https://doi.org/10.1007/978-1-4614-8721-0>`_ - for examples of each category: - - * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` - * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` - * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states - * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` - * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` - * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` - - - - - - - - - - - - - - - - - - - - - - - - - - Instances should use ion as a name prefix. - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml b/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml deleted file mode 100644 index e1e65dfc89..0000000000 --- a/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml +++ /dev/null @@ -1,168 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The number of also possible but different (molecular) ions. - - - - - Maximum number of allowed atoms per (molecular) ion (fragment). - - - - - Number of entries - - - - - Base class to document an algorithm for recovering charge state and nuclide composition of a (molecular) ion. - - Currently ranging definitions in the research field of atom probe face have limitations: - - 1. A ranging definition maps all signal within a mass-to-charge-state-ratio value interval - on one iontype. Facing limited mass-resolving-power, there are mass-to-charge-state-ratio - values, though, for which not only multiple (molecular) ions are indistinguishable but - also for which the current practice of documenting classical ranging definitions is incomplete. - 2. Indeed, ranging definitions often report only (for each interval) the - mass-to-charge-state-ratio intervals surplus the composition of elements - that build the (molecular) ion. - 3. Therefore, classical ranging definitions demand a post-processing with an algorithm - which can identify nuclides from which the (molecular) ion is constructed - and a charge state possibly recovered. Combinatorial algorithms are used for this purpose. - - This base class documents the configuration and results of such an algorithm. - - - - - Input constraint, list of nuclide_hash for typically elements used for the - ranging definition of the ion whose charge state the analyses covered. - The list contains each hash as many times as its multiplicity. - Nuclides are encoded using the hashing rule that is defined in :ref:`NXion`. - - As an example, a ranging definition H:2 O:1 is configured by setting nuclides to - a list with entries :math:`1 + 0 \cdot 256`, :math:`1 + 0 \cdot 256`, :math:`8 + 0 \cdot 256`. - An empty list does not release the constraint. Instead, a list with all elements - in the periodic table (encoded as nuclide_hash values) should be used, i.e. - :math:`1 + 0 \cdot 256`, :math:`2 + 0 \cdot 256`, and so on and so forth. - - Keep in mind that with a weakly constrained parameter space the combinatorial - analysis may become very time consuming! - - - - - - - - Input constraint, interval within which (molecular) ions need to have the - mass-to-charge-state-ratio such that an ion qualifies as a candidate. - - - - - - - - - Input constraint, minimum half life for how long each nuclide of each - (molecular) ion needs to be stable such that the ion qualifies as a candidate. - - - - - Input constraint, minimum natural abundance of each nuclide of each - (molecular) ion such that the ion qualifies as a candidate. - - - - - If the value is false, it means that non-unique solutions are accepted. - These are solutions where multiple candidates have been built from - different nuclide instances but the charge_state of all the ions is the same. - - - - - - - Signed charge, i.e. integer multiple of the elementary - charge of each candidate. - - - - - - - - Table of nuclide instances of which each candidate is composed. - Each row vector is sorted in descending order. Unused values are nullified. - - - - - - - - - Accumulated mass of the nuclides in each candidate. - Not corrected for quantum effects. - - - - - - - - The product of the natural abundances of the nuclides for each candidate. - - - - - - - - For each candidate the half life of that nuclide which has the shortest half - life. - - - - - - diff --git a/contributed_definitions/NXapm_compositionspace_config.nxdl.xml b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml index f6a7ce115c..dd02255eb9 100644 --- a/contributed_definitions/NXapm_compositionspace_config.nxdl.xml +++ b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml @@ -1,4 +1,4 @@ - + @@ -39,65 +38,63 @@ - - - + + + + Specification of the tomographic reconstruction used for this analysis. + Typically, reconstructions in the field of atom probe tomography are communicated via + files which store at least reconstructed ion positions and mass-to-charge-state-ratio + values. Container files like HDF5 though can store multiple reconstructions. + Therefore, the position and mass_to_charge concepts point to specific instances + to use for this analysis. + + + + + + - Specification of the tomographic reconstruction used for this analysis. - Typically, reconstructions in the field of atom probe tomography are communicated via - files which store at least reconstructed ion positions and mass-to-charge-state-ratio - values. Container files like HDF5 though can store multiple reconstructions. - Therefore, the position and mass_to_charge concepts point to specific instances - to use for this analysis. + Name of the node which resolves the reconstructed + ion position values to use for this analysis. - - - - - - - Name of the node which resolves the reconstructed - ion position values to use for this analysis. - - - - - Name of the node which resolves the mass-to-charge-state ratio - values for each reconstructed ion to use for this analysis. - - - - + + - Specification of the ranging definitions used for this analysis. - - Indices start from 1. The value 0 is reserved for the null model of unranged positions whose - iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. + Name of the node which resolves the mass-to-charge-state ratio + values for each reconstructed ion to use for this analysis. - - - - - - - Name of the (parent) node directly below which the ranging definitions for - (molecular) ions are stored. - - - - + + + + + Specification of the ranging definitions used for this analysis. + + Indices start from 1. The value 0 is reserved for the null model of unranged positions whose + iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. + + + + + + - Step during which the point cloud is discretized to compute element-specific composition fields. - Iontypes are atomically decomposed to correctly account for the multiplicity of each element that - was ranged for each ion. + Name of the (parent) node directly below which the ranging definitions for + (molecular) ions are stored. - - - Edge length of cubic voxels building the 3D grid that is used for discretizing - the point cloud. - - - + + + + + Step during which the point cloud is discretized to compute element-specific composition fields. + Iontypes are atomically decomposed to correctly account for the multiplicity of each element that + was ranged for each ion. + + + + Edge length of cubic voxels building the 3D grid that is used for discretizing + the point cloud. + + Optional step during which the subsequent segmentation step is prepared with the aim to eventually @@ -131,60 +128,71 @@ - + + + + Step during which the voxel set is segmented into voxel sets with different + chemical composition. + + + + A principal component analysis of the chemical space to guide a decision into how many sets of voxels + with different chemical composition the machine learning algorithm suggests to split the voxel set. + + + - Step during which the voxel set is segmented into voxel sets with different - chemical composition. + The decision is guided through the evaluation of the information criterion + minimization. - + - A principal component analysis of the chemical space to guide a decision into how many sets of voxels - with different chemical composition the machine learning algorithm suggests to split the voxel set. + The maximum number of chemical classes to probe with the Gaussian mixture model + with which the voxel set is segmented into a mixture of voxels with that many different + chemical compositions. - - + + - The decision is guided through the evaluation of the information criterion - minimization. + Configuration for the Gaussian mixture model that is used in the segmentation + step. - - - The maximum number of chemical classes to probe with the Gaussian mixture model - with which the voxel set is segmented into a mixture of voxels with that many different - chemical compositions. - - - - - Configuration for the Gaussian mixture model that is used in the segmentation - step. - - - + + + + Step during which the chemically segmented voxel sets are analyzed for their + spatial organization. + + - Step during which the chemically segmented voxel sets are analyzed for their - spatial organization. + Configuration for the DBScan algorithm that is used in the clustering step. - + - Configuration for the DBScan algorithm that is used in the clustering step. + The maximum distance between voxel pairs in a neighborhood to be considered + connected. - - - The maximum distance between voxel pairs in a neighborhood to be considered - connected. - - - - - The number of voxels in a neighborhood for a voxel to be considered as a core - point. - - - + + + + The number of voxels in a neighborhood for a voxel to be considered as a core + point. + + + diff --git a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml index 9f57f36c81..e1bcb394f8 100644 --- a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml +++ b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml @@ -1,9 +1,9 @@ - + @@ -59,14 +58,28 @@ - - + + + + + + + + - + + + Programs and libraries representing the computational environment + + + + + + + @@ -79,20 +92,19 @@ for if desired all the dependencies and libraries--> - + Contextualize back to the specimen from which the dataset was collected that was here analyzed with CompositionSpace tool. - + - A qualifier whether the specimen is a real one or a virtual one. + True, if the specimen that the reconstructed dataset + describes is a simulated one. + False, if the specimen that the reconstructed dataset + describes is a real one. - - - - @@ -150,7 +162,7 @@ for if desired all the dependencies and libraries--> - + Position of each cell in Euclidean space. @@ -170,7 +182,7 @@ for if desired all the dependencies and libraries--> - + For each ion, the identifier of the voxel into which the ion binned. @@ -188,7 +200,7 @@ for if desired all the dependencies and libraries--> - + Chemical symbol of the element from the periodic table. @@ -220,7 +232,7 @@ for if desired all the dependencies and libraries--> - + Element identifier stored sorted in descending order of feature importance. @@ -298,11 +310,9 @@ for if desired all the dependencies and libraries--> - + Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. - - Instances should use cluster_analysis as a name prefix. @@ -365,21 +375,16 @@ for if desired all the dependencies and libraries--> - + Respective DBScan clustering result for each segmentation/ic_opt case. - - - Instances should use cluster_analysis as a name prefix. - - + + The maximum distance between voxel pairs in a neighborhood to be considered connected. - - Instances should use dbscan as a name prefix. @@ -411,14 +416,5 @@ for if desired all the dependencies and libraries--> - - - - - - - diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml index abab0e3805..76bdb6a531 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml @@ -1,4 +1,4 @@ - + + Maximum number of atoms per molecular ion. Should be 32 for paraprobe. @@ -105,16 +104,14 @@ n_disjoint_clusters: Number of disjoint cluster.--> - + This process performs a cluster analysis on a reconstructed dataset or a ROI within it. - - Instances should use cluster_analysis as a name prefix. @@ -146,7 +143,7 @@ the region of interest.--> - + @@ -154,7 +151,7 @@ the region of interest.--> - + @@ -162,7 +159,7 @@ the region of interest.--> - + @@ -175,9 +172,6 @@ the region of interest.--> - diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml index e2e4349c72..bff207f5e1 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml @@ -1,4 +1,4 @@ - + - + - Results of a DBScan clustering analysis. - - Instances should use dbscan as a name prefix. + Results of a DBScan clustering analysis. - The epsilon (eps) parameter used. + The epsilon (eps) parameter used. - The minimum points (min_pts) parameter used. + The minimum points (min_pts) parameter used. - + - Number of members in the set which is partitioned into features. - Specifically, this is the total number of targets filtered from the - dataset, i.e. typically the number of clusters which is usually not and - for sure not necessarily the total number of ions in the dataset. + Number of members in the set which is partitioned into features. + Specifically, this is the total number of targets filtered from the + dataset, i.e. typically the number of clusters which is usually not and + for sure not necessarily the total number of ions in the dataset. - + - Which identifier is the first to be used to label a cluster. - - The value should be chosen in such a way that special values can be resolved: - * identifier_offset - 1 indicates an object belongs to no cluster. - * identifier_offset - 2 indicates an object belongs to the noise category. - - Setting for instance identifier_offset to 1 recovers the commonly used - case that objects of the noise category get the value of -1 and points of the - unassigned category get the value 0. + Which identifier is the first to be used to label a cluster. + + The value should be chosen in such a way that special values can be resolved: + * index_offset - 1 indicates an object belongs to no cluster. + * index_offset - 2 indicates an object belongs to the noise category. + + Setting for instance index_offset to 1 recovers the commonly used + case that objects of the noise category get the value of -1 and points of the + unassigned category get the value 0. - The evaporation (sequence) identifier (aka identifier_evaporation) to figure out - which ions from the reconstruction were considered targets. The length - of this array is not necessarily n_ions. - Instead, it is the value of cardinality. + The evaporation (sequence) id (aka evaporation_id) to figure out + which ions from the reconstruction were considered targets. The length + of this array is not necessarily n_ions. + Instead, it is the value of cardinality. @@ -116,11 +114,11 @@ - The number of solutions found for each target. Typically, - this value is 1 in which case the field can be omitted. - Otherwise, this array is the concatenated set of values of solution - tuples for each target that can be used to decode model_labels, - core_sample_indices, and weight. + The number of solutions found for each target. Typically, + this value is 1 in which case the field can be omitted. + Otherwise, this array is the concatenated set of values of solution + tuples for each target that can be used to decode model_labels, + core_sample_indices, and weight. @@ -128,12 +126,12 @@ - The raw labels from the DBScan clustering backend process. - The length of this array is not necessarily n_ions. - Instead, it is typically the value of cardinality provided that each - target has only one associated cluster. If targets are assigned to - multiple cluster this array is as long as the total number of solutions - found and + The raw labels from the DBScan clustering backend process. + The length of this array is not necessarily n_ions. + Instead, it is typically the value of cardinality provided that each + target has only one associated cluster. If targets are assigned to + multiple cluster this array is as long as the total number of solutions + found and @@ -141,8 +139,8 @@ - The raw array of core sample indices which specify which of the - targets are core points. + The raw array of core sample indices which specify which of the + targets are core points. @@ -150,7 +148,7 @@ - Numerical label for each target (member in the set) aka cluster identifier. + Numerical label for each target (member in the set) aka cluster identifier. @@ -158,7 +156,7 @@ - Categorical label(s) for each target (member in the set) aka cluster name(s). + Categorical label(s) for each target (member in the set) aka cluster name(s). @@ -166,39 +164,29 @@ - Weights for each target that specifies how probable the target is assigned to - a specific cluster. - - For the DBScan algorithm and atom probe tomography this value is the - multiplicity of each ion with respect to the cluster. That is how many times - should the position of the ion be accounted for because the ion is e.g. a - molecular ion with several elements or nuclides of requested type. + Weights for each target that specifies how probable the target is assigned to + a specific cluster. + + For the DBScan algorithm and atom probe tomography this value is the + multiplicity of each ion with respect to the cluster. That is how many times + should the position of the ion be accounted for because the ion is e.g. a + molecular ion with several elements or nuclides of requested type. - - Are targets assigned to the noise category or not. + Are targets assigned to the noise category or not. - - Are targets assumed a core point. + Are targets assumed a core point. @@ -206,44 +194,44 @@ number_of_objects(NX_UINT): - In addition to the detailed storage which members were grouped to which - feature here summary statistics are stored that communicate e.g. how many - cluster were found. + In addition to the detailed storage which members were grouped to which + feature here summary statistics are stored that communicate e.g. how many + cluster were found. - + - Total number of targets in the set, i.e. ions that were filtered - and considered in this cluster analysis. + Total number of targets in the set, i.e. ions that were filtered + and considered in this cluster analysis. - + - Total number of members in the set which are categorized as noise. + Total number of members in the set which are categorized as noise. - + - Total number of members in the set which are categorized as a core point. + Total number of members in the set which are categorized as a core point. - Total number of clusters (excluding noise and unassigned). + Total number of clusters (excluding noise and unassigned). - + - Numerical identifier of each feature aka identifier_cluster. + Numerical identifier of each feature aka cluster_id. - + - Number of members for each feature. + Number of members for each feature. @@ -265,36 +253,34 @@ number_of_objects(NX_UINT): - - - + + + - If used, metadata of at least the person who performed this analysis. + If used, metadata of at least the person who performed this analysis. - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml index 8a5cc44108..4b7127d3d8 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml @@ -1,4 +1,4 @@ - + - + @@ -108,12 +106,12 @@ - Specifies for which point the tool will compute distances. - - The value *default* configures that distances are computed for all points. - The value *skin* configures that distances are computed only for those - points which are not farther away located to a triangle than - threshold_distance. + Specifies for which point the tool will compute distances. + + The value *default* configures that distances are computed for all points. + The value *skin* configures that distances are computed only for those + points which are not farther away located to a triangle than + threshold_distance. @@ -122,27 +120,25 @@ - Maximum distance for which distances are - computed when *method* is *skin*. + Maximum distance for which distances are + computed when *method* is *skin*. - How many triangle sets to consider. - Multiple triangle sets can be defined which are - composed into one joint triangle set for the analysis. + How many triangle sets to consider. + Multiple triangle sets can be defined which are + composed into one joint triangle set for the analysis. - + - Each triangle_set that is referred to here should be a face_list_data_structure, - i.e. an array of (n_vertices, 3) of NX_FLOAT for vertex coordinates, an (n_facets, 3) - array of NX_UINT incident vertices of each facet. Vertex indices are assumed to - start at zero and must not exceed n_vertices - 1, i.e. the identifier_offset is 0. - Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. - - Instances should use triangle_set as a name prefix. + Each triangle_set that is referred to here should be a face_list_data_structure, + i.e. an array of (n_vertices, 3) of NX_FLOAT for vertex coordinates, an (n_facets, 3) + array of NX_UINT incident vertices of each facet. Vertex indices are assumed to + start at zero and must not exceed n_vertices - 1, i.e. the index_offset is 0. + Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. @@ -150,32 +146,32 @@ - Absolute path in the (HDF5) file that points to the array - of vertex positions for the triangles in that triangle_set. + Absolute path in the (HDF5) file that points to the array + of vertex positions for the triangles in that triangle_set. - Absolute path in the (HDF5) file that points to the array - of vertex indices for the triangles in that triangle_set. + Absolute path in the (HDF5) file that points to the array + of vertex indices for the triangles in that triangle_set. - Absolute path in the (HDF5) file that points to the array - of vertex normal vectors for the triangles in that triangle_set. + Absolute path in the (HDF5) file that points to the array + of vertex normal vectors for the triangles in that triangle_set. - Absolute path in the (HDF5) file that points to the array - of facet normal vectors for the triangles in that triangle_set. + Absolute path in the (HDF5) file that points to the array + of facet normal vectors for the triangles in that triangle_set. - + - Absolute path in the (HDF5) file that points to the array - of identifier for the triangles in that triangle_set. + Absolute path in the (HDF5) file that points to the array + of identifier for the triangles in that triangle_set. diff --git a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml index 163adca0de..931f0a115e 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml @@ -1,4 +1,4 @@ - + - - - + + + @@ -175,26 +175,24 @@ triangles in this case--> - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml index 095e23e4ef..e66e2acf32 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml @@ -1,9 +1,9 @@ - + @@ -123,14 +121,14 @@ next_set to nodes representing members of the current_set. - + Current set stores a set of members, meshes of volumetric features, which will be checked for proximity and/or volumetric intersection, to members of the current_set. The meshes were generated as a result of some other meshing process. - + This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k`) step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). @@ -154,7 +152,7 @@ current_set. - + Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the members of the set as instances of NXcg_polyhedron. @@ -182,7 +180,7 @@ - + Array of identifier whereby the path to the geometry data can be inferred automatically. @@ -193,14 +191,14 @@ - + Next set stores a set of members, meshes of volumetric features, which will be checked for proximity and/or volumetric intersection, to members of the next_set. The meshes were generated as a result of some other meshing process. - + This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k + 1`) step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). @@ -224,7 +222,7 @@ next_set. - + Descriptive category explaining what these features are. @@ -247,7 +245,7 @@ - + Array of identifier whereby the path to the geometry data can be inferred automatically. diff --git a/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml index 7b48475bcc..50883f97e8 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml @@ -1,4 +1,4 @@ - + - A matrix of identifier_feature that specifies which named features + A matrix of indices_feature that specifies which named features from the current_set have directed link(s) pointing to which named feature(s) from the next_set. @@ -98,7 +98,7 @@ - A matrix of identifier_feature which specifies which named feature(s) + A matrix of indices_feature which specifies which named feature(s) from the next_set have directed link(s) pointing to which named feature(s) from the current_set. Only if the mapping whereby the links are defined is symmetric it holds that next_to_current maps @@ -140,7 +140,7 @@ The third comparison is the current_set against the next_set. Once the (forward) links for these comparisons are ready, pair relations - are analyzed with respect to which objects with identifier_feature + are analyzed with respect to which objects with indices_feature cluster in identifier space. Thereby, a logical connection (link) is established between the features in the current_set and the next_set. Recall that these two sets typically represent different features @@ -158,8 +158,8 @@ - Matrix of identifier_feature and identifier_cluster pairs which - encodes the cluster to which each identifier_feature was assigned. + Matrix of indices_feature and cluster_id pairs which + encodes the cluster to which each indices_feature was assigned. Here for features of the current_set. @@ -169,8 +169,8 @@ - Matrix of identifier_feature and identifier_cluster pairs which - encodes the cluster to which each identifier_feature was assigned. + Matrix of indices_feature and cluster_id pairs which + encodes the cluster to which each indices_feature was assigned. Here for features of the next_set. @@ -178,7 +178,7 @@ - + The identifier (names) of the cluster. @@ -238,9 +238,9 @@ - - - + + + @@ -248,26 +248,24 @@ - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml index b4956764ae..4392766bdd 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml @@ -1,4 +1,4 @@ - + - + @@ -158,7 +158,7 @@ This can be achieved with the load_existent option.--> - + @@ -166,7 +166,7 @@ This can be achieved with the load_existent option.--> - + @@ -279,7 +279,7 @@ identifier(NX_UINT):--> accuracy of reconstruction protocols and their parameterization. Unused values in each row of the matrix are nullified. - Nuclides are identified as hashed nuclide (see :ref:`NXion`) for further details. + Nuclides are identified as hashed nuclide (see :ref:`NXatom`) for further details. @@ -417,6 +417,7 @@ identifier(NX_UINT):--> * candidates, total number of ions with type in the isotope_whitelist. * composition, candidates but normalized by composition, i.e. at.-% * concentration, candidates but normalized by voxel volume, i.e. ions/nm^3 + @@ -635,7 +636,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> - + @@ -643,7 +644,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> - + @@ -651,7 +652,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> - + @@ -943,7 +944,7 @@ from normals of neighboring facets, type of weighting schemes can affect results - + @@ -951,7 +952,7 @@ from normals of neighboring facets, type of weighting schemes can affect results - + @@ -959,7 +960,7 @@ from normals of neighboring facets, type of weighting schemes can affect results - + @@ -998,7 +999,7 @@ identifier(NX_UINT):--> - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml index 9384f40fcd..c1c1b20621 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml @@ -1,4 +1,4 @@ - + - - - Instances should use delocalization as a name prefix. - + @@ -131,14 +128,14 @@ The cardinality/total number of triangles in the triangle soup.--> The discretized domain/grid on which the delocalization is applied. - + - + The total number of cells/voxels of the grid. @@ -179,7 +176,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + Integer which specifies the first index to be used for distinguishing identifiers for cells. Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are @@ -232,7 +229,7 @@ The cardinality/total number of triangles in the triangle soup.--> For atom probe should be set to true. - + Integer which specifies the first index to be used for distinguishing hexahedra. Identifiers are defined either implicitly or explicitly. @@ -242,7 +239,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + Integer which specifies the first index to be used for distinguishing identifiers for vertices. Identifiers are defined either implicitly or explicitly. @@ -251,7 +248,7 @@ The cardinality/total number of triangles in the triangle soup.--> has to be defined. - + Integer which specifies the first index to be used for distinguishing identifiers for faces. Identifiers are defined either implicitly or explicitly. @@ -498,12 +495,10 @@ The cardinality/total number of triangles in the triangle soup.--> - + An iso-surface is the boundary between two regions across which the magnitude of a scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. - - Instances should iso_surface as a name prefix. For applications in atom probe microscopy, the location and shape of such a boundary (set) is typically approximated by discretization - triangulation to be specific. @@ -530,15 +525,9 @@ The cardinality/total number of triangles in the triangle soup.--> The resulting triangle soup computed via marching cubes. - - - - - Integer which specifies the first index to be used for distinguishing triangles. - Identifiers are defined either implicitly or explicitly. For implicit indexing the - identifiers are defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. - - + + + @@ -771,7 +760,7 @@ dim: (k,)--> - + The explicit identifier of features. @@ -792,9 +781,9 @@ dim: (k,)--> * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface - + - Explicit identifier of the feature a sub-set of the identifier_feature in the + Explicit identifier of the feature a sub-set of the indices_feature in the parent group. @@ -856,34 +845,27 @@ dim: (k,)--> - + - + - - - Instances should use object as a name prefix. - + - - + @@ -895,19 +877,19 @@ identifier_face_offset(NX_UINT):--> - + - + - + - Array of identifier_evaporation / identifier_ion which details which ions + Array of evaporation_id / identifier_ion which details which ions lie inside or on the surface of the feature. @@ -926,7 +908,7 @@ identifier_face_offset(NX_UINT):--> - + @@ -995,12 +977,10 @@ identifier_face_offset(NX_UINT):--> - + The triangle surface mesh representing the interface model. Exported at state before or after the next DCOM step. - - Instances should use mesh_state as a name prefix. @@ -1011,17 +991,17 @@ identifier_face_offset(NX_UINT):--> - - - + + + - - - - - - - + + + + + + + @@ -1054,7 +1034,7 @@ identifier_face_offset(NX_UINT):--> - + @@ -1131,8 +1111,8 @@ identifier_face_offset(NX_UINT):--> resolves the lateral surface of each cylinder such that their renditions are smooth in visualization software like Paraview. - - + + Position of the geometric center, which often is but not @@ -1154,7 +1134,7 @@ identifier_face_offset(NX_UINT):--> - + XDMF support to enable coloring each ROI by its identifier. @@ -1199,10 +1179,7 @@ identifier_face_offset(NX_UINT):--> are only expected to display pairwise the same values respectively, if all ions are built from a single atom only. - - - Instances should use roi as a name prefix. - + Sorted in increasing order projected along the positive direction @@ -1214,7 +1191,7 @@ identifier_face_offset(NX_UINT):--> - Hashvalue as defined in :ref:`NXion`. + Hashvalue as defined in :ref:`NXatom`. @@ -1243,9 +1220,9 @@ identifier_face_offset(NX_UINT):--> - - - + + + @@ -1253,26 +1230,24 @@ identifier_face_offset(NX_UINT):--> - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml index bf564c9705..5e3f50c4d3 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml @@ -1,4 +1,4 @@ - + - Paraprobe-ranger loads the iontypes and evaluates for each - ion on which iontype it matches. If it matches on None, the - ion is considered of the default *unknown_type*. This iontype - is marked with a 0 in the iontypes array. + Paraprobe-ranger loads the iontypes and evaluates for each + ion on which iontype it matches. If it matches on None, the + ion is considered of the default *unknown_type*. This iontype + is marked with a 0 in the iontypes array. - - + @@ -72,12 +70,12 @@ config--> - The iontype (identifier) for each ion that was best matching, stored - in the order of the evaporation sequence ID. The here computed iontypes - do not take into account the charge state of the ion which is - equivalent to interpreting a RNG and RRNG range files for each - ion in such a way that only the those elements are considered of which - a (molecular) ion is assumed composed according to the NXion instances. + The iontype (identifier) for each ion that was best matching, stored + in the order of the evaporation sequence ID. The here computed iontypes + do not take into account the charge state of the ion which is + equivalent to interpreting a RNG and RRNG range files for each + ion in such a way that only the those elements are considered of which + a (molecular) ion is assumed composed according to the NXatom instances. @@ -103,36 +101,34 @@ config--> - - - + + + - If used, metadata of at least the person who performed this analysis. + If used, metadata of at least the person who performed this analysis. - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml index 3a051b91ee..d3ffabb4d6 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml @@ -1,4 +1,4 @@ - + how iontypes are interpreted given an iontype represents in general a (molecular) ion with different isotopes that have individually different multiplicity. - + The value resolve_all will set an ion active in the analysis regardless of which iontype it is. Each active ion is accounted for once. diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml index e1e315dd36..b12422c928 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml @@ -1,4 +1,4 @@ - + - - - Instances should use spatial_statistics as a name prefix. - + @@ -67,13 +64,13 @@ - The iontype ID for each ion that was assigned to each ion during - the randomization of the ionlabels. Iontype labels are just permuted - but the total number of values for each iontype remain the same. - - The order matches the iontypes array from a given ranging results - as it is specified in the configuration settings inside the specific - config_filename that was used for this paraprobe-spatstat analysis. + The iontype ID for each ion that was assigned to each ion during + the randomization of the ionlabels. Iontype labels are just permuted + but the total number of values for each iontype remain the same. + + The order matches the iontypes array from a given ranging results + as it is specified in the configuration settings inside the specific + config_filename that was used for this paraprobe-spatstat analysis. @@ -81,11 +78,11 @@ - K-nearest neighbor statistics. + K-nearest neighbor statistics. - Right boundary of the binning. + Right boundary of the binning. @@ -98,7 +95,7 @@ - Cumulated not normalized by total counts. + Cumulated not normalized by total counts. @@ -106,7 +103,7 @@ - Cumulated and normalized by total counts. + Cumulated and normalized by total counts. @@ -115,11 +112,11 @@ - Radial distribution statistics. + Radial distribution statistics. - Right boundary of the binning. + Right boundary of the binning. @@ -132,7 +129,7 @@ - Cumulated not normalized by total counts. + Cumulated not normalized by total counts. @@ -140,7 +137,7 @@ - Cumulated and normalized by total counts. + Cumulated and normalized by total counts. @@ -167,36 +164,34 @@ - - - + + + - If used, metadata of at least the person who performed this analysis. + If used, metadata of at least the person who performed this analysis. - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml index 0a46542c87..e769564090 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml @@ -1,4 +1,4 @@ - + - + - - Instances should use alpha_complex as a name prefix. - A bitmask which identifies exactly all those ions whose positions @@ -129,7 +126,7 @@ for eventually performed preprocessing--> - + @@ -157,20 +154,20 @@ for eventually performed preprocessing--> The set of triangles in the coordinate system paraprobe which discretizes the exterior surface of the alpha complex. - + - - - - + + + + - + @@ -204,17 +201,17 @@ for eventually performed preprocessing--> The set of tetrahedra which represent the interior volume of the complex if that is a closed two-manifold. - + The accumulated volume of all interior tetrahedra. - - - - + + + + @@ -256,9 +253,9 @@ For the future as we may wish to wrap primitives other like triangles or polylin - - - + + + @@ -266,26 +263,24 @@ For the future as we may wish to wrap primitives other like triangles or polylin - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml index bebe5dc886..c576765007 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml @@ -1,4 +1,4 @@ - + - Base class documenting the information common to tools of the paraprobe-toolbox. - - The paraprobe-toolbox is a collection of open-source tools for performing - efficient analyses of point cloud data where each point can represent atoms or - (molecular) ions. A key application of the toolbox has been for research in the - field of Atom Probe Tomography (APT) and related Field Ion Microscopy (FIM): - - * `paraprobe-toolbox <https://www.gitlab.com/paraprobe/paraprobe-toolbox>`_ - * `M. Kühbach et al. <https://paraprobe-toolbox.readthedocs.io/en/main/>`_ - - The toolbox does not replace but complements existent software tools in this - research field. Given its capabilities of handling points as objects with - properties and enabling analyses of the spatial arrangement of and inter- - sections between geometric primitives, the software can equally be used - for analyzing data in Materials Science and Materials Engineering. - - The common section can be used as a place to store e.g. organizational - metadata and contextualization of that analysis in a research data - management system. + Base class documenting the information common to tools of the paraprobe-toolbox. + + The paraprobe-toolbox is a collection of open-source tools for performing + efficient analyses of point cloud data where each point can represent atoms or + (molecular) ions. A key application of the toolbox has been for research in the + field of Atom Probe Tomography (APT) and related Field Ion Microscopy (FIM): + + * `paraprobe-toolbox <https://www.gitlab.com/paraprobe/paraprobe-toolbox>`_ + * `M. Kühbach et al. <https://paraprobe-toolbox.readthedocs.io/en/main/>`_ + + The toolbox does not replace but complements existent software tools in this + research field. Given its capabilities of handling points as objects with + properties and enabling analyses of the spatial arrangement of and inter- + sections between geometric primitives, the software can equally be used + for analyzing data in Materials Science and Materials Engineering. + + The common section can be used as a place to store e.g. organizational + metadata and contextualization of that analysis in a research data + management system. - A statement whether the tool executable managed to process the analysis - or whether this failed. Status is written to the results file after the - end_time beyond which point in time the tool must no longer compute - any further analysis results but exit. - - Only when this status message is present and its value is `success`, - one should consider the results of the tool. In all other cases it might - be that the tool has terminated prematurely or another error occurred. + A statement whether the tool executable managed to process the analysis + or whether this failed. Status is written to the results file after the + end_time beyond which point in time the tool must no longer compute + any further analysis results but exit. + + Only when this status message is present and its value is `success`, + one should consider the results of the tool. In all other cases it might + be that the tool has terminated prematurely or another error occurred. @@ -60,69 +60,64 @@ - + - Internal identifier used by the tool to refer to an analysis (aka simulation - id). + Internal identifier used by the tool to refer to an analysis (aka simulation + id). - The configuration file that was used to parameterize - the algorithms that this tool has executed. + The configuration file that was used to parameterize + the algorithms that this tool has executed. +doc: | +Path where the tool stores tool-specific results. If not specified, +results will be stored in the current working directory.--> - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis in this results file was started, - i.e. when the respective executable/tool was started as a process. + ISO 8601 formatted time code with local time zone offset to UTC + information included when the analysis in this results file was started, + i.e. when the respective executable/tool was started as a process. - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis in this results file were - completed and the respective process of the tool exited. + ISO 8601 formatted time code with local time zone offset to UTC + information included when the analysis in this results file were + completed and the respective process of the tool exited. - Wall-clock time. + Wall-clock time. - + - Details about coordinate systems (reference frames) used. In atom probe several coordinate - systems have to be distinguished. Names of instances of such :ref:`NXcoordinate_system` - should be documented explicitly and doing so by picking from the - following controlled set of names: - - * paraprobe - * lab - * specimen - * laser - * instrument - * detector - * recon - - The aim of this convention is to support users with contextualizing which reference frame - each instance (coordinate system) is. If needed, instances of :ref:`NXtransformations` - are used to detail the explicit affine transformations whereby one can convert - representations between different reference frames. - Inspect :ref:`NXtransformations` for further details. + Details about coordinate systems (reference frames) used. In atom probe several coordinate + systems have to be distinguished. Names of instances of such :ref:`NXcoordinate_system` + should be documented explicitly and doing so by picking from the + following controlled set of names: + + * paraprobe + * lab + * specimen + * laser + * instrument + * detector + * recon + + The aim of this convention is to support users with contextualizing which reference frame + each instance (coordinate system) is. If needed, instances of :ref:`NXtransformations` + are used to detail the explicit affine transformations whereby one can convert + representations between different reference frames. + Inspect :ref:`NXtransformations` for further details. - - - - diff --git a/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml index b02983e163..88b2cd8b87 100644 --- a/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml @@ -1,4 +1,4 @@ - + +i be careful n_comb can vary for every instance of (NXatom) !--> - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - The total number of ions in the reconstruction. + The total number of ions in the reconstruction. - Maximum number of allowed atoms per (molecular) ion (fragment). - Needs to match maximum_number_of_atoms_per_molecular_ion. + Maximum number of allowed atoms per (molecular) ion (fragment). + Needs to match maximum_number_of_atoms_per_molecular_ion. - Total number of integers in the supplementary XDMF topology array. + Total number of integers in the supplementary XDMF topology array. - Number of entries + Number of entries - Application definition for results files of the paraprobe-transcoder tool. - - This tool is part of the paraprobe-toolbox. Inspect the base class :ref:`NXapm_paraprobe_tool_results`. - The purpose and need of the paraprobe-transcoder tool is to create a standardized representation - of reconstructed position and mass-to-charge-state-ratio values surplus other pieces of information - to enable working with atom probe data in reconstruction space in the paraprobe-toolbox. - This includes ranging definitions which map mass-to-charge-state ratio values onto iontypes. - - So far the atom probe community has not yet agreed upon a comprehensive standardization on how to - exchange information especially when it comes to the communication of configurations and results - from analyses of atom probe data. Instead, different simplistic file formats are used, such as POS, ePOS, - APT, or RNG and RRNG. None of these formats, though, are self-descriptive, standardize, or document - their origin and thus the sequence in which the file was generated during an analysis. - - Paraprobe-transcoder solves this limitation by interpreting the information content in such files - and standardize the representation prior injection into the scientific data analysis tools of the toolbox. - Therefore, the here proposed set of NeXus base classes and application definitions can be a useful - starting point for the atom probe community to take advantage of standardized information - exchange and improve the here proposed classes and concepts to become more inclusive. - - Paraprobe-transcoder uses a Python library developed based on efforts by members of the - global atom probe community `International Field Emission Society (IFES) Atom Probe Technical Committee (APT TC) <https://www.github.com/atomprobe-tc/ifes_apt_tc_data_modeling>`_. This library offers the - actual low-level I/O operations and respective information interpretation of above-mentioned file formats. + Application definition for results files of the paraprobe-transcoder tool. + + This tool is part of the paraprobe-toolbox. Inspect the base class :ref:`NXapm_paraprobe_tool_results`. + The purpose and need of the paraprobe-transcoder tool is to create a standardized representation + of reconstructed position and mass-to-charge-state-ratio values surplus other pieces of information + to enable working with atom probe data in reconstruction space in the paraprobe-toolbox. + This includes ranging definitions which map mass-to-charge-state ratio values onto iontypes. + + So far the atom probe community has not yet agreed upon a comprehensive standardization on how to + exchange information especially when it comes to the communication of configurations and results + from analyses of atom probe data. Instead, different simplistic file formats are used, such as POS, ePOS, + APT, or RNG and RRNG. None of these formats, though, are self-descriptive, standardize, or document + their origin and thus the sequence in which the file was generated during an analysis. + + Paraprobe-transcoder solves this limitation by interpreting the information content in such files + and standardize the representation prior injection into the scientific data analysis tools of the toolbox. + Therefore, the here proposed set of NeXus base classes and application definitions can be a useful + starting point for the atom probe community to take advantage of standardized information + exchange and improve the here proposed classes and concepts to become more inclusive. + + Paraprobe-transcoder uses a Python library developed based on efforts by members of the + global atom probe community `International Field Emission Society (IFES) Atom Probe Technical Committee (APT TC) <https://www.github.com/atomprobe-tc/ifes_apt_tc_data_modeling>`_. This library offers the + actual low-level I/O operations and respective information interpretation of above-mentioned file formats. @@ -95,9 +95,9 @@ config--> - By default the entire reconstructed volume is processed. - In this case, using window is also equivalent to an - NXspatial_filter that specified a window *entire_dataset*. + By default the entire reconstructed volume is processed. + In this case, using window is also equivalent to an + NXspatial_filter that specified a window *entire_dataset*. @@ -107,7 +107,7 @@ config--> - Mass-to-charge-state-ratio values. + Mass-to-charge-state-ratio values. @@ -117,8 +117,8 @@ config--> - Three-dimensional reconstructed positions of the ions. - Interleaved array of x, y, z positions in the specimen space. + Three-dimensional reconstructed positions of the ions. + Interleaved array of x, y, z positions in the specimen space. @@ -126,17 +126,17 @@ config--> - Defines in which reference frame the positions are defined. + Defines in which reference frame the positions are defined. - An array of triplets of integers which can serve as a supplementary - array for Paraview to display the reconstruction. The XDMF datatype - is here 1, the number of primitives 1 per triplet, the last integer - in each triplet is the identifier of each point starting from zero. + An array of triplets of integers which can serve as a supplementary + array for Paraview to display the reconstruction. The XDMF datatype + is here 1, the number of primitives 1 per triplet, the last integer + in each triplet is the identifier of each point starting from zero. @@ -147,9 +147,9 @@ config--> - Details about how peaks are interpreted as ion types or not. + Details about how peaks are interpreted as ion types or not. - + @@ -183,36 +183,34 @@ config--> - - - + + + - If used, metadata of at least the person who performed this analysis. + If used, metadata of at least the person who performed this analysis. - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_ranging.nxdl.xml b/contributed_definitions/NXapm_ranging.nxdl.xml deleted file mode 100644 index a7d7fb2c1a..0000000000 --- a/contributed_definitions/NXapm_ranging.nxdl.xml +++ /dev/null @@ -1,111 +0,0 @@ - - - - - - Base class for the configuration and results of ranging definitions. - - Ranging is a data post-processing step used in the research field of - atom probe during which elemental, isotopic, and/or molecular identities - are assigned to mass-to-charge-state-ratios within a certain interval. - The documentation of these steps is based on ideas that - have been described in the literature: - - * `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ - * `D. Haley et al. <https://doi.org/10.1017/S1431927620024290>`_ - * `M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - Specifies the mass-to-charge-state-ratio histogram. - - - - - Smallest, increment, and largest mass-to-charge-state ratio value. - - - - - - - - A default histogram aka mass spectrum of - the mass-to-charge-state ratio values. - - - - - - Details of the background model that was used to - correct the total counts per bin into counts. - - - - - To begin with we use a free-text field to learn how - atom probers define a background model. Future versions - of NXapm_ranging can then use this information to parameterize - these models. - - - - - - - How where peaks in the background-corrected in the histogram - of mass-to-charge-state ratio values identified? - - - - - - - Details about how peaks, with taking into account - error models, were interpreted as ion types or not. - - - - - How many ion types are distinguished. If no ranging was performed, each - ion is of the special unknown type. The iontype ID of this unknown type - is 0 representing a reserve value. Consequently, - iontypes start counting from 1. - - - - - Assumed maximum value that suffices to store all relevant - molecular ions, even the most complicated ones. - Currently, a value of 32 is used (see M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_). - - - - - diff --git a/contributed_definitions/NXapm_reconstruction.nxdl.xml b/contributed_definitions/NXapm_reconstruction.nxdl.xml deleted file mode 100644 index 95ef358785..0000000000 --- a/contributed_definitions/NXapm_reconstruction.nxdl.xml +++ /dev/null @@ -1,217 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of ions spatially filtered from results of the hit_finding algorithm - from which an instance of a reconstructed volume has been generated. - These ions get new identifier assigned in the process - the so-called - identifier_evaporation, which must not be confused with the identifier_pulse! - - - - - Base class for the configuration and results of a (static) reconstruction algorithm. - - Generating a tomographic reconstruction of the specimen uses selected and - calibrated ion hit positions, the evaporation sequence, and voltage curve data. - Very often scientists use own software scripts according to published procedures, - so-called reconstruction protocols. - - - - - - - - Different reconstruction protocols exist. Although these approaches - are qualitatively similar, each protocol uses different parameters - (and interprets these differently). The source code to IVAS/APSuite - is not open. For now users should store reconstruction parameter - in this free-text field to guide how to parameterize this better in the - future. For LEAP systems and reconstructions performed with IVAS/APSuite - see `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). - - - - - CAnalysis.CSpatial.fPrimaryElement - - - - - CAnalysis.CSpatial.fEfficiency - - - - - CAnalysis.CSpatial.fFlightPath - - - - - CAnalysis.CSpatial.fEvaporationField - - - - - CAnalysis.CSpatial.fImageCompression - - Image compression factor (ICF) - - - - - CAnalysis.CSpatial.fKfactor - - k factor - - - - - CAnalysis.CSpatial.fRecoVolume - - Sum of ion volumes - - - - - CAnalysis.CSpatial.fShankAngle - - Shank angle - - - - - CAnalysis.CSpatial.fTipRadius - - - - - CAnalysis.CSpatial.fTipRadius0 - - - - - CAnalysis.CSpatial.fVoltage0 - - - - - Tight, axis-aligned bounding box about the point cloud of the reconstruction. - - - - TODO - - - - - TODO - - - - - TODO - - - - - TODO - - - - - TODO - - - - - TODO - - - - - - Qualitative statement about which reconstruction protocol was used. - - - - - - - - - - - Different strategies for crystallographic calibration of the - reconstruction are possible. Therefore, we collect first such - feedback before parametrizing this further. - - If no crystallographic calibration was performed, the field - should be filled with the n/a, meaning not applied. - - - - - - - The nominal diameter of the specimen ROI which is measured in the - experiment. The physical specimen cannot be measured completely - because ions may launch but hit in locations other than the detector. - - - - - Three-dimensional reconstructed positions of the ions. - - - - - - - - The instance of :ref:`NXcoordinate_system` - in which the positions are defined. - - - - - - - - - To get a first visual overview of the reconstructed dataset, - here a 3d histogram of the ion is stored. Ion counts are characterized - using one nanometer cubic bins without applying position smoothening - algorithms during the histogram computation. - - - - diff --git a/contributed_definitions/NXatom.nxdl.xml b/contributed_definitions/NXatom.nxdl.xml deleted file mode 100644 index bdfca4aa77..0000000000 --- a/contributed_definitions/NXatom.nxdl.xml +++ /dev/null @@ -1,133 +0,0 @@ - - - - - - Base class for documenting a set of atoms. - - Atoms in the set may be bonded. - The set may have a net charge to represent - an ion. Ions can be molecular ions. - - - - Given name for the set. - - This field could for example be used in the research field - of atom probe tomography for storing a standardized - human-readable name of the element or (molecular) ion - like such as Al +++ or 12C +. - - - - - Identifier used to refer to if the set of atoms represents a substance. - - - - - - - - Signed net (partial) charge of the (molecular) ion. - - Different methods for computing charge are in use. - Care needs to be exercised with respect to the integration. - `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. - - - - - Charge reported in multiples of the charge of an electron. - - For research using atom probe tomography the value should be set to - zero if the charge_state is unknown and irrecoverable. This can happen - when classical ranging definition files in formats like RNG, RRNG are used. - These file formats do not document the charge state explicitly but only - the number of atoms of each element per molecular ion surplus the - respective mass-to-charge-state-ratio interval. - - Details on ranging definition files in the literature are `M. K. Miller <https://doi.org/10.1002/sia.1719>`_. - - - - - Assumed volume affected by the set of atoms. - - Neither individual atoms nor a set of cluster of these have a volume - that is unique as a some cut-off criterion is required. - - - - - - Identifier for each atom at locations as detailed by position. - - - - - - - - Nuclide information for each atom at locations as detailed by position. - - One `approach <https://doi.org/10.1017/S1431927621012241>`_ for storing nuclide information efficiently - is via hashing with the following formula - - :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - - the number of protons and :math:`N` the number of neutrons - of each nuclide given as 8-bit unsigned integer values. - - - - - - - - Position of each atom. - - - - - - - - Path to a reference frame in which positions are defined - to resolve ambiguity when the reference frame is different - to the NeXus default reference frame (McStas). - - - - - - Relative occupancy of the atom position. - - This field is useful for specifying the atomic motif in - instances of :ref:`NXunit_cell`. - - - - - - diff --git a/contributed_definitions/NXbeam_splitter.nxdl.xml b/contributed_definitions/NXbeam_splitter.nxdl.xml index 84eebbaa76..06d7d01bea 100644 --- a/contributed_definitions/NXbeam_splitter.nxdl.xml +++ b/contributed_definitions/NXbeam_splitter.nxdl.xml @@ -1,4 +1,4 @@ - + - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The cardinality of the set, i.e. the number of parallelograms. - - - - - Computational geometry description of a set of parallelograms. - - This class can also be used to describe rectangles or squares, irrespective - whether these are axis-aligned or not. The class represents different - access and description levels to embrace applied scientists and computational - geometry experts with their different views: - - * The simplest case is the communication of dimensions aka the size of a - region of interest in the 2D plane. In this case, communicating the - alignment with axes is maybe not as relevant as it is to report the area - of the ROI. - * In other cases the extent of the parallelogram is relevant though. - * Finally, in CAD models it should be possible to specify the polygons - which the parallelograms represent with exact numerical details. - - Parallelograms are important geometrical primitives as their usage for - describing many scanning experiments shows where typically parallelogram-shaped - ROIs are scanned across the surface of a sample. - - The term parallelogram will be used throughout this base class thus including - the important special cases rectangle, square, 2D box, axis-aligned bounding box - (AABB), or optimal bounding box (OBB) as analogous 2D variants to their 3D - counterparts. See :ref:`NXcg_hexahedron` for the generalization in 3D. - - An axis-aligned bounding box is a common data object in computational science - and simulation codes to represent a rectangle whose edges are aligned with the - axes of a coordinate system. As a part of binary trees AABBs are important data - objects for executing time- as well as space-efficient queries - of geometric primitives in techniques like kd-trees. - - An optimal bounding box is a common data object which provides the best, i.e. - most tightly fitting box about an arbitrary object. In general such boxes are - rotated. Other than in 3D dimensions, the rotation calipher method offers - a rigorous approach to compute an optimal bounding box to a point set in 2D. - - - - - To specify which parallelogram is a rectangle. - - - - - - - - Only to be used if is_rectangle is present. In this case, this field - describes whether parallelograms are rectangles whose primary edges - are parallel to the axes of the coordinate system. - - - - - - - - - Combined storage of all parallelograms. - - - - - Individual storage of each parallelogram. - - Instances should use parallelogram as a name prefix. - - - diff --git a/contributed_definitions/NXcg_polygon.nxdl.xml b/contributed_definitions/NXcg_polygon.nxdl.xml deleted file mode 100644 index 7cb6cb5739..0000000000 --- a/contributed_definitions/NXcg_polygon.nxdl.xml +++ /dev/null @@ -1,130 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be either 2 or 3. - - - - - The cardinality of the set, i.e. the number of polygons. - - - - - - The total number of vertices when visiting every polygon. - - - - - - Computational geometry description of a set of polygons in Euclidean space. - - Polygons are specialized polylines: - - * A polygon is a geometric primitive that is bounded by a closed polyline - * All vertices of this polyline lay in the d-1 dimensional plane. - whereas vertices of a polyline do not necessarily lay on a plane. - * A polygon has at least three vertices. - - Each polygon is built from a sequence of vertices (points with identifiers). - The members of a set of polygons may have a different number of vertices. - Sometimes a collection/set of polygons is referred to as a soup of polygons. - - As three-dimensional objects, a set of polygons can be used to define the - hull of what is effectively a polyhedron; however users are advised to use - the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed - polyhedra. Even more general complexes can be thought of. An example are the - so-called piecewise-linear complexes used in the TetGen library. - - As these complexes can have holes though, polyhedra without holes are one - subclass of such complexes, users should rather design an own base class - e.g. NXcg_polytope to describe such even more complex primitives instead - of abusing this base class for such purposes. - - - - The total number of vertices in the set. - - - - - - Combined storage of all primitives of all polygons. - - - - - Individual storage of the mesh of each polygon. - - Instances should use polygon as a name prefix. - - - - - Individual storage of each polygon as a graph. - - Instances should use polygon_half_edge as a name prefix. - - - - - - For each polygon its accumulated length along its edges. - - - - - - - - Interior angles for each polygon. There are as many values per polygon - as the are number_of_vertices. - The angle is the angle at the specific vertex, i.e. between the adjoining - edges of the vertex according to the sequence in the polygons array. - Usually, the winding_order field is required to interpret the value. - - - - - - - - Curvature type: - - * 0 - unspecified, - * 1 - convex, - * 2 - concave - - - - - - diff --git a/contributed_definitions/NXcoordinate_system_set.nxdl.xml b/contributed_definitions/NXcoordinate_system_set.nxdl.xml deleted file mode 100644 index 36d58e9337..0000000000 --- a/contributed_definitions/NXcoordinate_system_set.nxdl.xml +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - Base class to hold different coordinate systems and representation conversions. - - How many nodes of type :ref:`NXcoordinate_system_set` should be used in an application definition? - - * 0; if there is no instance of :ref:`NXcoordinate_system_set` and therein or elsewhere across - the application definition, an instance of NXcoordinate_system is defined, - the default NeXus `McStas <https://mailman2.mcstas.org/pipermail/mcstas-users/2021q2/001431.html>`_ - coordinate system is assumed. This makes :ref:`NXcoordinate_system_set` and - NXcoordinate_system base classes backwards compatible to older - NeXus conventions and classes. - * 1; if only one :ref:`NXcoordinate_system_set` is defined, it should be placed - as high up in the node hierarchy (ideally right below an instance of NXentry) - of the application definition tree as possible. - This :ref:`NXcoordinate_system_set` should define at least one NXcoordinate_system - instance. This shall be named such that it is clear how this coordinate system is - typically referred to in a community. For the NeXus `McStas coordinate system, it is - advised to call it mcstas for the sake of improved clarity. - Additional NXcoordinate_system instances should be specified if possible in that same - :ref:`NXcoordinate_system_set` instead of cluttering them across the tree. - - If this is the case, it is assumed that the NXcoordinate_system_members - overwrite the NeXus default McStas coordinate system, i.e. users can thereby - conveniently and explicitly specify the coordinate system(s) that - they wish to use. - - Users are encouraged to write also explicit and clean depends_on fields in - all groups that encode information about where the interpretation of coordinate - systems is relevant. If these depends_on hints are not provided, it is - automatically assumed that all children (to arbitrary depth) - of that branch and sub-branches below the one in which that - :ref:`NXcoordinate_system_set` is defined use either the only NXcoordinate_system_set - instance in that set or the application definition is considered - underconstrained which should at all costs be avoided and in which case - again McStas is assumed. - * 2 and more; as soon as more than one :ref:`NXcoordinate_system_set` is specified - somewhere in the tree, different interpretations are possible as to which - of these coordinate system sets and instances apply or take preference. - We realize that such ambiguities should at all costs be avoided. - However, the opportunity for multiple sets and their instances enables to - have branch-specific coordinate system conventions which could especially - be useful for deep classes where multiple scientific methods are combined or - cases where having a definition of global translation and conversion tables - how to convert between representations in different coordinate systems - is not desired or available for now. - We argue that having 2 or more :ref:`NXcoordinate_system_set` instances and respective - NXcoordinate_system instances makes the interpretation eventually unnecessary - complicated. Instead, developers of application definitions should always try - to work for clarity and thus use only one top-level coordinate system set. - - For these reasons we conclude that the option with one top-level - :ref:`NXcoordinate_system_set` instance is the preferred choice. - - McStas is used if neither an instance of :ref:`NXcoordinate_system_set` nor an instance - of NXcoordinate_system is specified. However, even in this case it is better - to be explicit like for every other coordinate system definition to support - users with interpreting the content and logic behind every instance of the tree. - - How to store coordinate systems inside :ref:`NXcoordinate_system_set`? - Individual coordinate systems should be specified as members of the - :ref:`NXcoordinate_system_set` instance using instances of NXcoordinate_system. - - How many individual instances of NXcoordinate_system to allow within one - instance of :ref:`NXcoordinate_system_set`? - - * 0; This case should be avoided for the sake of clarity but this case could - mean the authors of the definition meant that McStas is used. We conclude, - McStas is used in this case. - * 1; Like above-mentioned this case has the advantage that it is explicit - and faces no ambiguities. However, in reality typically multiple - coordinate systems have to be mastered especially for complex - multi-signal modality experiments. - * 2 or more; If this case is realized, the best practice is that in every - case where a coordinate system should be referred to the respective class - has a depends_on field which resolves the possible ambiguities which specific - coordinate systems is referred to. The benefit of this explicit and clear - specifying of the coordinate system used in every case is that especially - in combination with having coordinate systems inside deeper branches - makes up for a very versatile, backwards compatible, but powerful system - to express different types of coordinate systems using NeXus. In the case - of two or more instances of NXcoordinate_system in one :ref:`NXcoordinate_system_set`, - it is also advised to specify the relationship between the two coordinate systems by - using the (NXtransformations) group within NXcoordinate_system. - - In effect, 1 should be the preferred choice. However, if more than one coordinate - system is defined for practical purposes, explicit depends_on fields should - always guide the user for each group and field which of the coordinate system - one refers to. - - - - Convention how a positive rotation angle is defined when viewing - from the end of the rotation unit vector towards its origin. - This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - Counter_clockwise is equivalent to a right-handed choice. - Clockwise is equivalent to a left-handed choice. - - - - - - - - - How are rotations interpreted into an orientation according to convention 3 - of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - - How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) - according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - The most frequently used convention is zxz, which is based on the work of H.-J. Bunge - but other conventions are possible. Apart from undefined, proper Euler angles - are distinguished from (improper) Tait-Bryan angles. - - - - - - - - - - - - - - - - - - - To which angular range is the rotation angle argument of an - axis-angle pair parameterization constrained according to - convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - Which sign convention is followed when converting orientations - between different parametrizations/representations according - to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - - - - - Details about eventually relevant named directions that may give reasons for anisotropies. - The classical example is mechanical processing where one has to specify which directions - (e.g. rolling, transverse, and normal direction) align how with the direction of the base - vectors of the sample_reference_frame. - - It is assumed that the configuration is inspected by looking towards the sample surface. - If a detector is involved, it is assumed that the configuration is inspected from a position - that is located behind this detector. - - If any of these assumptions is not met, the user is required to explicitly state this. - - Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the - base vectors of this coordinate system as Xp, Yp, Zp. - - - - - Details about the sample_reference_frame that is typically overlaid onto the surface of the sample. - - It is assumed that the configuration is inspected by looking towards the sample surface. - If a detector is involved, it is assumed that the configuration is inspected from a position - that is located behind this detector. - - If any of these assumptions is not met, the user is required to explicitly state this. - - Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the - base vectors of this coordinate system as Xs, Ys, Zs. - - - - - Details about the detector_reference_frame for a specific detector. - - Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the - base vectors of this coordinate system as Xd, Yd, Zd. - - It is assumed that the configuration is inspected by looking towards the sample surface - from a position that is located behind the detector. - - If any of these assumptions is not met, the user is required to explicitly state this. - - Instances should use detector_reference_frame as a name prefix. - - - diff --git a/contributed_definitions/NXcs_computer.nxdl.xml b/contributed_definitions/NXcs_computer.nxdl.xml deleted file mode 100644 index 3378c51a5c..0000000000 --- a/contributed_definitions/NXcs_computer.nxdl.xml +++ /dev/null @@ -1,145 +0,0 @@ - - - - - - Base class for reporting the description of a computer - - - - Given name/alias to the computing system, e.g. MyDesktop. - - - - - Name of the operating system, e.g. Windows, Linux, Mac, Android. - - - - Version plus build number, commit hash, or description of an ever - persistent resource where the source code of the program and build - instructions can be found so that the program can be configured in - such a manner that the result file is ideally recreatable yielding - the same results. - - - - - - - Ideally a (globally) unique persistent identifier of the computer, i.e. - the Universally Unique Identifier (UUID) of the computing node. - - - - - - Details about the system of processing units e.g. (classical) processing units (CPUs), - coprocessor, graphic cards, accelerator processing units or a system of these. - - - - Granularizing the processing units. Typical examples, a desktop computer - with a single CPU one could describe using one instance of NXcircuit. - A dual-socket server one could describe using two instances NXcircuit - A server with two dual-socket server nodes one could describe with - four instances of NXcircuit surplus a field with their level in the hierarchy. - - - - General type of the processing unit - - - - - - - - - - Given name - - - - - - - Details about the memory system. - - - - Granularizing the components of the memory system. - - - - Qualifier for the type of random access memory. - - - - - - - - - Total amount of data which the medium can hold. - - - - - Given name - - - - - - - Details about the I/O system. - - - - Granularizing the components of the I/O system. - - - - Qualifier for the type of storage medium used. - - - - - - - - - - Total amount of data which the medium can hold. - - - - - Given name - - - - - - diff --git a/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml b/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml deleted file mode 100644 index 23717c288d..0000000000 --- a/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml +++ /dev/null @@ -1,114 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of entries (e.g. number of points or objects). - - - - - Number of bits assumed for the container datatype used. - - - - - Length of mask considering the eventual need for padding. - - - - - Base class for packing and unpacking booleans. - - This base class bookkeeps metadata to inform software about necessary modulo - operations to decode e.g. set membership of objects in sets which are encoded - as a packed array of boolean values. - - One use case is processing of object sets (e.g. point cloud data). If e.g. a - spatial filter has been applied to a set of points we may wish to store - document efficiently which points were analyzed. Array of boolean values - is one option to achieve this. A value is true if the point is included. - The resulting boolean array will be filled with true and false values - in a manner that is often arbitrary and in general case-dependent. - - Especially when the number of points is large, for instance several thousands - or more, some situations can be more efficiently stored if one does not store - the boolean array but just lists the identifiers of the points taken. - - For example, if within a set of 1000 points only one point is included, it would - take (naively) 4000 bits to store the array but only 32 bits to store e.g. the - ID of the single point that is taken. Of course the 4000 bit field is so - sparse that it could be compressed resulting also in a substantial reduction - of the storage demands. Therefore, boolean masks are useful in that - they store compact representation of set memberships. - - This base class can deal with the situation when the number of objects - is not an integer multiple of the bit depth used for storing the states. - - - - Possibility to refer to which set this mask applies. - - If depends_on is not provided, it is assumed that the mask - applies to its direct parent. - - - - - Number of objects represented by the mask. - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The content of the mask. If padding is used, - padding bits have to be set to 0. - - - - - - - - Link to/or array of identifiers for the objects. The decoded mask is - interpreted consecutively, i.e. the first bit in the mask matches - to the first identifier, the second bit in the mask to the second - identifier and so on and so forth. Resolving of identifier follows - the conventions made for depends_on, so consult also the description - of th content to which depends_on refers. - - - - - - diff --git a/contributed_definitions/NXcs_prng.nxdl.xml b/contributed_definitions/NXcs_prng.nxdl.xml deleted file mode 100644 index c5d96bf5dc..0000000000 --- a/contributed_definitions/NXcs_prng.nxdl.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computer science description of pseudo-random number generator. - - The purpose of this base class is to identify if exactly the same sequence - can be reproduced, like for a PRNG or not (for a true physically random source). - - - - Physical approach or algorithm whereby random numbers are generated. - - Different approaches for generating random numbers with a computer exists. - Some use a dedicated physical device whose the state is unpredictable - (physically). Some use a strategy of mangling information from the system - clock. Also in this case the sequence is not reproducible without having - additional pieces of information. - - In most cases though so-called pseudo-random number generator (PRNG) - algorithms are used. These yield a deterministic sequence of practically - randomly appearing numbers. These algorithms differ in their quality in - how close the resulting sequences are random, i.e. sequentially - uncorrelated. Nowadays one of the most commonly used algorithm is the - MersenneTwister (mt19937). - - - - - - - - - - - Name of the PRNG implementation and version. If such information is not - available or if the PRNG type was set to other the DOI to the publication - or the source code should be given. - - - - - Parameter of the PRNG controlling its initialization - and thus controlling the specific sequence generated. - - - - - Number of initial draws from the PRNG after its initialized with the seed. - These initial draws are typically discarded in an effort to equilibrate the - sequence. If no warmup was performed or if warmup procedures are unclear, - users should set the value to zero. - - - - diff --git a/contributed_definitions/NXcs_profiling.nxdl.xml b/contributed_definitions/NXcs_profiling.nxdl.xml deleted file mode 100644 index 206d09daa6..0000000000 --- a/contributed_definitions/NXcs_profiling.nxdl.xml +++ /dev/null @@ -1,149 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computer science description for performance and profiling data of an application. - - Performance monitoring and benchmarking of software is a task where questions - can be asked at various levels of detail. In general, there are three main - contributions to performance: - - * Hardware capabilities and configuration - * Software configuration and capabilities - * Dynamic effects of the system in operation and the system working together - with eventually multiple computers, especially when these have to exchange - information across a network and these are used usually by multiple users. - - At the most basic level users may wish to document how long e.g. a data - analysis with a scientific software (app) took. - A frequent idea is here to answer practical questions like how critical is the - effect on the workflow of the scientists, i.e. is the analysis possible in - a few seconds or would it take days if I were to run this analysis on a - comparable machine? - For this more qualitative performance monitoring, mainly the order of - magnitude is relevant, as well as how this was achieved using parallelization - (i.e. reporting the number of CPU and GPU resources used, the number of - processes and threads configured, and providing basic details about the computer). - - At more advanced levels benchmarks may go as deep as detailed temporal tracking - of individual processor instructions, their relation to other instructions, the - state of call stacks; in short eventually the entire app execution history - and hardware state history. Such analyses are mainly used for performance - optimization, i.e. by software and hardware developers as well as for - tracking bugs. Specialized software exists which documents such performance - data in specifically-formatted event log files or databases. - - This base class cannot and should not replace these specific solutions for now. - Instead, the intention of the base class is to serve scientists at the - basic level to enable simple monitoring of performance data and log profiling - data of key algorithmic steps or parts of computational workflows, so that - these pieces of information can guide users which order of magnitude differences - should be expected or not. - - Developers of application definitions should add additional fields and - references to e.g. more detailed performance data to which they wish to link - the metadata in this base class. - - - - - Path to the directory from which the tool was called. - - - - - Command line call with arguments if applicable. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the app was started. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the app terminated or crashed. - - - - - Wall-clock time how long the app execution took. This may be in principle - end_time minus start_time; however usage of eventually more precise timers - may warrant to use a finer temporal discretization, - and thus demands a more precise record of the wall-clock time. - - - - - Qualifier which specifies with how many nominal processes the app was - invoked. The main idea behind this field e.g. for apps which use e.g. MPI - (Message Passing Interface) parallelization is to communicate - how many processes were used. - - For sequentially running apps number_of_processes and number_of_threads - is 1. If the app uses exclusively GPU parallelization number_of_gpus - can be larger than 1. If no GPU is used number_of_gpus is 0 even though - the hardware may have GPUs installed, thus indicating these were not - used though. - - - - - Qualifier how many nominal threads were used at runtime. - Specifically here the maximum number of threads used for the - high-level threading library used (e.g. OMP_NUM_THREADS), posix. - - - - - Qualifier with how many nominal GPUs the app was invoked at runtime. - - - - - - A collection with one or more computing nodes each with own resources. - This can be as simple as a laptop or the nodes of a cluster computer. - - - - - A collection of individual profiling event data which detail e.g. how - much time the app took for certain computational steps and/or how much - memory was consumed during these operations. - - - - diff --git a/contributed_definitions/NXdelocalization.nxdl.xml b/contributed_definitions/NXdelocalization.nxdl.xml index b1e3915218..9b3cfb7ce1 100644 --- a/contributed_definitions/NXdelocalization.nxdl.xml +++ b/contributed_definitions/NXdelocalization.nxdl.xml @@ -1,4 +1,4 @@ - + - - - Application definition for normalized representation of electron microscopy research. - - This application definition is a comprehensive example for a general description - with which to normalize specific (meta)data collected from the research field - of electron microscopy - - NXem is designed to be used for documenting experiments or computer simulations in which - controlled electron beams are used for studying electron-beam matter interaction to explore - physical mechanisms and phenomena or to characterize materials with an electron microscope. - - - - - - - - - - - The configuration of the software that was used to generate this NeXus file. - - - - A collection of all programs and libraries that are considered as relevant - to understand with which software tools this NeXus file instance was - generated. Ideally, to enable a binary recreation from the input data. - - Examples include the name and version of the libraries used to write the - instance. Ideally, the software which writes these NXprogram instances - also includes the version of the set of NeXus classes i.e. the specific set - of base classes, application definitions, and contributed definitions - with which the here described concepts can be resolved. - - For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ - which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ - research data management system, it makes sense to store e.g. the GitHub - repository commit and respective submodule references used. - - Instances can also be used to document the modules and libraries that - are offered by the computational environment such as those parsed - from conda or python virtualenv environments. - - - - - - - - - Alias (short name) which scientists can use to refer to this experiment. - - - - - Free-text description about the experiment. - - Users are strongly advised to parameterize the description of their experiment - by using respective groups and fields and base classes instead of writing prose - into the field. The reason is that such free-text field is difficult to machine-interpret. - The motivation behind keeping this field for now is to learn in how far the - current base classes need extension based on user feedback. - - - - - ISO 8601 time code with local time zone offset to UTC information included - when the microscope session started. If the application demands that time - codes in this section of the application definition should only be used - for specifying when the experiment was performed - and the exact - duration is not relevant - use this start_time field. - - Often though it is useful to specify a time interval via setting both a start_time - and an end_time because this enables software tools and users to collect a - more detailed bookkeeping of the experiment. - - Users should be aware though that even using only start_time and end_time - may not be sufficient to infer how long the experiment took or for how long - data were acquired. To bookkeep more fine-grained timestamps over the - course of the experiment is possible with start_time and end_time fields - of respective :ref:`NXevent_data_em` instances. - - - - - ISO 8601 time code with local time zone offset to UTC included when - the microscope session ended. - - See docstring of the start_time field to see how to use the - start_time and end_time together. - - - - - - Collection of serialized resources associated with the experiment. - - An example how to use this set is to document from which files in formatting - of technology partners, the (meta)data in an instance of NXem were filled with - during parsing to NeXus. - - - - - - - - - Information about persons who performed or were involved in the microscope - session or simulation run. - - Examples could be to put here the principle investigator who performed this - experiment or students who performed simulations to name but a few. - Adding multiple users if relevant is recommended. - - The protection of personal data by laws is in different stages of development - and strictness. Therefore, the existence of user data has not been made - required. - - Instances should use user as a name prefix. - - - - - - - Given (first) name and surname. - - - - - Name of the affiliation at the point in time when the experiment was performed. - - - - - Postal address of the affiliation. - - - - - Email address at the point in time when the experiment was performed. - - Writing the most permanently used email is recommended. - - - - - Telephone number at the point in time when the experiment was performed. - - - - - User role at the point in time when the experiment was performed. - - Examples are technician operating the microscope, student, postdoc, - principle investigator, or guest. - - - - - - A physical entity which contains material intended to be investigated. - Sample and specimen are treated as de facto synonyms. - Samples can be real or virtual ones as annotated via is_simulation. - - The suggested best practice is to call this group sample. In those cases when - multiple samples need to be grouped inside one entry, these SAMPLE groups - should be named using the prefix sample followed an index starting from 1, i.e. - (sample1, sample2). - - There are at least two strategies how to store (meta)data when one analyzes multiple - samples - not different ROIs on a single sample though - in one session. - - One strategy is to store each sample and its results under an own NXem/ENTRY. - This is one of the most frequent use cases as during most sessions typically only a - single sample is investigated. In this case the name of this group should be NXem/ENTRY/sample. - - If multiple samples are investigated storing each of them in an own ENTRY group eventually will - demand an unnecessary duplication though of many details about the instrument. - - This can be avoided by using another strategy how to store all samples and their results. - Namely, by using only one instance of NXem/ENTRY. That NXem/ENTRY should then be named, - like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., - i.e. instances should use sample as a name prefix. - - In this case though the collection of events demands to use identifier_sample to state clearly - for which of the samples loaded the (characterization) event was detected. - - This concept is related to term `Specimen`_ of the EMglossary standard. - - .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 - - - - Qualifier whether the sample is a real (in which case is_simulation should be set to false) - or a virtual one (in which case is_simulation should be set to true). - - - - - - - - - - - - - Ideally, (globally) unique persistent identifier which distinguishes this sample from all others - and especially the predecessor/origin from where that sample was cut. The terms sample - and specimen are here considered as exact synonyms. - - This field must not be used for an alias for the sample! Instead, use name. - - In cases where multiple specimens were loaded into the microscope, the identifier has to resolve - the specific sample, whose results are stored by this :ref:`NXentry` instance because a single - NXentry should be used for the characterization of a single specimen. - - Details about the specimen preparation should be stored in resources referring to identifier_parent. - - - - - - Identifier of the sample from which the sample was cut or the string *None*, - i.e. the parent to this sample. - - The purpose of this field is to support functionalities for tracking - sample provenance in a research data management system. - - - - - - ISO 8601 time code with local time zone offset to UTC information - when the specimen was prepared. - - Ideally, report the end of the preparation, i.e. the last known timestamp when - the measured specimen surface was actively prepared. Ideally, this matches - the last timestamp that is mentioned in the digital resource pointed to by - identifier_parent. - - Knowing when the specimen was exposed to e.g. specific atmosphere is especially - required for material that is sensitive to the environment such as specimens that were - charged with fast diffusing elements or short-lived radioactive tracers. - - Additional time stamps prior to preparation_date should better be placed in resources - which describe but do not pollute the description here with prose. Resolving these - connected metadata is considered as within the responsibility of the - research data management system and not the a NeXus file. - - - - - An alias used to refer to the specimen to please readability for humans. - - - - - List of comma-separated elements from the periodic table that are contained in the sample. - If the sample substance has multiple components, all elements from each component - must be included in atom_types. - - The purpose of the field is to offer research data management systems an opportunity - to parse the relevant elements without having to interpret these from the resources - pointed to by identifier_parent or walk through eventually deeply nested groups in - individual data instances. - - - - - (Measured) sample thickness. - - The information is recorded to qualify if the beam used was likely - able to shine through the specimen. For scanning electron microscopy, - in many cases the specimen is typically thicker than what is - illuminatable by the electron beam. - - In this case the value should be set to the actual thickness of the specimen - viewed for an illumination situation where the nominal surface normal of the - specimen is parallel to the optical axis. - - - - - (Measured) density of the specimen. - - For multi-layered specimens this field should only be used to describe - the density of the excited volume. For scanning electron microscopy - the usage of this field is discouraged and instead an instance of a region-of-interest within connection to individual :ref:`NXevent_data_em` - instances can provide a cleaner description of the relevant details - why one may wish to store the density of the specimen. - - - - - Discouraged free-text field to provide further detail. - - - - - - The conventions used when reporting crystal orientations. - We follow the best practices of the Material Science community - that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - Convention how a positive rotation angle is defined when viewing - from the end of the rotation unit vector towards its origin. - This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - Counter_clockwise is equivalent to a right-handed choice. - Clockwise is equivalent to a left-handed choice. - - - - - - - - - How are rotations interpreted into an orientation according to convention 3 - of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - - How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) - according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - The most frequently used convention is zxz, which is based on the work of H.-J. Bunge - but other conventions are possible. Apart from undefined, proper Euler angles - are distinguished from (improper) Tait-Bryan angles. - - - - - - - - - - - - - - - - - - - To which angular range is the rotation angle argument of an - axis-angle pair parameterization constrained according to - convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - Which sign convention is followed when converting orientations - between different parametrizations/representations according - to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. - - - - - - - - - - - - - - - - - - - - Location of the origin of the processing_reference_frame. - - It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. - Edges are interpreted by inspecting the direction of their outer unit normals - (which point either parallel or antiparallel) along respective base vector direction - of the reference frame. - - If any of these assumptions is not met, the user is required to explicitly state this. - - - - - - - - - - - - - - - Direction of the positively pointing x-axis base vector of the - processing_reference_frame. - - - - - - - - - - - - - Direction of the positively pointing y-axis base vector of the - processing_reference_frame. - - - - - - - - - - - - - Direction of the positively pointing z-axis base vector of the - processing_reference_frame. - - - - - - - - - - - - - - - Reference to the specifically named :ref:`NXsample` instance(s) for - which these conventions apply (e.g. /entry1/sample1). - - - - - - - - Location of the origin of the sample_reference_frame. - - It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. - Edges are interpreted by inspecting the direction of their outer unit normals - (which point either parallel or antiparallel) along respective base vector direction - of the reference frame. - - If any of these assumptions is not met, the user is required to explicitly state this. - - - - - - - - - - - - - - - Direction of the positively pointing x-axis base vector of the - sample_reference_frame. - - - - - - - - - - - - - Direction of the positively pointing y-axis base vector of the - sample_reference_frame. - - - - - - - - - - - - - Direction of the positively pointing z-axis base vector of the - sample_reference_frame. - - - - - - - - - - - - - - Instances should use detector_reference_frame as a name prefix. - - - - Reference to the specifically named :ref:`NXdetector` instance for - which these conventions apply (e.g. /entry1/instrument/detector1). - - Instances should use detector_reference_frame as a name prefix. - - - - - - - - Location of the origin of the detector_reference_frame. - - If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted - by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) - along respective base vector direction of the reference frame. - - If any of these assumptions is not met, the user is required to explicitly state this. - - - - - - - - - - - - - - - Direction of the positively pointing x-axis base vector of the - detector_reference_frame. - - - - - - - - - - - - - Direction of the positively pointing y-axis base vector of the - detector_reference_frame. - - - - - - - - - - - - - Direction of the positively pointing z-axis base vector of the - detector_reference_frame. - - - - - - - - - - - - - - - - - - - - - - - - - Details about the control program used for operating the microscope. - - Instances should use control_software as a name prefix. - - - - - - - - - - - - - - - - - - - - - - - - Instances should use lens as a name prefix. - - - - - - - - - - - Instances should use aperture as a name prefix. - - - - - - - - - - - Instances should use monochromator as a name prefix. - - - - - - - - - - - - - - - - - - - - - - - - - Instances should use biprism as a name prefix. - - - - - - - - - - Instances should use phaseplate as a name prefix. - - - - - - - - - - - Instances should use sensor as a name prefix. - - - - - Instances should use actuator as a name prefix. - - - - - Instances should use beam as a name prefix. - - - - - Instances should use deflector as a name prefix. - - - - - - - - - - - - - - - - - - - - - - Instances should use lens as a name prefix. - - - - - - - - - - - Instances should use aperture as a name prefix. - - - - - - - - - - - Instances should use monochromator as a name prefix. - - - - - - - - - - - Instances should use sensor as a name prefix. - - - - - Instances should use actuator as a name prefix. - - - - - Instances should use beam as a name prefix. - - - - - Instances should use deflector as a name prefix. - - - - - - Instances should use detector as a name prefix. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Instances should use pump as a name prefix. - - - - - - Instances should use sensor as a name prefix. - - - - - Instances should use actuator as a name prefix. - - - - - - - This group should be used to store all event-related (meta)data, - which are typically measured datasets like images and spectra. - To avoid that static instrument-related metadata need to be stored - repetitively the NXem application definitions splits the storage of the - dynamic (meta)data that typically change for each image and spectrum - from the static one. - - - - Instances should use event as a name prefix. - - - - - - - - Instances should use image as a name prefix. - Each NXimage instance must use only one image or stack instance. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Instances should use spectrum as a name prefix. - Each NXspectrum instance must use only one spectrum or stack instance. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Instances should use lens as a name prefix. - - - - - - Instances should use aperture as a name prefix. - - - - Descriptor for the aperture setting when the exact technical details - are unknown or not directly controllable as the control software of - the microscope does not enable or was not configured to display these - values for users. - - - - - - - Instances should use monochromator as a name prefix. - - - - - - - - - - - - Instances should use tableau as a name prefix. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Instances should use sensor as a name prefix. - - - - - Instances should use actuator as a name prefix. - - - - - Instances should use beam as a name prefix. - - - - - Instances should use deflector as a name prefix. - - - - - - - - - - - - Instances should use lens as a name prefix. - - - - - - Instances should use aperture as a name prefix. - - - - Descriptor for the aperture setting when the exact technical details - are unknown or not directly controllable as the control software of - the microscope does not enable or was not configured to display these - values for users. - - - - - - Instances should use monochromator as a name prefix. - - - - - - Instances should use sensor as a name prefix. - - - - - Instances should use actuator as a name prefix. - - - - - Instances should use beam as a name prefix. - - - - - Instances should use deflector as a name prefix. - - - - - - Instances should use detector as a name prefix. - - - - Operation mode of the detector as displayed by the control software. - - - - - - - - - - Instances should use sensor as a name prefix. - - - - - Instances should use actuator as a name prefix. - - - - - - - - - - - - - Nominal current of the heater. - - - - - Nominal voltage of the heater. - - - - - - - - - - - - - - Possibility for documenting a set of simulations of electron beam matter interaction. - - Instances should use simulation as a name prefix. - - - - The program with which the simulation was performed. - - - - - - - - Programs and libraries representing the computational environment - - - - - - - - - - Configuration of the simulation - - - - - Results of the simulation - - - - - - Description of the volume of interaction between of particle-matter interaction. - - Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam - interaction simulations can be used to qualify and (or) quantify the shape of - the interaction volume. Results of such simulations can be summary statistics - or single-particle-resolved sets of trajectories. - - Explicit or implicit descriptions of the geometry of this - interaction volume are possible: - - * An implicit description is via a set of electron/specimen interactions - represented ideally as trajectory data from the computer simulation. - * An explicit description is via iso-contour surface using either - a simulation grid or a triangulated surface mesh of the approximated - iso-contour surface evaluated at specific threshold values. - Iso-contours could be computed from electron or particle flux through - an imaginary control surface (the iso-surface) or energy-levels - (e.g. the case of X-rays). Details depend on the model. - * Another explicit description is via theoretical models which may - be relevant e.g. for X-ray spectroscopy - - Further details on how the interaction volume can be quantified - is available in the literature for example: - - * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ - * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ - * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ - - Instances should use interaction_volume as a name prefix. - - - - - - - - - - A region-of-interest analyzed either during or after the session for which specific - processed data are available. Instances should use roi as a name prefix. - - This concept is related to term `Region Of Interest`_ of the EMglossary standard. - - .. _Region Of Interest: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 - - - - - - Instances should use image as a name prefix. - Each NXimage instance must use only one image or stack instance. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Instances should use phase as a name prefix. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/contributed_definitions/NXem_calorimetry.nxdl.xml b/contributed_definitions/NXem_calorimetry.nxdl.xml index 1e762e1687..a095cc0780 100644 --- a/contributed_definitions/NXem_calorimetry.nxdl.xml +++ b/contributed_definitions/NXem_calorimetry.nxdl.xml @@ -1,4 +1,4 @@ - + + Details about performance, profiling, etc. @@ -82,7 +83,7 @@ are aligned with what and how to name things--> - + Programs and libraries representing the computational environment @@ -94,14 +95,11 @@ are aligned with what and how to name things--> - + - A qualifier whether the sample is a real one or a virtual one. + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). - - - - @@ -112,8 +110,7 @@ are aligned with what and how to name things--> The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by identifier_parent or walk through - eventually deeply nested groups in data instances. + these from the resources. @@ -167,7 +164,7 @@ are aligned with what and how to name things--> delta_time. - + @@ -193,18 +190,18 @@ Timestamp that is used for each diffraction pattern to correlate the results obtained from that pattern with associated actuator data. ISO8601 with local time zone information if possible and as precise as practically possible. The indices follow the same order as -used for identifier_pattern. +used for indices_pattern. dim: (n_p,)--> - Computation of the centre for each pattern using e.g. a Circular Hough + Computation of the center for each pattern using e.g. a Circular Hough Transformation. - Computed centre for each pattern. + Computed center for each pattern. @@ -215,7 +212,7 @@ dim: (n_p,)--> - Elliptical distortion correction as a step when computing the centre for + Elliptical distortion correction as a step when computing the center for patterns. @@ -223,7 +220,7 @@ dim: (n_p,)--> NXcg_ellipsoid--> - Computed centre for each pattern. + Computed center for each pattern. @@ -234,7 +231,7 @@ NXcg_ellipsoid--> - Integrated diffraction pattern intensity as a function of radial distance from the centre + Integrated diffraction pattern intensity as a function of radial distance from the center azimuthally integrated as a function of time. @@ -253,7 +250,7 @@ NXcg_ellipsoid--> Integrated intensity as a function of time and the radial distance from the - pattern centre. + pattern center. @@ -261,7 +258,7 @@ NXcg_ellipsoid--> - + Identifier for each pattern. diff --git a/contributed_definitions/NXevent_data_apm.nxdl.xml b/contributed_definitions/NXevent_data_apm.nxdl.xml deleted file mode 100644 index 80b0f7daf6..0000000000 --- a/contributed_definitions/NXevent_data_apm.nxdl.xml +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of pulses collected in between start_time and end_time. - - - - - Base class to store state and (meta)data of events over the course of an atom probe experiment. - - Having at least one instance for an instance of NXapm is recommended. - - This base class applies the concept of the NXevent_data_em base class to the specific needs - of atom probe research. Against static and dynamic quantities are split to avoid a duplication - of information. Specifically, the time interval considered is the entire time - starting at start_time until end_time during which we assume the pulser triggered named pulses. - These pulses are identified via the identifier_pulse field. The point in time when each was issued - is specified via the combination of start_time and delta_time. - - Conceptually and technically NeXus currently stores tensorial information as arrays of values - (with each value of the same datatype). For instance, a field temperature(NX_FLOAT) stores - a set of temperature values but that field when used somewhere is a concept. However, that - concept has no information at which point in time these temperatures were taken. - An existent functional relationship between the two concepts is not defined. - - However, a correct interpretation of the temperature values demands knowledge about what is - the independent quantity on which temperature depends on or according to which frequency - temperature values were sampled. - In NeXus there are two approaches which cope with such correlations: - One is :ref:`NXdata` where the attribute signal specifies the correlation. - The other one is :ref:`NXlog` which, like NXdata, demands to granularize logged_against - (dependent signal) and independent quantities into an own group. - In many cases this additional grouping is not desired though. - - One naive solution typically employed is then to store the independent variable values via a second - vector e.g. time_stamp with the same number of entries (with dimensionality defined through symbols). - However, there is no independent logical connection between these two concepts, i.e. temperature - and time_stamp. - - In the case of atom probe though the time that one would use in NXlog is defined implicitly via identifier_pulse, - which is the independent variable vector against which eventually dozens of channels of data are logged. - Not only are these channels logged they should ideally also be self-descriptive in that these channels have - identifier_pulse as the independent variable but we do not wish to duplicate this information all the time but - reference it. - - Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the - symbol depends_on but this is easily to be confused with depends_on that is used for instances of - :ref:`NXtransformations`. Consequently, if depends_on were to be used extra logic is needed by consuming - applications to understand that the here build correlations are conceptually different ones. - - This issue should be discussed further by the NeXus community. - - - - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval started. If the user wishes to specify an - interval of time that the snapshot should represent during which the instrument - was stable and configured using specific settings and calibrations, - the start_time is the start (left bound of the time interval) while - the end_time specifies the end (right bound) of the time interval. - - - - - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval ended. - - - - - Delta time array which resolves for each identifier_pulse the time difference - between when that pulse was issued and start_time. - - In summary, using start_time, end_time, delta_time, identifier_pulse_offset, - and identifier_pulse exactly specifies the connection between when a pulse was - issued relative to start and absolute in UTC. - - - - - - - - Integer used to name the first pulse to know if there is an - offset of the identifiers to zero. - - Identifiers can be defined either implicitly or explicitly. - For implicit indexing identifiers are defined on the interval - :math:`[identifier\_offset, identifier\_offset + c - 1]`. - - Therefore, implicit identifier are completely defined by the value of - identifier_offset and cardinality. For example if identifier run from - -2 to 3 the value for identifier_offset is -2. - - For explicit indexing the field identifier has to be used. - Fortran-/Matlab- and C-/Python-style indexing have specific implicit - identifier conventions where identifier_offset is 1 and 0 respectively. - - - - - Identifier that contextualizes how the detector and pulser of an atom probe - instrument follows a sequence of pulses to trigger field evaporation. - - The identifier_pulse is used to associate thus an information about time - when quantities have been collected via sampling. - - In virtually all cases the pulser is a blackbox. Depending on how the - instrument is configured during a measurement the target - values and thus also the actual values may change. - - Maybe the first part of the experiment is run at a certain pulse fraction but thereafter - the pulse_fraction is changed. In this case the field pulse_fraction is a vector which - collects all measured values of the pulse_fraction, identifier_pulse is then an equally - long vector which stores the set of events (e.g. pulsing events) when that value was - measured. - - This may cause several situations: In the case that e.g. the pulse_fraction is never changed - and also exact details not interesting, one stores the set value for the pulse_fraction - and a single value for the identifier_pulse e.g. 0 to indicate that the pulse_fraction was set - at the beginning and it was maintained constant during the measurement. - If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a - vector with two values one for the first and another one for the value from the 100000-th - pulse onwards. The values of identifier_pulse are then [0, 99999] respectively. - - - - - - - diff --git a/contributed_definitions/NXibeam_column.nxdl.xml b/contributed_definitions/NXibeam_column.nxdl.xml deleted file mode 100644 index 24d14b47a8..0000000000 --- a/contributed_definitions/NXibeam_column.nxdl.xml +++ /dev/null @@ -1,134 +0,0 @@ - - - - - - - Base class for a set of components equipping an instrument with FIB capabilities. - - Focused-ion-beam (FIB) capabilities turn especially scanning electron microscopes - into specimen preparation labs. FIB is a material preparation technique whereby - portions of the sample are illuminated with a focused ion beam with controlled - intensity. The beam is intense enough and with sufficient ion momentum to - remove material in a controlled manner. - - The fact that an electron microscope with FIB capabilities has needs a - second gun with own relevant control circuits, focusing lenses, and other - components, warrants the definition of an own base class to group these - components and distinguish them from the lenses and components for creating - and shaping the electron beam. - - For more details about the relevant physics and application examples - consult the literature, for example: - - * `L. A. Giannuzzi et al. <https://doi.org/10.1007/b101190>`_ - * `E. I. Preiß et al. <https://link.springer.com/content/pdf/10.1557/s43578-020-00045-w.pdf>`_ - * `J. F. Ziegler et al. <https://www.sciencedirect.com/science/article/pii/S0168583X10001862>`_ - * `J. Lili <https://www.osti.gov/servlets/purl/924801>`_ - - - - The source which creates the ion beam. - - - - Given name/alias for the ion gun. - - - - - Emitter type used to create the ion beam. - - If the emitter type is other, give further - details in the description field. - - - - - - - - - - - Ideally, a (globally) unique persistent identifier, link, - or text to a resource which gives further details. - - - - - Which ionized elements or molecular ions form the beam. - Examples are gallium, helium, neon, argon, krypton, - or xenon, O2+. - - - - - Average/nominal flux - - - - - Average/nominal brightness - - - - - - Charge current - - - - - Ion acceleration voltage upon source exit and - entering the vacuum flight path. - - - - - To be defined more specifically. Community suggestions are welcome. - - - - - - - - - - - - - Individual characterization results for the position, shape, - and characteristics of the ion beam. - - :ref:`NXtransformations` should be used to specify the location or position - at which details about the ion beam are probed. - - - - - diff --git a/contributed_definitions/NXion.nxdl.xml b/contributed_definitions/NXion.nxdl.xml deleted file mode 100644 index 02c6812fab..0000000000 --- a/contributed_definitions/NXion.nxdl.xml +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Maximum number of atoms/isotopes allowed per (molecular) ion (fragment). - - - - - Number of mass-to-charge-state-ratio range intervals for ion type. - - - - - Base class for documenting the set of atoms of a (molecular) ion. - - - - A unique identifier whereby such an ion can be referred to - via the service offered as described in identifier_type. - - - - - How can the identifier be resolved? - - - - - - - - Ion type (ion species) identifier. - - The identifier zero is reserved for the special unknown ion type. - - - - - Vector of nuclide hash values. - - Individual hash values :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - encode the number of protons :math:`Z` and the number of neutrons :math:`N` - of each nuclide respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - - The array is sorted in decreasing order. For the rationale behind this see `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - - - Table which decodes the entries in nuclide_hash into a human-readable matrix of instances. - The first column specifies the nuclide mass number, i.e. using the hashvalues - from the isotope_vector this is :math:`Z + N` or 0. The value 0 documents that no - isotope-specific information about the element encoded is relevant. - The second row specifies the number of protons :math:`Z` or 0. - The value 0 in this case documents a placeholder or that no element-specific - information is relevant. - Taking a carbon-14 nuclide as an example the mass number is 14. - That is encoded as a value pair (14, 6) as one row of the table. - - Therefore, this notation is the typical superscribed nuclide mass number - and subscripted number of protons element notation e.g. :math:`^{14}C`. - The array is stored matching the order of nuclide_hash. - - - - - - - - - - Assumed volume of the ion. - - In atom probe microscopy this field can be used to store the reconstructed - volume per ion (average) which is typically stored alongside ranging - definitions. - - - - - Charge of the ion. - - - - - Signed charge state of the ion in multiples of electron charge. - - In the example of atom probe microscopy, only positive values will be measured - as the ions are accelerated by a negatively signed bias electric field. - In the case that the charge state is not explicitly recoverable, the value should - be set to zero. - - In atom probe microscopy this is for example the case when using - classical ranging definition files in formats like RNG, RRNG. - These file formats do not document the charge state explicitly - but the number of atoms of each element per molecular ion - surplus the mass-to-charge-state-ratio interval. - Details on ranging definition files can be found in the literature: - `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ - - - - - Human-readable ion type name (e.g. Al +++) - The string should consists of UTF-8 characters, ideally using LaTeX - notation to specify the isotopes, ions, and charge state. - Examples are 12C + or Al +++. - - To ease automated parsing, isotope_vector should be the - preferred machine-readable information used. - - - - - Associated lower (mqmin) and upper (mqmax) bounds of the - mass-to-charge-state ratio interval(s) [mqmin, mqmax] - (boundaries inclusive). This field is primarily of interest - for documenting :ref:`NXprocess` steps of indexing a - ToF/mass-to-charge state histogram. - - - - - - - diff --git a/contributed_definitions/NXisocontour.nxdl.xml b/contributed_definitions/NXisocontour.nxdl.xml index 3c2cb16c48..eace731923 100644 --- a/contributed_definitions/NXisocontour.nxdl.xml +++ b/contributed_definitions/NXisocontour.nxdl.xml @@ -1,4 +1,4 @@ - + - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Grinding and polishing of a sample using abrasives in a wet lab. - Manual procedures, electro-chemical, vibropolishing. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - - - - - - - - - - A preparation step performed by a human or a robot/automated system. - - - - - - - - Carrier/plate used on which the abrasive/(lubricant) mixture was applied. - - - - - - Medium on the abrasive_medium_carrier (cloth or grinding plate) - whereby material is abrasively weared. - - - - - - Lubricant - - - - - - Qualitative statement how the revelation of the machine was configured. - If the rotation was controlled manually, e.g. by turning knobs - choose manual and estimate the nominal average rotation. - If the rotation was controlled via choosing from a fixed set - of options offered by the machine choose fixed and - specify the nominal rotation. - If programmed use rotation_history (e.g. for automated/robot systems). - - - - - - - - - - - Qualitative statement how the (piston) force with which the sample - was pressed into/against the abrasive medium was controlled if at all. - If the force was controlled manually e.g. by turning knobs - choose manual and estimate nominal average force. - If the force was controlled via choosing from a fixed set - of options offered by the machine choose fixed and - specify the nominal force. - If programmed use force_history (e.g. for automated/robot systems). - - - - - - - - - - - Qualitative statement for how long (assuming regular uninterrupted) - preparation at the specified conditions the preparation step was - applied. - - - - - - - - - - - Turns per unit time. - - - - - - Force exerted on the sample to press it into the abrasive. - - - - - - Seconds - - - - - Qualitative statement how the material removal was characterized. - - - - - - - - - - How thick a layer was removed. - - - - - - - A preparation step performed by a human or a robot/automated system - with the aim to remove residual abrasive medium from the specimen surface. - - - - - diff --git a/contributed_definitions/NXlab_sample_mounting.nxdl.xml b/contributed_definitions/NXlab_sample_mounting.nxdl.xml deleted file mode 100644 index 88d753c106..0000000000 --- a/contributed_definitions/NXlab_sample_mounting.nxdl.xml +++ /dev/null @@ -1,93 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Embedding of a sample in a medium for easing processability. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - - - - - - - - - - Qualitative statement how the sample was mounted. - - - - - - - - - Type of material. - - - - - - - - - Electrical conductivity of the embedding medium. - - - - - diff --git a/contributed_definitions/NXlockin.nxdl.xml b/contributed_definitions/NXlockin.nxdl.xml index 1a4acfdf8f..a0d0081667 100644 --- a/contributed_definitions/NXlockin.nxdl.xml +++ b/contributed_definitions/NXlockin.nxdl.xml @@ -1,4 +1,4 @@ - + @@ -101,57 +121,83 @@ The number of line defects.--> Whether one uses a continuum or atomic scale description of materials, these are always a model only of the true internal structure of a material. Such models are useful as they enable a coarse-graining and categorizing of properties and representational aspects from which measured or simulated descriptions - can be correlated with properties, i.e. descriptor values. + can be correlated with properties, i.e. descriptor values. The base class here can be used to describe + the structural aspect of a region-of-interest for a specimen that was investigated or a computer + simulation that was performed for a virtual specimen. - Keep in mind that most specimens are thermo-chemo-mechanically processed prior characterization. - Therefore, the characterized microstructure may not have probed the same structure as of the untreated + Specimens experience thermo-chemo-mechanical processing (steps) before characterization. Therefore, + the characterized microstructure may not turn out to be the same structure as of the untreated sample from which the region-of-interests on the specimen were sampled. Fields such as time and increment enable a quantification of the spatiotemporal evolution of a materials' structure by using multiple instances of NXmicrostructure. Both measurements and simulation virtually - always sample this evolution. Most microscopy techniques support to generate only a two-dimensional - representation (projection) of the characterized material. Often materials are characterized only for - specific states or via sampling coarsely in time relative to the timescale at which the - physical phenomena take place. This is typically a compromise between the research questions at hand and technical surplus practical limitations. + always sample this evolution. Most microscopy techniques characterize only a two-dimensional representation + (projection) of the characterized material volume. Often materials are characterized only for specific states + or via sampling coarsely in time relative to the timescale at which the physical phenomena take place. + This is typically a compromise between the research questions and technical surplus practical limitations. - The term microstructural feature covers here crystals and all sorts of crystal defects within the material. - A key challenge with the description of representations and properties of microstructural features is that - features with different dimensionality exist and combinations of features of different dimensionality are - frequently expected to be documented with intuitive naming conventions using flat property lists. - For these key-value dictionaries often folksonomies are used. These can be based on ad hoc documentation - of such dictionaries in the literature and the metadata section of public data repositories. + The term microstructural feature covers here crystals and all sorts of crystal defects within the material + (interfaces, triple junctions, dislocations, pores, etc.). + A key challenge with the description of representations and properties of such microstructural features is that + they can be represented and view as features with different dimensionality. Furthermore, combinations of features of + different dimensionality are frequently expected to be documented with intuitive naming conventions when + flat property lists are used. For these key-value dictionaries often folksonomies are used. These can be based + on ad hoc documentation of such dictionaries in the literature and the metadata section of public data repositories. NXmicrostructure is an attempt to standardize these descriptions stronger. - The descriptive variety is large especially for junctions. Like crystals and interfaces, junctions are features in - three-dimensional Euclidean space even if they are formed maybe only through a monolayer or pearl chain of atoms. - Either way the local atomic and electronic environment is different compared to the situation of an ideal crystal, - which gives typically rise to a plethora of configurations of which some yield useful properties. + For crystals the number of typically used technical terms are smaller than for interfaces or line like defects and + junctions of different types of crystal defects. The term grain describes a contiguous region of material that is + delineated by interfaces (phase or grain boundaries). With its origin motivated by light optical microscopy though + a grain is not necessarily a single crystal but can have an internal structure of defect such as dislocations. + In this base class we use the term and respective group crystals though for single crystals and grains. + The reason why this is possible is that when e.g. materials engineers talk about grains they inherently assume + that the internal structure of these grains can be described with homogenized effective properties. + If alternatively the individual structural crystalline or features of this grain should be distinguished + it is useful to instantiate these as individual instances of crystals. + + Grain boundaries and phase boundaries are two main categories of interfaces. + A grain boundary delineates two regions with similar crystal structure and phase but different orientation. + A grain boundary is thus a homophase interface. By contrast, a heterophase boundary delineates two regions with typically + but not necessarily dissimilar crystal structure but a different atomic occupation that justifies to distinguish two + phases. There is a substantial variety of interfaces whose distinction was classically based on geometrical arguments + but considers that atomic segregation is an equally important structural aspect to consider when classifying grain + boundaries. A concise overview on theoretical aspect of and the semantics for characterizing interfaces and their properties + is provided in e.g. `W. Bollmann <https://doi.org/10.1007/978-3-642-49173-3>`_ and A. Sutton and R. W. Baluffi, + Interfaces in Crystalline Materials, Clarendon Press, ISBN 9780198500612. + + Also for junctions between crystal defects there is a considerable variety of terms. Junctions are features in + three-dimensional Euclidean space even if they are formed maybe only through a monolayer or a pearl chain of atoms. + Either way their local atomic and electronic environment is different compared to the situation of an ideal crystal, + or the adjoining defects, which gives typically rise to a plethora of configurations of which some yield useful material + properties or affect material properties. Like crystals and interfaces, junctions are assumed to represent groups of atoms that have specific descriptor values which are different to other features. Taking an example, a triple junction is practically a three-dimensional defect as its atoms are arranged in three-dimensional space but the characteristics of that defect can often be reduced to a lower-dimensional - description such as a triple point or a triple line. Therefore, different representations can be used to describe the location, - shape, and structure of the defect. As different types of crystal defects can interact, there is a substantial number of - in principle characterizable and representable objects. Take again a triple line as an example. It is a tubular feature built from three - adjoining interfaces. However, dislocations as line defects can interact with triple lines. Therefore, one can also argue that - along a triple line there can be dislocation-line-triple-line junctions, likewise dislocations form own junctions. + description such as a triple line or a triple point as the projection of a line. Therefore, different representations can + be used to describe the location, shape, and structure of such defect. - It is not the aim of this base class to cover all these cases, rather this base class currently provides examples how the - typically most relevant types of features can be represented using a combination of base classes in NeXus. Currently, - these are crystals, interfaces, triple lines, quadruple junctions. + This base class provides definitions for crystals, grains, interfaces, triple junctions, and quadruple junctions thus covering, + volumetric, patch, line, and point like features that can serve as examples for future extension. - The description attempt here took inspiration from `E. E. Underwood <https://doi.org/10.1111/j.1365-2818.1972.tb03709.x>`_ - and E. E. Underwood's book on Quantitative Stereology published 1970 to categorize features based on their dimensionality. + As different types of crystal defects can interact, there is a substantial number of in principle characterizable and representable + objects. Take again a triple line as an example. It is a tubular feature built from three adjoining interfaces. However, dislocations + as line defects can interact with triple lines. Therefore, one can also argue that along a triple line there exist dislocation-line- + triple-line junctions, likewise dislocations form own junctions. - Identifiers can be defined either implicitly or explicitly. Identifiers for implicit indexing are defined - on the interval :math:`[identifier\_offset, identifier\_offset + cardinality - 1]`. + The description took inspiration from `E. E. Underwood <https://doi.org/10.1111/j.1365-2818.1972.tb03709.x>`_ + and E. E. Underwood's book on Quantitative Stereology published in 1970 to categorize features based on their dimensionality. + + Indices can be defined either implicitly or explicitly. Indices for implicit indexing are defined + on the interval :math:`[index\_offset, index\_offset + cardinality - 1]`. Indices can be used as identifiers + for distinguishing instances, i.e. indices are equivalent to instance names of individual crystals. - Discouraged free-text field for leaving comments. + Discouraged free-text field for leaving comments @@ -220,6 +266,9 @@ the idea is we may wish to run as many grain reconstructions as we want and add + @@ -227,18 +276,24 @@ the idea is we may wish to run as many grain reconstructions as we want and add (NXcsg): (NXcontinuous_function): examples for specific frequently discussed microstructural features--> - + The chemical composition of this microstructure (region). - - - - - - - + + + Different (thermodynamic) phases can be distinguished for the region-of- + interest. + + + + First identifier whereby to identify phases implicitly. + + + + + One- or two-dimensional projections, or three-dimensional representations of crystals. @@ -259,8 +314,7 @@ examples for specific frequently discussed microstructural features--> * :ref:`NXcg_polyline` for a one-dimensional representation as only a projection is available (like in linear intercept analysis) * :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) - * :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions - (like in computer simulations or 3D experiments) + * :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) which represent the geometrical entities of the discretization. @@ -279,40 +333,37 @@ examples for specific frequently discussed microstructural features--> Phases are typically distinguished based on statistical thermodynamics argument and crystal structure. - + First identifier whereby to identify crystals implicitly. - + Identifier whereby to identify each crystal explicitly. - + - - - First identifier whereby to identify phases implicitly. - - - + Identifier whereby to identify phase for each crystal explicitly. - + - - + + - True or false value, one for each crystal, to communicate whether that feature - makes contact with the edge of the ROI. + True, if the feature makes contact with the edge of the ROI. + False, if the feature does not make contact with the edge of the ROI. - + @@ -322,7 +373,7 @@ examples for specific frequently discussed microstructural features--> average disorientation of that crystal. - + @@ -330,7 +381,7 @@ examples for specific frequently discussed microstructural features--> Length of each crystal - + @@ -338,7 +389,7 @@ examples for specific frequently discussed microstructural features--> Area of each crystal. - + @@ -346,11 +397,16 @@ examples for specific frequently discussed microstructural features--> Volume of each crystal - + + + + Possibility to store the mean orientation of the grain. + + - + One- or two-dimensional projections or three-dimensional representation of interfaces between crystals as topological entities equivalent to dual_junctions. @@ -358,6 +414,14 @@ examples for specific frequently discussed microstructural features--> An example for a surface defect. Most important are interfaces such as grain and phase boundaries but factually interfaces also exist between the environment and crystals exposed at the surface of the specimen or internal surfaces like between crystals, cracks, or pores. + + Interfaces are typically reported as discretized features. For interface projections on the 2D plane + these are most frequently polyline segments. For interface patches in 3D these are most frequently + triangulations. Descriptions with continuous functions are seldom used unless simplified configurations + are studied in modeling and theoretical studies. + + When using discretizations the individual interface segments need to be distinguished from the interfaces + themselves. Consequently, there are two sets of indices. @@ -365,7 +429,7 @@ examples for specific frequently discussed microstructural features--> * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) * :ref:`NXcg_polyline` or :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) - * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks + * :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) using (boolean) masks (like in computer simulations or 3D experiments) which represent the geometrical entities of the discretization. @@ -376,26 +440,30 @@ examples for specific frequently discussed microstructural features--> How many interfaces are distinguished. - + First identifier whereby to identify interfaces implicitly. - + Identifier whereby to identify each interface explicitly. + + An array with as many entries as interfaces or their projections. - + - + - Set of pairs of identifier_crystal for each interface. + Set of pairs of indices_crystal values, for each interface one value pair. + + An array with as many pairs as interfaces or their projections. - + @@ -404,12 +472,14 @@ examples for specific frequently discussed microstructural features--> - + - Set of pairs of identifier_phase for each interface. + Set of pairs of indices_phase values, for each interface one value pair. + + An array with as many pairs as interfaces or their projections. - + @@ -419,13 +489,32 @@ examples for specific frequently discussed microstructural features--> - + - Set of pairs of identifier_triple_junction for each interface. + Interfaces can be the physical three-dimensional surfaces or two- or one-dimensional + projections. The latter situation applies typically for characterization with electron + microscopy. + + In the case of a two-dimensional projection interfaces are interface traces. These have + two terminating junctions. In three dimensions though the interface is a surface patch + that is bounded by multiple triple lines. + + Number of triple_junctions adjoining each interface. This array resolves the number of + values along the second dimension for the field indices_triple_junctions. + + + + + + + + Set of pairs of indices_triple_junction for each interface. + + An array with as many tuples of pairs to describe + all junctions about all interfaces. - @@ -434,13 +523,13 @@ examples for specific frequently discussed microstructural features--> - + - True or false value, one for each crystal, to communicate whether that feature - makes contact with the edge of the ROI. + True, if the interface makes contact with the edge of the ROI. + False, if the interface does not make contact with the edge of the ROI. - + @@ -448,7 +537,7 @@ examples for specific frequently discussed microstructural features--> Gibbs free surface energy for each interface. - + @@ -456,7 +545,7 @@ examples for specific frequently discussed microstructural features--> Non-intrinsic mobility of each interface. - + @@ -467,7 +556,7 @@ examples for specific frequently discussed microstructural features--> polyline segments whereby the interface is discretized. - + @@ -475,11 +564,11 @@ examples for specific frequently discussed microstructural features--> The surface area of all interfaces. - + - + Projections or representations of junctions at which three interfaces meet. @@ -506,17 +595,17 @@ examples for specific frequently discussed microstructural features--> Number of triple junctions. - + First identifier to identify triple junctions implicitly. - + Identifier to identify each triple junction explicitly. - + junction. - + @@ -535,33 +624,33 @@ example i) triple points as projections of triple lines have locations--> - + Explicit positions. - + - + Set of tuples of identifier of crystals connected to the junction for each triple junction. - + - + Set of tuples of identifier of interfaces connected to the junction for each triple junction. - + @@ -571,30 +660,30 @@ example i) triple points as projections of triple lines have locations--> - + Set of tuples of identifier for polyline segments connected to the junction for each triple junction. - + - The specific identifier_polyline whereby to resolve ambiguities. + The specific indices_polyline whereby to resolve ambiguities. - + - True or false value, one for each crystal, to communicate whether that feature - makes contact with the edge of the ROI. + True, if the triple line makes contact with the edge of the ROI. + False, if the triple line does not make contact with the edge of the ROI. - + @@ -602,7 +691,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> Specific line energy of each triple junction - + @@ -610,7 +699,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> Non-intrinsic mobility of each triple junction. - + @@ -621,30 +710,40 @@ EXAMPLES FOR DESCRIPTOR VALUES--> polyline segments whereby the junction is discretized. - + - The volume of the each triple junction + The volume about each triple junction. + + Respective cut-off criteria need to be specified. - + - + Quadruple junctions as a region where four crystals meet. - An example for a point defect. + An example for a point (like) defect. + + Thermodynamically such junctions can be unstable. + Specifically when discretizations are used in simulations + that do not address the thermodynamics of and splitting characteristics + of junctions in cases when more than four crystals meet, it is possible + that so-called higher-order junctions are observed. Reference to an instance of: * :ref:`NXcg_point` - * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks + * :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) using (boolean) masks + + which represent the geometrical entities of the discretization. @@ -652,12 +751,12 @@ EXAMPLES FOR DESCRIPTOR VALUES--> Number of quadruple junctions. - + First identifier to identify quadruple junctions implicitly. - + Identifier to identify each quadruple junction explicitly. @@ -673,7 +772,7 @@ example i) quadruple point locations explicitly--> junction. - + @@ -681,23 +780,23 @@ example i) quadruple point locations explicitly--> - + Explicit positions. - - + + - + Set of tuples of identifier of crystals connected to the junction for each junction. - + @@ -707,13 +806,13 @@ example i) quadruple point locations explicitly--> - + Set of tuples of identifier of interfaces connected to the junction for each junction. - + @@ -724,13 +823,13 @@ example i) quadruple point locations explicitly--> - + Set of tuples of identifier for triple junctions connected to the junction for each quadruple junction. - + @@ -741,13 +840,13 @@ example i) quadruple point locations explicitly--> - + Set of tuples of identifier for phases of crystals connected to the junction for each quadruple junction. - + @@ -758,13 +857,13 @@ example i) quadruple point locations explicitly--> - + - True or false value, one for each crystal, to communicate whether that feature - makes contact with the edge of the ROI. + True, if the junction makes contact with the edge of the ROI. + True, if the junction does not make contact with the edge of the ROI. - + @@ -772,7 +871,7 @@ example i) quadruple point locations explicitly--> Energy of the quadruple_junction as a defect. - + @@ -780,7 +879,7 @@ example i) quadruple point locations explicitly--> Non-intrinsic mobility of each quadruple_junction. - + diff --git a/contributed_definitions/NXmicrostructure_feature.nxdl.xml b/contributed_definitions/NXmicrostructure_feature.nxdl.xml new file mode 100644 index 0000000000..3af8dbeea6 --- /dev/null +++ b/contributed_definitions/NXmicrostructure_feature.nxdl.xml @@ -0,0 +1,37 @@ + + + + + + Base class for documenting structuring features of a microstructure. + + Instances of the class enable sub-grouping of microstructural features + as the abstract base class NXobject should not be used for this purpose. + + + + The chemical composition of this microstructural feature or this set of + features. + + + diff --git a/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml b/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml deleted file mode 100644 index 8ff6e704ed..0000000000 --- a/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - Application definition for configuring GraGLeS. - - GraGLeS is a continuum-scale model for shared-memory-parallelized simulations - of the isothermal evolution of 2D and 3D grain boundary networks with a level-set approach. - CPU parallelization is achieved with OpenMP. - - The code has been implemented by C. Mießen in the group of G. Gottstein - at the Institute für Metallkunde und Metallphysik, RWTH Aachen University. - - Details of the model are summarized in `C. Mießen <https://publications.rwth-aachen.de/record/709678>`_. - - - - - - - - - - Simulation ID as an alias to refer to this simulation. - - - - - Discouraged free-text field to add further details to the computation. - - - - - - - - - - - - - - - Programs and libraries representing the computational environment - - - - - - - - - - - - From which file should the microstructure be instantiated. - - - - - - - - - The formulation of mean curvature flow in the GraGLeS model is scale invariant. - Therefore, the discretization has to be scaled to the actual physical length - of the simulation domain (ve, ROI). - For GraGLeS the discretization is always a square or cubic axis-aligned - bounding box with a regular tiling into material points - (either squares or cubes respectively). - - Edge_length is the length of the entire domain along its edge not - the length of the Wigner-Seitz cell about each material point! - - - - - - Configuration when snapshots of the system should be taken. - - Keep in mind that essentially geometry snapshot data store the - polylines and polyhedra of all grains which can take substantial disk - space. - - - - Generate a snapshot of the properties of the grains to follow - the evolution of the microstructure every :math:`n`-th iteration. - Setting zero causes that no property snapshots are taken. - - - - - Generate a snapshot of the geometry of the entire grain boundary network - every :math:`n`-th iteration. Setting zero instructs to store no geometry data. - - - - - - - Configuration when the simulation should be stopped in a controlled manner. - Whichever criterion is fulfilled first triggers the controlled stop of - and termination of GraGLeS. - - - - The simulation stops if the total number of grains - becomes smaller than this criterion. - - - - - The simulation stops if more iterations than this criterion have been computed. - - - - - - Configuration of numerical details of the solver. - - - - - Which type of convolution kernel and model is used. - - - - - - - - - - Constant to calibrate the real time scaling of the simulation. - - - - - - - Configuration of the grid coarsement algorithm whereby the representation - of the system is continuously rediscretized such that on average grains - are discretized with discretization many material points along each - direction. - - Grid coarsement can reduce the computational costs substantially although - it cannot be ruled out completely that the rediscretizing may have an effect - on the system evolution. Without grid coarsement the total number of material - points to consider stays the same throughout the simulation. - - - - Number of material points along each direction to discretize the - average grain. The larger this value is chosen the finer the curvature - details are that can be resolved but also the longer the simulation - takes. - - - - - If true grid coarsement is active, otherwise it is not. - - - - - Fraction how strongly the number of grains has to reduce - to trigger a grid coarsement step in an iteration. - - - - - - - Physically-based model of the assumed mobility of the grain boundaries. - - Grain boundary mobility is not an intrinsic property of a grain boundary but system-dependent - especially as grain boundaries in reality are decorated with defects as a consequence of which - the actual mobility is a combination of the mobility of the individual defects and the attached - boundary patches. Grain boundaries have different degrees of microscopic freedom. - Therefore, their mobility follows a distribution. - - - - - Fundamental model how :math:`m` is assumed a function of the disorientation - angle :math:`\Theta`. - - - - - - - - - The assumed mobility :math:`m_0` of the fastest grain boundary in the system at the assumed - temperature. GraGLeS was developed for modelling isothermal annealing. - - - - - Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not one. - - - - - - Mobility scaling factor :math:`c_2`. Typically 5. - - - - - Mobility scaling factor :math:`c_3`. Typically 9. - - - - - - Physically-based model of the assumed grain boundary surface energy. - - Like for the grain boundary mobility, defects cause a distribution of energies for the - patches of which the boundary is composed. In practice a too complicated dependency - of the energy and mobility model is observed as a function of the type and chemical - decoration of the defects. Therefore, simplifying assumptions are typically made. - - - - Fundamental type of assumption if energies are considered isotropic or not. - - - - - - - - - Fundamental model how :math:`\gamma` is assumed a function of the disorientation - angle :math:`\Theta`. - - - - - - - - Mean grain boundary surface energy that is assumed a function of the - disorientation angle :math:`\Theta` of the adjoining grains :math:`\gamma(\Theta)`. - This value factorizes the curvature_driving_force model. - - - - - - - A continuum-scale curvature of an interface causes the interface to - migrate towards the center of the curvature radius. - - - - If true the curvature_driving_force is considered, otherwise it is not. - - - - - - A continuum-scale difference of the stored elastic energy in dislocation - configurations across a grain boundary can exert a driving force on the - grain boundary such that the boundary migrates into the volume with the - higher stored elastic energy. - - - - If true the dislocation_driving_force is considered, otherwise it is not. - - - - - Prefactor :math:`0.5Gb^2` that factorizes the average - stored elastic energy per length dislocation line. - - - - - - In case of an applied magnetic field, a difference of the magnetic - susceptibility can exert a driving force on the grain boundary such that - the boundary migrates into the volume with the higher magnetic energy. - - - - If true the magnetic_driving_force is considered, otherwise it is not. - - - - - - - A triple line mediates the atomic arrangement differences between three - interface patches. Therefore, the triple line is a defect that may not - have the same mobility as adjoining grain boundaries and thus it may - exert what can be conceptualized as a drag (resistance) to the motion - of the adjoining interface patches. - - - - Assumed triple junction drag. - - - - - - diff --git a/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml b/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml deleted file mode 100644 index f5aba4d74f..0000000000 --- a/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of summary statistic log entries. - - - - - Number of grains in the computer simulation. - - - - - Number of interfaces in the computer simulation. - - - - - Application definition for documenting results with GraGLeS. - - - - - - - - - - - Simulation ID as an alias to refer to this simulation. - - - - - Discouraged free-text field to add further details to the computation. - - - - - - - - - - - - - - Programs and libraries representing the computational environment - - - - - - - - - - - - - - - - - - - - - - - - - - - - Documentation of the spatiotemporal evolution - - Instances should use spatiotemporal as a name prefix. - - - - - Summary quantities which are the result of some post-processing of the snapshot data - (averaging, integrating, interpolating) happening in for practical reasons though in while - running the simulation. Place used for storing descriptors from continuum mechanics - and thermodynamics at the scale of the entire ROI. - - - - Evolution of the recrystallized volume fraction over time. - - - - Evolution of the physical time not to be confused with wall-clock time or - profiling data. - - - - - - - - Iteration or increment counter. - - - - - How many crystals are distinguished. - Crystals are listed irrespective of the phase to which these are assigned. - - - - - - - - - - Which type of stress. - - - - - - - - Applied external stress tensor on the ROI. - - - - - - - - - - - - Which type of strain. - - - - - Applied external strain tensor on the ROI. - - - - - - - - - - - - Which type of deformation gradient. - - - - - - - - Applied deformation gradient tensor on the ROI. - - - - - - - - - - - - Applied external magnetic field on the ROI. - - - - - - - - - - - - - Applied external electrical field on the ROI. - - - - - - - - - - - - - Instances should use microstructure as a name prefix. - - - - - - Simulated temperature for this snapshot. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set of pairs of identifier_crystal for each interface. - - - - - - - - - - Mobility times surface energy density of the interface normalized - to the maximum such product of the interface set. - - - - - - - - - - - - - - - diff --git a/contributed_definitions/NXmicrostructure_imm_config.nxdl.xml b/contributed_definitions/NXmicrostructure_imm_config.nxdl.xml deleted file mode 100644 index 9767e5951a..0000000000 --- a/contributed_definitions/NXmicrostructure_imm_config.nxdl.xml +++ /dev/null @@ -1,242 +0,0 @@ - - - - - - - - How many texture components are distinguished, minimum is 1. - - - - - How many special texture components are distinguished if any. - - - - - Number of discrete orientations that are distributed across the grains. - - - - - Application definition for the configuration of the legacy (micro)structure generator - developed by the Institut für Metallkunde und Metallphysik at RWTH Aachen University. - - * `N. Leuning et al. <https://doi.org/10.3390/ma14216588>`_ - * `C. Mießen <https://doi.org/10.18154/RWTH-2017-10148>`_ - * `M. Kühbach <https://doi.org/10.18154/RWTH-2018-00294>`_ - * `M. Kühbach et al. <https://github.com/mkuehbach/GraGLeS>`_ - - The tool can be used to instantiate specific configurations for two- and three-dimensional discretized microstructures. - Specifically, single-phase material that is composed of crystals, so-called (parent) grains which are tessellated into so-called sub-grains. - Grains are modelled as elongated crystals to mimic fundamental geometrical constraints of the interface network in deformed material. - - - - - - - - - - The computational domain will be synthesized either as a square (for dimensionality = 2) - or a cube (for dimensionality = 3) with axis-aligned cuboidal parent grains. The domain is - discretized into material points using either square pixel or cubic voxel as the tessellating - unit cells. - - - - Two-dimensional or three-dimensional simulation. - - - - - - - - - Target value for the number of material points per equivalent - discrete diameter of the arithmetic average sub-grain. - - - - - Assumed space group of the material. - - - - - - - - - - - Target value for the number of grains. The actual domain size and grid will be configured - based on the choices for discretization, number_of_grains, and shape of these grains. - - - - - Target value for the average number of sub-grains per grain. - - - - - - If available used to define the sequence of relative extent of grains along the y (first value) - and z-axis (second value) assuming the relative shape along the x-axis is 1. If not provided, - the relative extent of the grains will be 1 one average along each axis (globulitic structure). - - - - - - - - - - In texture research component analyses set on the idea that properties - of grains different based on orientation with certain regions in orientation - space show similar trends like a different average dislocation density - or orientation_spread. - - - - The first entry is always the null model None which means that an orientation - is not categorized as a special component. Examples for special components are - Dillamore, Copper, Cube, Y, P and Q. - - - - - - - - Bunge-Euler angle parameterization of the texture components - location in orientation space for which specifically different settings - should be configured. - - - - - - - - - Disorientation angle below which an orientation is categorized as one of the - components. - - - - - - - - - Dislocations are modelled as Rayleigh-distributed mean-field density that - can differ between but is constant within grains and sub-grains. - - - - The minimum and the maximum dislocation density to distribute across grains. - - - - - - - - - The minimum and the maximum dislocation density to distribute across sub-grains. - - - - - - - - - - - The variance of the dislocation density distribution across the grains. - - - - - - - - The variance of the dislocation density distribution across the sub-grains. - - - - - - - - - Orientations of the grains are sampled from a set of Bunge-Euler angle triplets. - Orientations of the sub-grains are sampled by scattering the orientation - of the (parent) grain and with optional Rayleigh-distributed scatter. - - - - Bunge-Euler angle parameterization of the texture components - location in orientation space for which specifically different settings - should be configured. - - - - - - - - - The variance of the disorientation of the sub-grain to their parent grain. - - - - - - - - - diff --git a/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml b/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml deleted file mode 100644 index c7074ace67..0000000000 --- a/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml +++ /dev/null @@ -1,192 +0,0 @@ - - - - - - - - Number of material points along the edge of the square- or cube-shaped domain. - - - - - Number of crystals. - - - - - Application definition for the results of the legacy (micro)structure generator developed - by the Institut für Metallkunde und Metallphysik at RWTH Aachen University. - - * `N. Leuning et al. <https://doi.org/10.3390/ma14216588>`_ - * `C. Mießen <https://doi.org/10.18154/RWTH-2017-10148>`_ - * `M. Kühbach <https://doi.org/10.18154/RWTH-2018-00294>`_ - * `M. Kühbach et al. <https://github.com/mkuehbach/GraGLeS>`_ - - The tool can be used to instantiate specific configurations for two- and three-dimensional discretized microstructures. - Specifically, single-phase material that is composed of crystals, so-called (parent) grains which are tessellated into so-called sub-grains. - Grains are modelled as elongated crystals to mimic fundamental geometrical constraints of the interface network in deformed material. - - - - - - - - - - Discouraged free-text field to add further details to the computation. - - - - - - - - - - - - - - - Programs and libraries representing the computational environment - - - - - - - - - - Instances should use microstructure as a name prefix. - - - - - - - Default plot showing the grid. - - - - - - - - Crystal identifier that was assigned to each material point. - - - - - - Material point barycenter coordinate along z direction. - - - - - - - Coordinate along z direction. - - - - - - Material point barycenter coordinate along y direction. - - - - - - - Coordinate along y direction. - - - - - - Material point barycenter coordinate along x direction. - - - - - - - Coordinate along x direction. - - - - - - - - - - - - - - - - - - - - - - - - - - True if the crystal is considered a sub-grain. - False if the crystal is considered a grain. - - - - - - - - Bunge-Euler angle orientation of each crystal. - - - - - - - - - Mean-field dislocation density as a measure of the stored elastic energy - content that is stored in the dislocation network of this grain and related - defects within each crystal. - - - - - - - - - diff --git a/contributed_definitions/NXmicrostructure_ipf.nxdl.xml b/contributed_definitions/NXmicrostructure_ipf.nxdl.xml index 20b3ad99f0..b4c9f1b38d 100644 --- a/contributed_definitions/NXmicrostructure_ipf.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_ipf.nxdl.xml @@ -1,9 +1,9 @@ - + + + + Number of pixel along the slow direction used for the IPF color key. + + + + + Number of pixel along the fast direction used for the IPF color key. + + - Number of pixel along the z slowest direction. + Number of pixel along the slowest direction, typically labeled z or k. - Number of pixel along the y slow direction. + Number of pixel along the slow direction, typically labeled y or j. - Number of pixel along the x fast direction. + Number of pixel along the fast direction, typically labeled x or i. - Number of RGB values along the fastest direction, always three. + Number of RGB values along the fastest direction, always three. - Base class to store an inverse pole figure (IPF) mapping (IPF map). + Base class to store an inverse pole figure (IPF) mapping (IPF map). - Reference to an :ref:`NXcoordinate_system` in which the projection_direction is defined. - - If the field depends_on is not provided but parents of the instance of this base class or its - specializations define an instance of :ref:`NXcoordinate_system`, projection_direction - is defined in this coordinate system. - - If nothing is provided it is assumed that projection_direction is defined in the McStas coordinate system. + Reference to an instance of :ref:`NXcoordinate_system` in which the axes axis_z, + axis_y, and axis_x are defined. + + + The algorithm whereby orientations are colored. + + + + + + - The direction along which orientations are projected. + The direction normal vector along which orientations are projected. + + + Reference to an instance of :ref:`NXcoordinate_system` in which the projection_direction is defined. + + If the field depends_on is not provided but parents of the instance of this base class or its + specializations define an instance of :ref:`NXcoordinate_system`, projection_direction + is defined in this coordinate system. + + If nothing is provided, it is assumed that projection_direction is defined in the McStas coordinate system. + + - Details about the original grid. - - Here original grid means the grid for which the IPF map was computed when that - IPF map was exported from the tech partner's file format representation. + Details about the original grid, i.e. the grid for which the IPF map was computed + when that IPF map was exported from the tech partner's file format representation. - Details about the grid onto which the IPF is recomputed. - - Rescaling the visualization of the IPF map may be needed to enable - visualization in specific software tools like H5Web. + Details about the grid onto which the IPF is recomputed. + + Rescaling the visualization of the IPF map may be needed to enable + visualization in specific software tools like H5Web. - How where orientation values at positions of input_grid computed to values on output_grid. - - Nearest neighbour means the orientation of the closed (Euclidean distance) grid point of the input_grid was taken. + How where orientation values at positions of input_grid computed to values on output_grid. + + Nearest neighbour means the orientation of the closed (Euclidean distance) grid point of the input_grid was taken. @@ -94,149 +117,129 @@ - Inverse pole figure mapping. - - Instances named phase0 should by definition refer to the null phase notIndexed. - Inspect the definition of :ref:`NXphase` and its field identifier_phase - for further details. - - Details about possible regridding and associated interpolation - during the computation of the IPF map visualization can be stored - using the input_grid, output_grid, and interpolation fields. - - The main purpose of this map is to offer a normalized default representation - of the IPF map for consumption by a research data management system (RDMS). - This is aligned with the first aim of :ref:`NXmicrostructure_ipf`, to bring colleagues - and users of IPF maps together to discuss which pieces of information need storage. - - We are convinced a step-by-step design and community-driven discussion is a practical - strategy to work towards an interoperable description and data model for exchanging - IPF maps as a specific community-accepted method to convey orientation maps. - - With this design the individual RDMS solutions and tools can still continue - to support specific custom data analyses workflow and routes but at least - there is one common understanding which enables also those users who are - not necessarily experts in all the details of the underlying techniques an - understanding if the dataset is worth to become reused or repurposed. + Inverse pole figure mapping. + + Instances named phase0 should by definition refer to the null phase notIndexed. + Inspect the definition of :ref:`NXphase` and its field identifier_phase + for further details. + + Details about possible regridding and associated interpolation + during the computation of the IPF map visualization can be stored + using the input_grid, output_grid, and interpolation fields. + + The main purpose of this map is to offer a normalized default representation + of the IPF map for consumption by a research data management system (RDMS). - - - Inverse pole figure color code for each map coordinate. + Inverse pole figure color code for each map coordinate. + + Different types of AXISNAME dimensional scale axes are found in practice. A few examples: + + * No scaling, e.g. pixel position values like 0, 1, 2, 3 pixel. + Pixels on the map can be distinguished but that map is disconnected from + any sample surface context and eventually physical scaling + * Scaling but no offset, e.g. calibrated pixel position 0., 0.5, 1.0, 1.5 micron. + Pixels on the map can be compared for their distance to obtain e.g. size of features + but the position of the map relative to the e.g. the sample surface is unclear. + For IPF maps this is the most frequently reported situation. + * Scaling and offset, which resolves also the absolute position of the map in + relation to the sample surface. This is useful information for stitching multiple + mappings together and other processing where precise and accurate + position data are relevant e.g. for correlative materials characterization. + + Three types of dimensional constraints for maps are possible: + + * (n_x, 3), a one-dimensional map, + typically used for coarse sampling and crystal size statistics. + * (n_y, n_x, 3), a two-dimensional map, + the most frequently found reported + * (n_z, n_y, n_x, 3), a three-dimensional map, + these are commonly generated using computational methods, + or in cases multiple EBSD maps have been stitched/reconstructed + into a three-dimensional map. - - - - - + - Pixel center coordinate calibrated for step size along the z axis of the map. + Pixel center coordinate calibrated for step size along the z axis of the map. - - Pixel center coordinate calibrated for step size along the y axis of the map. + Pixel center coordinate calibrated for step size along the y axis of the map. - - Pixel center coordinate calibrated for step size along the x axis of the map. + Pixel center coordinate calibrated for step size along the x axis of the map. - - The color code which maps colors to orientation in the fundamental zone. - - For each stereographic standard triangle (SST), i.e. a rendering of the - fundamental zone of the crystal-symmetry-reduced orientation space - SO3, it is possible to define a color model which assigns a color to each - point in the fundamental zone. - - Different mapping models are used. These implement (slightly) different - scaling relations. Differences exist across representations of tech partners. - - Differences are which base colors of the RGB color model are placed in - which extremal position of the SST and where the white point is located. - - For further details see: - - * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) - * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). - - Details are implementation-specific and not standardized yet. - - Given that the SST has a complicated geometry, it can not yet be - visualized using tools like H5Web, which is why for now the matrix - of a rasterized image which is rendered by the backend tool gets - copied into an RGB matrix to offer a default plot. + The color code which maps color to orientation in the fundamental zone. + + For each stereographic standard triangle (SST), i.e. a rendering of the + fundamental zone of the crystal-symmetry-reduced orientation space + SO3, it is possible to define a color model which assigns a color to each + point in the fundamental zone. + + Different mapping models are used. These implement (slightly) different + scaling relations. Differences exist across representations of tech partners. + + Differences are which base colors of the RGB color model are placed in + which extremal position of the SST and where the white point is located. + + For further details see: + + * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) + * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). + + Details are implementation-specific and not standardized yet. - - - + + + - Inverse pole figure color code for each map coordinate. + Inverse pole figure color code for each map coordinate. - - + + - Pixel along the y-axis. + Pixel along the y-axis. - + - - Pixel along the x-axis. + Pixel along the x-axis. - + - diff --git a/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml b/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml index 50c49766ba..40dc06c9f8 100644 --- a/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml @@ -1,4 +1,4 @@ - + - - - Instances should use microstructure as a name prefix. - + @@ -109,7 +106,7 @@ - + Crystal identifier that was assigned to each material point. @@ -157,16 +154,16 @@ - + - + - + diff --git a/contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml b/contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml index 6442eba21c..c33566afcc 100644 --- a/contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml @@ -1,9 +1,9 @@ - + - True if MTex renders a scale bar with figures. + True, if MTex renders a scale bar with figures. - True if MTex renders a grid with figures. + True, if MTex renders a grid with figures. @@ -145,9 +145,9 @@ check against v5.12--> +doc: | +TODO with MTex developers +unit: NX_UNITLESS--> @@ -209,7 +209,11 @@ check against v5.12--> TODO with MTex developers - + + + TODO with MTex developers + + diff --git a/contributed_definitions/NXmicrostructure_odf.nxdl.xml b/contributed_definitions/NXmicrostructure_odf.nxdl.xml index f3541c3f1b..2dbe76ea49 100644 --- a/contributed_definitions/NXmicrostructure_odf.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_odf.nxdl.xml @@ -1,9 +1,9 @@ - + - + - Number of pixel per varphi section plot along the :math:`\varphi_1` fastest + Number of pixel per varphi section plot along the :math:`\varphi_2` slow direction. @@ -34,9 +34,9 @@ Number of pixel per varphi section plot along the :math:`\Phi` fast direction. - + - Number of pixel per varphi section plot along the :math:`\varphi_2` slow + Number of pixel per varphi section plot along the :math:`\varphi_1` fastest direction. @@ -58,20 +58,21 @@ much volume of material has a specific orientation. An ODF is computed from pole figure data in a computational process called `pole figure inversion <https://doi.org/10.1107/S0021889808030112>`_. - + Details about the algorithm used for computing the ODF. - Point group of the crystal structure of the phase for which the here documented phase- - dependent ODF was computed.(following the notation of the International Table of Crystallography). + Point group of the crystal structure of the phase for which the here documented + phase-dependent ODF was computed following the notation of the + International Table of Crystallography. Point group assumed for additionally considered sample symmetries - following the notation of the International Table of Crystallography). + following the notation of the International Table of Crystallography. @@ -91,7 +92,7 @@ - + Group to store descriptors and summary statistics for extrema of the ODF. @@ -121,8 +122,8 @@ - Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the kth-most - maxima in decreasing order of the intensity maximum. + Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the + kth-most maxima in decreasing order of the intensity maximum. @@ -131,7 +132,7 @@ - Integrated ODF intensity within a theta angular region of the orientation space (SO3) + Integrated ODF intensity within a theta angular region of the orientation space :math:`SO3` about each location (obeying symmetries) as specified for each location. @@ -139,9 +140,9 @@ - + - The ODF intensity values (weights) as sampled with a software + The ODF intensity values (weights) as sampled with a software. @@ -174,7 +175,7 @@ This is one example of typical default plots used in the texture community in materials engineering. - Mind that when parameterized using Euler angles the orientation space is a distorted space. + Mind that the orientation space is a distorted space when it using an Euler angle parameterization. Therefore, equivalent orientations show intensity contributions in eventually multiple locations. Pixel center angular position along the :math:`\Phi` direction. @@ -210,7 +210,6 @@ - Pixel center angular position along the :math:`\varphi_2` direction. @@ -220,5 +219,4 @@ - diff --git a/contributed_definitions/NXmicrostructure_pf.nxdl.xml b/contributed_definitions/NXmicrostructure_pf.nxdl.xml index 18809d66a2..3c8285419c 100644 --- a/contributed_definitions/NXmicrostructure_pf.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_pf.nxdl.xml @@ -1,9 +1,9 @@ - + @@ -64,7 +64,8 @@ - Miller indices (:math:`(hkl)[uvw]`) to specify the pole figure. + Miller (:math:`(hkl)[uvw]`) or Miller-Bravais indices used to specify the pole + figure. @@ -99,7 +100,6 @@ - Pixel center along x direction in the equatorial plane of @@ -110,5 +110,4 @@ - diff --git a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml index 81a2d79eba..12ccf6dfb9 100644 --- a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml @@ -1,4 +1,4 @@ - + - + Dimensionality of the simulation. @@ -129,8 +129,7 @@ exists: optional--> The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by identifier_parent or walk through - eventually deeply nested groups in data instances. + these from other sources. @@ -142,7 +141,7 @@ exists: optional--> - + Programs and libraries representing the computational environment @@ -152,7 +151,7 @@ exists: optional--> - + (Mechanical) properties of the material which scale the amount of stored (elastic) energy in the system and @@ -178,7 +177,7 @@ SecondOrderThermalExpCoeff--> - + Details about the geometry and properties of the polycrystal that represents the starting configuration (typically a deformed microstructure) for the simulation. @@ -214,7 +213,7 @@ SecondOrderThermalExpCoeff--> Average spherical diameter when model is poisson_voronoi. - + Settings for instantiating properties of deformed grains when model is cuboidal or poisson. @@ -281,7 +280,7 @@ SecondOrderThermalExpCoeff--> - + Phenomenological model according to which recrystallization nuclei are placed into the domain whose growth is studied with the simulation. @@ -321,7 +320,7 @@ SecondOrderThermalExpCoeff--> - + Settings for instantiating properties of nuclei for recrystallizing grains. @@ -347,7 +346,7 @@ SecondOrderThermalExpCoeff--> - + Model for the assumed mobility of grain boundaries with different disorientation implemented as parameterized Turnbull's model for thermally-activated @@ -367,7 +366,7 @@ TODO: add equation for the Rollett-Holm model the following equation--> - + Parameter of the Sebald-Gottstein migration model. @@ -414,7 +413,7 @@ unit: NX_ANGLE--> - + Parameter of the Rollett-Holm migration model. @@ -446,7 +445,7 @@ unit: NX_ANGLE--> - + Time-dependent reduction of the stored energy to account for recovery effects. @@ -459,7 +458,7 @@ unit: NX_ANGLE--> - + Reduction of the grain boundary migration speed due to the presence of dispersoids through which the total grain boundary area of the recrystallization front can be reduced @@ -474,7 +473,7 @@ unit: NX_ANGLE--> - + Parameter of the Zener-Smith drag model when model is zener_smith. @@ -524,7 +523,7 @@ like showing a r(t) plot--> - + Given name of a texture component. @@ -617,7 +616,7 @@ like showing a r(t) plot--> - + Criteria which enable to stop the simulation in a controlled manner. Whichever criterion is fulfilled first stops the simulation. @@ -665,7 +664,7 @@ like showing a r(t) plot--> - + Parameter which control the memory management of cells in the recrystallization front. @@ -704,7 +703,7 @@ like showing a r(t) plot--> - + Perform a statistical analyses of the results as it was proposed @@ -725,10 +724,4 @@ like showing a r(t) plot--> - diff --git a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml index 1a8453c870..b456748e3f 100644 --- a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml @@ -1,4 +1,4 @@ - + - + Programs and libraries representing the computational environment @@ -143,11 +143,11 @@ inspect comments behind NXmicrostructure--> +rotation_handedness(NX_CHAR): +rotation_convention(NX_CHAR): +euler_angle_convention(NX_CHAR): +axis_angle_convention(NX_CHAR): +sign_convention(NX_CHAR):--> @@ -203,7 +203,7 @@ inspect comments behind NXmicrostructure--> - + @@ -211,7 +211,7 @@ inspect comments behind NXmicrostructure--> - + How many distinct boundaries are distinguished? Most grids discretize a cubic or cuboidal region. In this case @@ -244,21 +244,19 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele - + Documentation of the spatiotemporal evolution for each CA domain. SCORE is a hybrid parallelized code that can evolve multiple replicas in parallel. The set of replicas is distributed across MPI processes. Each such replica is then evolved via OpenMP multi-threading. - - Instances should use spatiotemporal as a name prefix. Summary quantities which are the result of some post-processing of the snapshot data - (averaging, integrating, interpolating) happening for practical and performance reasons + (averaging, integrating, interpolating) happening for practical and performance reasons during the simulation. Place used for storing descriptors from continuum mechanics and thermodynamics at the scale of the entire ROI. @@ -366,24 +364,21 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele - - - Instances should use microstructure as a name prefix. - + @@ -409,9 +404,9 @@ the typically storage-costlier snapshot data--> - + - Grain identifier for each cell. + Index for each crystal whereby its metadata can be retrieved. @@ -419,9 +414,9 @@ the typically storage-costlier snapshot data--> - + - Identifier of the OpenMP thread which processed this part of the grid. + Identifier of the OpenMP thread that processed this part of the grid. @@ -430,18 +425,18 @@ the typically storage-costlier snapshot data--> - + - - + + - - + + @@ -490,7 +485,7 @@ the typically storage-costlier snapshot data--> - + Details about those cells which in this time step represent the discrete recrystallization front. @@ -522,7 +517,7 @@ the typically storage-costlier snapshot data--> - + Grain identifier assigned to each cell in the recrystallization front. @@ -530,7 +525,7 @@ the typically storage-costlier snapshot data--> - + Grain identifier assigned to each nucleus which affected that cell in the recrystallization front. @@ -539,7 +534,7 @@ the typically storage-costlier snapshot data--> - + Identifier of the OpenMP thread processing each cell in the recrystallization front. diff --git a/contributed_definitions/NXmicrostructure_slip_system.nxdl.xml b/contributed_definitions/NXmicrostructure_slip_system.nxdl.xml index e4a4cdd616..f9387095c3 100644 --- a/contributed_definitions/NXmicrostructure_slip_system.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_slip_system.nxdl.xml @@ -1,4 +1,4 @@ - + - Array of Miller indices which describe the crystallographic direction. + Array of Miller or Miller-Bravais indices that describe the crystallographic + direction. - + - For each slip system a marker whether the specified Miller indices refer to - a specific or a crystallographic equivalent set of the slip system. + For each slip system a marker whether the Miller indices refer to a specific slip system + or to a set of equivalent crystallographic slip systems. diff --git a/contributed_definitions/NXpiezo_config_spm.nxdl.xml b/contributed_definitions/NXpiezo_config_spm.nxdl.xml index 9c4bab1e03..36122baa6e 100644 --- a/contributed_definitions/NXpiezo_config_spm.nxdl.xml +++ b/contributed_definitions/NXpiezo_config_spm.nxdl.xml @@ -1,4 +1,4 @@ - + - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The cardinality of the set, i.e. the number of value tuples. - - - - - How many phases with usually different crystal and symmetry are distinguished. - - - - - - Base class to detail a set of rotations, orientations, and disorientations. - - For getting a more detailed insight into the discussion of the - parameterized description of orientations in materials science see: - - * `H.-J. Bunge <https://doi.org/10.1016/C2013-0-11769-2>`_ - * `T. B. Britton et al. <https://doi.org/10.1016/j.matchar.2016.04.008>`_ - * `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_ - * `A. Morawiec <https://doi.org/10.1007/978-3-662-09156-2>`_ - - Once orientations are defined, one can continue to characterize the - misorientation and specifically the disorientation. The misorientation describes - the rotation that is required to register the lattices of two oriented objects - (like crystal lattice) into a crystallographic equivalent orientation: - - * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ - - - - Reference to an instance of :ref:`NXcoordinate_system` which contextualizes - how the here reported parameterized quantities can be interpreted. - - - - - Point group which defines the symmetry of the crystal. - - This has to be at least a single string. If crystal_symmetry is not - provided, point group 1 is assumed. - - In the case that misorientation or disorientation fields are used - and the two crystal sets resolve for phases with a different - crystal symmetry, this field needs to encode two strings: - The first string is for phase A. The second string is for phase B. - An example of this most complex case is the description of the - disorientation between crystals adjoining a hetero-phase boundary. - - - - - - - - Point group which defines an assumed symmetry imprinted upon processing - the material/sample which could give rise to or may justify to use a - simplified description of rotations, orientations, misorientations, - and disorientations via numerical procedures that are known as - symmetrization. - - If sample_symmetry is not provided, point group 1 is assumed. - - The traditionally used symmetrization operations within the texture - community in Materials Science, though, have become obsolete thanks - to improvements in methods, software, and available computing power. - - Therefore, users are encouraged to set the sample_symmetry to 1 (triclinic). - - In practice one often faces situations where indeed these assumed - symmetries are anyway not fully observed, and thus an accepting of - eventual inaccuracies just for the sake of reporting a simplified - symmetrized description should be avoided. - - - - - - - - The set of rotations expressed in quaternion parameterization considering - crystal_symmetry and sample_symmetry. Rotations which should be - interpreted as antipodal are not marked as such. - - - - - - - - - The set of rotations expressed in Euler angle parameterization considering - the same applied symmetries as detailed for the field rotation_quaternion. - To interpret Euler angles correctly, it is necessary to inspect the rotation - conventions behind reference_frame to resolve which of the many possible - Euler-angle conventions (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. - - - - - - - - - - - True for all those value tuples which have assumed antipodal symmetry. - False for all others. - - - - - - - - The set of orientations expressed in quaternion parameterization and - obeying symmetry for equivalent cases as detailed in crystal_symmetry - and sample_symmetry. The supplementary field is_antipodal can be used - to mark orientations with the antipodal property. - - - - - - - - - The set of orientations expressed in Euler angle parameterization following - the same assumptions like for orientation_quaternion. - To interpret Euler angles correctly, it is necessary to inspect the rotation - conventions behind reference_frame to resolve which of the many Euler-angle - conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. - - - - - - - - - - The set of misorientations expressed in quaternion parameterization - obeying symmetry operations for equivalent misorientations - as defined by crystal_symmetry and sample_symmetry. - - The misorientation should not be confused with the disorientation, - as for the latter the angular argument is expected to be the minimal - obeying symmetries. - - - - - - - - - Misorientation angular argument (eventually signed) following the same - symmetry assumptions as expressed for the field misorientation_quaternion. - - - - - - - - Misorientation axis (normalized) and signed following the same - symmetry assumptions as expressed for the field misorientation_angle. - - - - - - - - - - The set of disorientations expressed in quaternion parameterization - obeying symmetry operations for equivalent disorientations - as defined by crystal_symmetry and sample_symmetry. - - - - - - - - - Disorientations angular argument (should not be signed, see - `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) - following the same symmetry assumptions as expressed for the field - disorientation_quaternion. - - - - - - - - Disorientations axis (normalized) following the same symmetry assumptions - as expressed for the field disorientation_angle. - - - - - - - diff --git a/contributed_definitions/NXsample_component_set.nxdl.xml b/contributed_definitions/NXsample_component_set.nxdl.xml deleted file mode 100644 index af33885be3..0000000000 --- a/contributed_definitions/NXsample_component_set.nxdl.xml +++ /dev/null @@ -1,78 +0,0 @@ - - - - - - - - number of components - - - - - Set of sample components and their configuration. - - The idea here is to have a united place for all materials descriptors that are not - part of the individual sample components, but rather their configuration. - - - - Array of strings referring to the names of the NXsample_components. - The order of these components serves as an index (starting at 1). - - - - - Concentration of each component - - - - - - - - Volume fraction of each component - - - - - - - - Scattering length density of each component - - - - - - - - Each component set can contain multiple components. - - - - - For description of a sub-component set. Can contain multiple components itself. - - - diff --git a/contributed_definitions/NXscan_control.nxdl.xml b/contributed_definitions/NXscan_control.nxdl.xml index cec34cf5d3..0a3a5b91f7 100644 --- a/contributed_definitions/NXscan_control.nxdl.xml +++ b/contributed_definitions/NXscan_control.nxdl.xml @@ -1,4 +1,4 @@ - + - + - Which numerical identifier is the first to be used to label a feature. + Which numerical index is the first to be used to label a feature. The value should be chosen in such a way that special values can be resolved: - * identifier_offset - 1 indicates that an object belongs to no cluster. - * identifier_offset - 2 indicates that an object belongs to the noise category. - Setting for instance identifier_offset to 1 recovers the commonly used + * index_offset - 1 indicates that an object belongs to no cluster. + * index_offset - 2 indicates that an object belongs to the noise category. + Setting for instance index_offset to 1 recovers the commonly used case that objects of the noise category get values to -1 and unassigned points to 0. Numerical identifier have to be strictly increasing. @@ -97,7 +97,7 @@ results for the object set--> Matrix of numerical label for each member in the set. For classical clustering algorithms this can for instance - encode the identifier_cluster. + encode the indices_cluster. @@ -137,7 +137,7 @@ at the level of the feature set--> - + Array of numerical identifier of each feature. diff --git a/contributed_definitions/NXspatial_filter.nxdl.xml b/contributed_definitions/NXspatial_filter.nxdl.xml index eff7718777..f4a3e54ac1 100644 --- a/contributed_definitions/NXspatial_filter.nxdl.xml +++ b/contributed_definitions/NXspatial_filter.nxdl.xml @@ -1,4 +1,4 @@ - + -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Number of hit qualities (hit types) distinguished. -# -# -# -# -# Number of delay-line wires of the detector. -# -# -# -# -# Number of bins used in the mass-to-charge-state-ratio spectrum. -# -# -# -# -# Number of pulses collected in between start_time and end_time resolved by an -# instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of -# ions included in the reconstructed volume if the application definition is used -# to store results of an already reconstructed datasets. -# -# -# -# -# Number of pulses returned by the hit finding algorithm. -# Neither necessarily equal to p nor to n. -# -# -# -# -# Number of ions spatially filtered from results of the hit_finding algorithm -# from which an instance of a reconstructed volume has been generated. -# These ions get new identifier assigned in the process (the so-called -# identifier_evaporation). This identifier must not be confused with -# the identifier_pulse. Typically smaller than both p_out and p_out. -# -# -# -# -# Application definition for atom probe and field ion microscopy experiments. -# -# -# -# -# -# -# -# -# -# -# The configuration of the I/O writer software (e.g. `pynxtools <https://github.com/FAIRmat-NFDI/pynxtools>`_ or its plugins) -# which was used to generate this NeXus file instance. -# -# -# -# -# A collection of all programs and libraries which are considered relevant -# to understand with which software tools this NeXus file instance was -# generated. Ideally, to enable a binary recreation from the input data. -# -# Examples include the name and version of the libraries used to write the -# instance. Ideally, the software which writes these NXprogram instances -# also includes the version of the set of NeXus classes i.e. the specific -# set of base classes, application definitions, and contributed definitions -# with which the here described concepts can be resolved. -# -# For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ -# which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ -# research data management system, it makes sense to store e.g. the GitHub -# repository commit and respective submodule references used. -# -# -# -# -# -# -# -# -# -# -# The identifier whereby the experiment is referred to in the control software. -# This is neither the specimen_name nor the experiment_identifier. For -# Local Electrode Atom Probe (LEAP) instruments, it is recommended to use the -# run_number from the proprietary software IVAS/APSuite of AMETEK/Cameca. -# For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, -# or the instruments at GPM in Rouen, use the identifier which matches -# best conceptually to the LEAP run number. -# The field does not have to be required if the information is recoverable -# in the dataset which for LEAP instruments is the case (provided these -# RHIT or HITS files respectively are stored alongside a data artifact). -# With NXapm the RHIT or HITS can be stored via NXnote in the -# hit_finding algorithm section. -# -# As a destructive microscopy technique, a run can be performed only once. -# It is possible, however, to interrupt a run and restart data acquisition -# while still using the same specimen. In this case, each evaporation run -# needs to be distinguished with different run numbers. -# We follow this habit of most atom probe groups. Such interrupted runs -# should be stored as individual :ref:`NXentry` instances in one NeXus file. -# -# -# -# -# Either an identifier or an alias that is human-friendly so that scientists find that experiment again. -# For experiments usually this is the run_number but for simulation typically no run_numbers are issued. -# -# -# -# -# Free-text description about the experiment. -# -# Users are strongly advised to parameterize the description of their experiment -# by using respective groups and fields and base classes instead of writing prose -# into this field. -# -# The reason is that such free-text field is difficult to machine-interpret. -# The motivation behind keeping this field for now is to learn in how far the -# current base classes need extension based on user feedback. -# -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information -# included when the atom probe session started. If the exact duration of -# the measurement is not relevant start_time only should be used. -# -# Often though it is useful to specify both start_time and end_time to -# capture more detailed bookkeeping of the experiment. The user should -# be aware that even with having both dates specified, it may not be -# possible to infer how long the experiment took or for how long data -# were collected. -# -# More detailed timing data over the course of the experiment have to be -# collected to compute this event chain during the experiment. For this -# purpose the :ref:`NXevent_data_apm` instance should be used. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC included -# when the atom probe session ended. -# -# -# -# -# How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime -# -# -# -# -# -# -# -# -# -# -# -# -# -# What type of atom probe experiment is performed? This field is meant to -# inform research data management systems to allow filtering: -# -# * apt are experiments where the analysis_chamber has no imaging gas. -# experiment with LEAP instruments are typically performed such. -# * fim are experiments where the analysis_chamber has an imaging gas, -# which should be specified with the atmosphere in the analysis_chamber group. -# * apt_fim should be used for combinations of the two imaging modes. -# few experiments of this type have been performed as this can be detrimental -# to LEAP systems (see `S. Katnagallu et al. <https://doi.org/10.1017/S1431927621012381>`_). -# * other should be used in combination with the user specifying details -# in the experiment_documentation field. -# -# If NXapm is used for storing details about a simulation use other for now. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Description of the sample from which the specimen was prepared or -# site-specifically cut out using e.g. a focused-ion beam instrument. -# -# The sample group is currently a place for storing suggestions from -# atom probers about knowledge they have gained about the sample. -# There are cases where the specimen is machined further or exposed to -# external stimuli during the experiment. In this case, these details should -# not be stored under sample but suggestions should be made -# how this application definition can be improved. -# -# In the future also details like how the grain_diameter was characterized, -# how the sample was prepared, how the material was heat-treated etc., -# should be stored. For this specific application definitions/schemas can be -# used which are then arranged and documented with a description of the -# workflow so that actionable graphs become instantiatable. -# -# -# -# -# Qualifier whether the sample is a real (in which case is_simulation should be set to false) -# or a virtual one (in which case is_simulation should be set to true). -# -# -# -# -# Given name/alias for the sample. -# -# -# -# -# Qualitative information about the grain size, here specifically -# described as the equivalent spherical diameter of an assumed -# average grain size for the crystal ensemble. -# Users of this information should be aware that although the grain -# diameter or radius is often referred to as grain size. -# -# In atom probe it is possible that the specimen may contain a few -# crystals only. In this case the grain_diameter is not a reliable -# descriptor. Reporting a grain size may be useful though as it allows -# judging if specific features are expected to be found in the -# detector hit map. -# -# -# -# -# Magnitude of the standard deviation of the grain_diameter. -# -# -# -# -# -# The temperature of the last heat treatment step before quenching. -# Knowledge about this value can give an idea how the sample -# was heat treated. However, if a documentation of the annealing -# treatment as a function of time is available one should better -# rely on this information and have it stored alongside the NeXus file. -# -# -# -# -# Magnitude of the standard deviation of the heat_treatment_temperature. -# -# -# -# -# Rate of the last quenching step. Knowledge about this value can give -# an idea how the sample was heat treated. However, there are many -# situations where one can imagine that the scalar value for just the -# quenching rate is insufficient. -# -# An example is when the sample was left in the furnace after the -# furnace was switched off. In this case the sample cools down with -# a specific rate of how this furnace cools down in the lab. -# Processes which in practice are often not documented. -# -# This can be problematic though because when the furnace door was left open -# or the ambient temperature in the lab changed, i.e. for a series of -# experiments where one is conducted on a hot summer day and the next -# during winter this can have an effect on the evolution of the microstructure. -# There are many cases where this has been reported to be an QA issue in industry, -# e.g. think about aging aluminum samples left on the factory -# parking lot on a hot summer day. -# -# -# -# -# Magnitude of the standard deviation of the heat_treatment_quenching_rate. -# -# -# -# -# -# The chemical composition of the sample. Typically, it is assumed that -# this more macroscopic composition is representative for the material -# so that the composition of the typically substantially less voluminous -# specimen probes from the more voluminous sample. -# -# -# -# -# -# -# -# -# -# -# -# -# -# Qualifier whether the specimen is a real (in which case is_simulation should be set to false) -# or a virtual one (in which case is_simulation should be set to true). -# -# -# -# -# Given name an alias. Better use identifierNAME and identifier_parent instead. -# A single NXentry should be used only for the characterization of a single specimen. -# -# -# -# -# Identifier of the sample from which the specimen was cut or the string -# n/a. The purpose of this field is to support functionalities for -# tracking sample provenance via a research data management system. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information -# when the specimen was prepared. -# -# Ideally, report the end of the preparation, i.e. the last known time -# the measured specimen surface was actively prepared. Ideally, this -# matches the last timestamp that is mentioned in the digital resource -# pointed to by identifier_parent. -# -# Knowing when the specimen was exposed to e.g. specific atmosphere is -# especially required for environmentally sensitive material such as -# hydrogen charged specimens or experiments including tracers with a -# short half time. Additional time stamps prior to preparation_date -# should better be placed in resources which describe but which do not -# pollute the description here with prose. Resolving these connected -# pieces of information is considered within the responsibility of the -# research data management system. -# -# -# -# -# List of comma-separated elements from the periodic table that are -# contained in the specimen. If the specimen substance has multiple -# components, all elements from each component must be included in -# `atom_types`. -# -# The purpose of the field is to offer research data management systems an -# opportunity to parse the relevant elements without having to interpret -# these from the resources pointed to by identifier_parent or walk through -# eventually deeply nested groups in data instances. -# -# -# -# -# Discouraged free-text field. -# -# -# -# -# Report if the specimen is polycrystalline, in which case it -# contains a grain or phase boundary, or if the specimen is a -# single crystal. -# -# -# -# -# Report if the specimen is amorphous. -# -# -# -# -# Ideally measured otherwise best elaborated guess of the initial radius of the -# specimen. -# -# -# -# -# Ideally measured otherwise best elaborated guess of the (initial) shank angle. -# This is a measure of the specimen taper. Define it in such a way that the base of the specimen -# is modelled as a conical frustrum so that the shank angle is the (shortest) angle between -# the specimen space z-axis and a vector on the lateral surface of the cone. -# -# -# -# -# -# The conventions used when reporting crystal orientations. -# We follow the best practices of the Material Science community -# that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# Convention how a positive rotation angle is defined when viewing -# from the end of the rotation unit vector towards its origin. -# This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# Counter_clockwise is equivalent to a right-handed choice. -# Clockwise is equivalent to a left-handed choice. -# -# -# -# -# -# -# -# -# How are rotations interpreted into an orientation according to convention 3 -# of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# -# How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) -# according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# The most frequently used convention is zxz, which is based on the work of H.-J. Bunge -# but other conventions are possible. Apart from undefined, proper Euler angles -# are distinguished from (improper) Tait-Bryan angles. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# To which angular range is the rotation angle argument of an -# axis-angle pair parameterization constrained according to -# convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# Which sign convention is followed when converting orientations -# between different parametrizations/representations according -# to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# -# -# A collection of coordinate systems. Several Euclidean -# coordinate systems (CS) are used in the field of atom probe: -# -# * World space; -# a CS specifying a local coordinate system of the planet earth which -# identifies into which direction gravity is pointing such that -# the laboratory space CS can be rotated into this world CS. -# * The laboratory space; -# a CS specifying the room where the instrument is located in or -# a physical landmark on the instrument, e.g. the direction of the -# transfer rod where positive is the direction how the rod -# has to be pushed during loading a specimen into the instrument. -# In summary, this CS is defined by the chassis of the instrument. -# * The specimen space; -# a CS affixed to either the base or the initial apex of the specimen, -# whose z axis points towards the detector. -# * The detector space; -# a CS affixed to the detector plane whose xy plane is usually in the -# detector and whose z axis points towards the specimen. -# This is a distorted space with respect to the reconstructed ion -# positions. -# * The reconstruction space; -# a CS in which the reconstructed ion positions are defined. -# The orientation depends on the analysis software used. -# * Eventually further coordinate systems attached to the -# flight path of individual ions might be defined. -# -# In atom probe microscopy a frequently used choice for the detector -# space (CS) is discussed with the so-called detector space image -# (stack). This is a stack of two-dimensional histograms of detected ions -# within a predefined evaporation identifier interval. Typically, the set of -# ion evaporation sequence identifiers is grouped into chunks. -# -# For each chunk a histogram of the ion hit positions on the detector -# is computed. This leaves the possibility for inconsistency between -# the so-called detector space and the e.g. specimen space. -# -# To avoid these ambiguities, instances of :ref:`NXtransformations` should be used. -# -# -# -# -# -# -# -# -# -# -# -# Base class for collecting a session with a real atom probe or field-ion microscope. -# -# Workflows used during experiments or simulations of atom probe and related field-evaporation -# research should be documented in more detail and be better contextualized not only because of -# ongoing developments and the tighter becoming connection between atom probe and other -# methods for material characterization foremost electron microscopy see e.g.: -# -# * `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_ -# * `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_ -# * `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_ -# * `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_ -# * `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ -# -# to mention but a few. -# -# To arrive at a design of base classes and an application definition that can be used -# for both real and simulated atom probe experiments it is worthwhile to recall concepts that are -# related to events and (molecular) ions: -# -# * Pulsing events which are used to trigger ion extraction events. -# * Physical events and corresponding signal triggered by an ion hitting the detector. -# Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. -# * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input -# and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are -# worthwhile to be considered further and eventually included in the reconstructed volume. -# * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually -# selected (molecular) ions based on which an instance of a reconstruction is created. -# * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values -# and charge states of the (molecular) ions to substantiate that some of these ions can be considered -# as rangeable ions and hence an iontype can be assigned to these via running peak finding algorithms -# and subsequent peak labeling. In the field of atom probe this these peak identification methods -# are known as ranging definitions. -# -# Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts -# are well distinguished. However, the algorithms used to transform correlations between pulses and physical events -# into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. -# -# Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme -# where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier -# i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. -# That is identifier_evaporation values take the role of an implicit time and course of the experiment given that -# ion extraction physically is a sequential process. -# -# There is a number of research groups who build own instruments and share different aspects of their technical -# specifications and approaches how they apply data processing e.g.: -# -# * `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_ -# * `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ -# * `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ -# -# to name but a few. -# -# Despite some of these activities embrace practices of open-source development, they use essentially the same -# workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface -# software is used to explore and thus analyze reconstructed atom probe datasets. -# -# Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. -# Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which -# scientific conclusions about the characterized material volume are made. Also here a reconstruction is -# point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. -# -# By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all -# the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. -# Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. -# We argue that this divide can be bridged with realizing the above-mentioned context and the realization that -# similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. -# -# A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed -# datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment -# and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting -# a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as -# (spatial) filtering and reconstruction algorithms. -# -# Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation -# simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. -# Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. -# Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. -# Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require -# simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps -# in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. -# Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) -# than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path -# such as local electrodes or physical obstacles and electric fields (controlled or stray fields). -# -# -# -# A statement whether the measurement was successful or failed prematurely. -# -# -# -# -# -# -# -# -# CAnalysis.CResults.fQuality -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Free text field for additional comments. -# -# -# -# -# -# -# Group to hold instances of :ref:`NXevent_data_apm`. -# -# Which temporal granularity is adequate depends on the situation and research -# question. Using a model which enables a collection of events offers the most -# flexible way to cater for both atom probe experiments or simulation. -# -# To monitor the course of an ion extraction experiment (or simulation) -# it makes sense to track time explicitly via time stamps or implicitly -# via e.g. a clock inside the instrument, such as the clock of the pulser -# and respective pulsing event identifier. -# -# As set and measured quantities typically change over time and we do not -# yet know during the measurement which of the events have associated -# (molecular) ions that will end up in the reconstructed volume, we must not -# document quantities as a function of the identifier_evaporation but as a -# function of the (pulsing) identifier_event. -# -# -# -# -# Instances should use event as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Simulation of ion extraction from matter via laser and/or voltage pulsing. -# -# -# -# -# -# A region-of-interest analyzed either during or after the session for which -# specific processed data of the measured or simulated data are available. -# -# -# -# -# SEM or TEM image of the initial specimen (ideally taken prior data acquisition). -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# For almost atom probe instruments (meta)data about raw data follow proprietary semantics. -# Therefore, this group can currently be used only to point to these digital artifacts -# in an effort to document all step of an analysis workflow. -# -# The physical quantities measured in an atom probe experiment are time-of-flight and -# tuples of arrival_time_pairs as a function of the event chain on the pulser. -# From these tuples hits are computed in a process called hit_finding. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# The number of wires in the detector. -# -# -# -# -# -# -# -# -# -# Alias tuple (begin, end) of each DLD wire of the detector. -# Order follows arrival_time_pairs. -# -# -# -# -# -# -# -# -# Raw readings from the analog-to-digital-converter -# timing circuits of the detector wires. -# -# -# -# -# -# -# -# -# -# -# Configuration of and results obtained from a hit finding algorithm. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Evaluated ion impact coordinates on the detector. -# Use the depends_on field to specify which reference -# frame the positions are defined. -# -# -# -# -# -# -# -# Defines in which reference frame the positions are defined. -# -# -# -# -# -# CRunHeader.fTotalEventGolden -# -# -# -# -# CRunHeader.fTotalEventIncomplete -# -# -# -# -# CRunHeader.fTotalEventMultiple -# -# -# -# -# CRunHeader.fTotalEventPartials -# -# -# -# -# CRunHeader.fTotalEventRecords -# -# -# -# -# Identifier used for each hit_quality type. -# Following the order of hit_quality_types. -# -# -# -# -# -# -# -# Hit quality identifier for each pulse. -# Identifier have to be within identifier_hit_quality. -# -# -# -# -# -# -# -# This processing yields for each ion with how many others it evaporated -# if these were collected on the same pulse. Extraction of multiple ions -# on one pulse on different or even the same pixel of the detector are possible. -# -# Multiplicity must not be confused with how many atoms of the same element -# a molecular ion contains. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Integer used to name the first pulse to know if there is an -# offset of the identifier_evaporation to zero. -# -# Identifiers can be defined either implicitly or explicitly. -# For implicit indexing identifiers are defined on the interval -# :math:`[identifier\_offset, identifier\_offset + c - 1]`. -# -# Therefore, implicit identifier are completely defined by the value of -# identifier_offset and cardinality. For example if identifier run from -# -2 to 3 the value for identifier_offset is -2. -# -# For explicit indexing the field identifier has to be used. -# Fortran-/Matlab- and C-/Python-style indexing have specific implicit -# identifier conventions where identifier_offset is 1 and 0 respectively. -# -# -# -# -# (Molecular) ion identifier which resolves the sequence in which -# the ions were evaporated but taking into account that a hit_finding -# and spatial_filtering was applied. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. -# -# The voltage-and-bowl correction is a data post-processing step to correct ion impact -# positions for flight path differences, detector bias, and nonlinearities. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Raw time-of-flight data without corrections. -# -# -# -# -# -# -# -# -# The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate -# -# -# -# -# Calibrated time-of-flight. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# For LEAP and IVAS/APSuite-based analyses root file which stores -# the settings whereby an RHIT/HITS file can be used to regenerate the -# reconstruction that is here referred to. -# -# The respective RHIT/HITS file should ideally be specified in the serialized -# group of the hit_finding section of this application definition. -# -# -# -# -# -# -# -# -# For LEAP and IVAS/APSuite-based analyses the resulting typically -# file with the reconstructed positions and (calibrated) mass-to-charge -# state ratio values. -# -# For other data collection/analysis software the data artifact which comes -# closest conceptually to AMETEK/Cameca's typical file formats. -# -# These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, -# which should be stored alongside this record in the research data -# management system. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# The respective ranging definitions file RNG/RRNG/ENV/HDF5. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# (Out-of-sync) background levels in ppm/ns -# reported by e.g. IVAS/APSuite for LEAP systems. -# -# -# -# -# MRP, mass-resolving power, `D. Larson et al. -# <https://doi.org/10.1007/978-1-4614-8721-0>`_ (p282, Eqs. D.7 and D.8). -# -# -# -# -# MRP, at which mrp_value was specified. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Category for the peak offering a qualitative statement of the location of the peak -# in light of limited mass-resolving power that is relevant for -# composition quantification. See `D. Larson et al. (p172) <https://doi.org/10.1007/978-1-4614-8721-0>`_ -# for examples of each category: -# -# * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` -# * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` -# * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states -# * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` -# * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` -# * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use ion as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXapm_charge_state_analysis.yaml b/contributed_definitions/nyaml/NXapm_charge_state_analysis.yaml deleted file mode 100644 index 5c24a66930..0000000000 --- a/contributed_definitions/nyaml/NXapm_charge_state_analysis.yaml +++ /dev/null @@ -1,295 +0,0 @@ -category: base -doc: | - Base class to document an algorithm for recovering charge state and nuclide composition of a (molecular) ion. - - Currently ranging definitions in the research field of atom probe face have limitations: - - 1. A ranging definition maps all signal within a mass-to-charge-state-ratio value interval - on one iontype. Facing limited mass-resolving-power, there are mass-to-charge-state-ratio - values, though, for which not only multiple (molecular) ions are indistinguishable but - also for which the current practice of documenting classical ranging definitions is incomplete. - 2. Indeed, ranging definitions often report only (for each interval) the - mass-to-charge-state-ratio intervals surplus the composition of elements - that build the (molecular) ion. - 3. Therefore, classical ranging definitions demand a post-processing with an algorithm - which can identify nuclides from which the (molecular) ion is constructed - and a charge state possibly recovered. Combinatorial algorithms are used for this purpose. - - This base class documents the configuration and results of such an algorithm. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n_cand: | - The number of also possible but different (molecular) ions. - n_ivec_max: | - Maximum number of allowed atoms per (molecular) ion (fragment). - n_variable: | - Number of entries -type: group -NXapm_charge_state_analysis(NXprocess): - - # Details and results of the combinatorial analyses of a ranging definition - # to clarify (if possible) the charge_state of an ion and its (not necessarily) - # unique combination of nuclides contained including their multiplicity. - # input/config - nuclides(NX_UINT): - unit: NX_UNITLESS - doc: | - Input constraint, list of nuclide_hash for typically elements used for the - ranging definition of the ion whose charge state the analyses covered. - The list contains each hash as many times as its multiplicity. - Nuclides are encoded using the hashing rule that is defined in :ref:`NXion`. - - As an example, a ranging definition H:2 O:1 is configured by setting nuclides to - a list with entries :math:`1 + 0 \cdot 256`, :math:`1 + 0 \cdot 256`, :math:`8 + 0 \cdot 256`. - An empty list does not release the constraint. Instead, a list with all elements - in the periodic table (encoded as nuclide_hash values) should be used, i.e. - :math:`1 + 0 \cdot 256`, :math:`2 + 0 \cdot 256`, and so on and so forth. - - Keep in mind that with a weakly constrained parameter space the combinatorial - analysis may become very time consuming! - dimensions: - rank: 1 - dim: (n_ivec_max,) - mass_to_charge_range(NX_FLOAT): - unit: NX_ANY - doc: | - Input constraint, interval within which (molecular) ions need to have the - mass-to-charge-state-ratio such that an ion qualifies as a candidate. - dimensions: - rank: 2 - dim: (1, 2) - min_half_life(NX_FLOAT): - unit: NX_TIME - doc: | - Input constraint, minimum half life for how long each nuclide of each - (molecular) ion needs to be stable such that the ion qualifies as a candidate. - min_abundance(NX_FLOAT): - unit: NX_DIMENSIONLESS - doc: | - Input constraint, minimum natural abundance of each nuclide of each - (molecular) ion such that the ion qualifies as a candidate. - sacrifice_isotopic_uniqueness(NX_BOOLEAN): - doc: | - If the value is false, it means that non-unique solutions are accepted. - These are solutions where multiple candidates have been built from - different nuclide instances but the charge_state of all the ions is the same. - - # min_abundance_product(NX_FLOAT): - # doc: | - # For each candidate TO BE DEFINED. - # unit: NX_DIMENSIONLESS - # dim: (n_cand,) - - # output/results - # the n_cand can be 1 in which case all quantities below are scalar - charge_state(NX_INT): - unit: NX_UNITLESS - doc: | - Signed charge, i.e. integer multiple of the elementary - charge of each candidate. - dimensions: - rank: 1 - dim: (n_cand,) - nuclide_hash(NX_UINT): - unit: NX_UNITLESS - doc: | - Table of nuclide instances of which each candidate is composed. - Each row vector is sorted in descending order. Unused values are nullified. - dimensions: - rank: 2 - dim: (n_cand, n_ivec_max) - mass(NX_FLOAT): - unit: NX_MASS - doc: | - Accumulated mass of the nuclides in each candidate. - Not corrected for quantum effects. - dimensions: - rank: 1 - dim: (n_cand,) - natural_abundance_product(NX_FLOAT): - unit: NX_DIMENSIONLESS - doc: | - The product of the natural abundances of the nuclides for each candidate. - dimensions: - rank: 1 - dim: (n_cand,) - shortest_half_life(NX_FLOAT): - unit: NX_TIME - doc: | - For each candidate the half life of that nuclide which has the shortest half - life. - dimensions: - rank: 1 - dim: (n_cand,) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 269baf13dc37b92fc6b8296cc469bae9de49ac49186adf2fde60b28e9dda1272 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# The number of also possible but different (molecular) ions. -# -# -# -# -# Maximum number of allowed atoms per (molecular) ion (fragment). -# -# -# -# -# Number of entries -# -# -# -# -# Base class to document an algorithm for recovering charge state and nuclide composition of a (molecular) ion. -# -# Currently ranging definitions in the research field of atom probe face have limitations: -# -# 1. A ranging definition maps all signal within a mass-to-charge-state-ratio value interval -# on one iontype. Facing limited mass-resolving-power, there are mass-to-charge-state-ratio -# values, though, for which not only multiple (molecular) ions are indistinguishable but -# also for which the current practice of documenting classical ranging definitions is incomplete. -# 2. Indeed, ranging definitions often report only (for each interval) the -# mass-to-charge-state-ratio intervals surplus the composition of elements -# that build the (molecular) ion. -# 3. Therefore, classical ranging definitions demand a post-processing with an algorithm -# which can identify nuclides from which the (molecular) ion is constructed -# and a charge state possibly recovered. Combinatorial algorithms are used for this purpose. -# -# This base class documents the configuration and results of such an algorithm. -# -# -# -# -# Input constraint, list of nuclide_hash for typically elements used for the -# ranging definition of the ion whose charge state the analyses covered. -# The list contains each hash as many times as its multiplicity. -# Nuclides are encoded using the hashing rule that is defined in :ref:`NXion`. -# -# As an example, a ranging definition H:2 O:1 is configured by setting nuclides to -# a list with entries :math:`1 + 0 \cdot 256`, :math:`1 + 0 \cdot 256`, :math:`8 + 0 \cdot 256`. -# An empty list does not release the constraint. Instead, a list with all elements -# in the periodic table (encoded as nuclide_hash values) should be used, i.e. -# :math:`1 + 0 \cdot 256`, :math:`2 + 0 \cdot 256`, and so on and so forth. -# -# Keep in mind that with a weakly constrained parameter space the combinatorial -# analysis may become very time consuming! -# -# -# -# -# -# -# -# Input constraint, interval within which (molecular) ions need to have the -# mass-to-charge-state-ratio such that an ion qualifies as a candidate. -# -# -# -# -# -# -# -# -# Input constraint, minimum half life for how long each nuclide of each -# (molecular) ion needs to be stable such that the ion qualifies as a candidate. -# -# -# -# -# Input constraint, minimum natural abundance of each nuclide of each -# (molecular) ion such that the ion qualifies as a candidate. -# -# -# -# -# If the value is false, it means that non-unique solutions are accepted. -# These are solutions where multiple candidates have been built from -# different nuclide instances but the charge_state of all the ions is the same. -# -# -# -# -# -# -# Signed charge, i.e. integer multiple of the elementary -# charge of each candidate. -# -# -# -# -# -# -# -# Table of nuclide instances of which each candidate is composed. -# Each row vector is sorted in descending order. Unused values are nullified. -# -# -# -# -# -# -# -# -# Accumulated mass of the nuclides in each candidate. -# Not corrected for quantum effects. -# -# -# -# -# -# -# -# The product of the natural abundances of the nuclides for each candidate. -# -# -# -# -# -# -# -# For each candidate the half life of that nuclide which has the shortest half -# life. -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml index 2b134ba74d..be057b2356 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml @@ -9,68 +9,65 @@ doc: | CompositionSpace tool by using the NeXus data model and semantics. type: group NXapm_compositionspace_config(NXobject): - - # by default for application definitions the value of the exists keyword is required unless it is explicitly specified differently (NXentry): exists: ['min', '1', 'max', '1'] definition(NX_CHAR): \@version(NX_CHAR): exists: optional enumeration: [NXapm_compositionspace_config] - config(NXobject): - identifier_analysis(NX_UINT): + identifier_analysis(NX_UINT): + exists: recommended + reconstruction(NXnote): + doc: | + Specification of the tomographic reconstruction used for this analysis. + Typically, reconstructions in the field of atom probe tomography are communicated via + files which store at least reconstructed ion positions and mass-to-charge-state-ratio + values. Container files like HDF5 though can store multiple reconstructions. + Therefore, the position and mass_to_charge concepts point to specific instances + to use for this analysis. + type(NX_CHAR): + exists: optional + file_name(NX_CHAR): + checksum(NX_CHAR): exists: recommended - reconstruction(NXnote): + algorithm(NX_CHAR): + exists: recommended + position(NX_CHAR): doc: | - Specification of the tomographic reconstruction used for this analysis. - Typically, reconstructions in the field of atom probe tomography are communicated via - files which store at least reconstructed ion positions and mass-to-charge-state-ratio - values. Container files like HDF5 though can store multiple reconstructions. - Therefore, the position and mass_to_charge concepts point to specific instances - to use for this analysis. - type(NX_CHAR): - exists: optional - file_path(NX_CHAR): - checksum(NX_CHAR): - exists: recommended - algorithm(NX_CHAR): - exists: recommended - position(NX_CHAR): - doc: | - Name of the node which resolves the reconstructed - ion position values to use for this analysis. - mass_to_charge(NX_CHAR): - exists: optional - doc: | - Name of the node which resolves the mass-to-charge-state ratio - values for each reconstructed ion to use for this analysis. - ranging(NXnote): + Name of the node which resolves the reconstructed + ion position values to use for this analysis. + mass_to_charge(NX_CHAR): + exists: optional doc: | - Specification of the ranging definitions used for this analysis. - - Indices start from 1. The value 0 is reserved for the null model of unranged positions whose - iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. - type(NX_CHAR): - exists: optional - file_path(NX_CHAR): - checksum(NX_CHAR): - exists: recommended - algorithm(NX_CHAR): - exists: recommended - ranging_definitions(NX_CHAR): - doc: | - Name of the (parent) node directly below which the ranging definitions for - (molecular) ions are stored. - voxelization(NXprocess): + Name of the node which resolves the mass-to-charge-state ratio + values for each reconstructed ion to use for this analysis. + ranging(NXnote): + doc: | + Specification of the ranging definitions used for this analysis. + + Indices start from 1. The value 0 is reserved for the null model of unranged positions whose + iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. + type(NX_CHAR): + exists: optional + file_name(NX_CHAR): + checksum(NX_CHAR): + exists: recommended + algorithm(NX_CHAR): + exists: recommended + ranging_definitions(NX_CHAR): doc: | - Step during which the point cloud is discretized to compute element-specific composition fields. - Iontypes are atomically decomposed to correctly account for the multiplicity of each element that - was ranged for each ion. - edge_length(NX_NUMBER): - unit: NX_LENGTH - doc: | - Edge length of cubic voxels building the 3D grid that is used for discretizing - the point cloud. + Name of the (parent) node directly below which the ranging definitions for + (molecular) ions are stored. + voxelization(NXprocess): + doc: | + Step during which the point cloud is discretized to compute element-specific composition fields. + Iontypes are atomically decomposed to correctly account for the multiplicity of each element that + was ranged for each ion. + edge_length(NX_NUMBER): + unit: NX_LENGTH + doc: | + Edge length of cubic voxels building the 3D grid that is used for discretizing + the point cloud. autophase(NXprocess): doc: | Optional step during which the subsequent segmentation step is prepared with the aim to eventually @@ -97,51 +94,63 @@ NXapm_compositionspace_config(NXobject): exists: optional doc: | Configuration for the random forest classification model. - segmentation(NXprocess): + segmentation(NXprocess): + doc: | + Step during which the voxel set is segmented into voxel sets with different + chemical composition. + pca(NXprocess): + exists: optional doc: | - Step during which the voxel set is segmented into voxel sets with different - chemical composition. - pca(NXprocess): - exists: optional + A principal component analysis of the chemical space to guide a decision into how many sets of voxels + with different chemical composition the machine learning algorithm suggests to split the voxel set. + ic_opt(NXprocess): + doc: | + The decision is guided through the evaluation of the information criterion + minimization. + n_max_ic_cluster(NX_POSINT): + unit: NX_UNITLESS doc: | - A principal component analysis of the chemical space to guide a decision into how many sets of voxels - with different chemical composition the machine learning algorithm suggests to split the voxel set. - ic_opt(NXprocess): + The maximum number of chemical classes to probe with the Gaussian mixture model + with which the voxel set is segmented into a mixture of voxels with that many different + chemical compositions. + gaussian_mixture(NXprocess): + exists: optional doc: | - The decision is guided through the evaluation of the information criterion - minimization. - n_max_ic_cluster(NX_POSINT): - unit: NX_UNITLESS - doc: | - The maximum number of chemical classes to probe with the Gaussian mixture model - with which the voxel set is segmented into a mixture of voxels with that many different - chemical compositions. - gaussian_mixture(NXprocess): - exists: optional - doc: | - Configuration for the Gaussian mixture model that is used in the segmentation - step. - clustering(NXprocess): + Configuration for the Gaussian mixture model that is used in the segmentation + step. + clustering(NXprocess): + doc: | + Step during which the chemically segmented voxel sets are analyzed for their + spatial organization. + dbscan(NXparameters): doc: | - Step during which the chemically segmented voxel sets are analyzed for their - spatial organization. - dbscan(NXobject): + Configuration for the DBScan algorithm that is used in the clustering step. + eps(NX_FLOAT): + unit: NX_LENGTH + doc: | + The maximum distance between voxel pairs in a neighborhood to be considered + connected. + min_samples(NX_UINT): + unit: NX_UNITLESS doc: | - Configuration for the DBScan algorithm that is used in the clustering step. - eps(NX_FLOAT): - unit: NX_LENGTH - doc: | - The maximum distance between voxel pairs in a neighborhood to be considered - connected. - min_samples(NX_UINT): - unit: NX_UNITLESS - doc: | - The number of voxels in a neighborhood for a voxel to be considered as a core - point. + The number of voxels in a neighborhood for a voxel to be considered as a core + point. + + # meshing(NXprocess): + # doc: | + # TODO + # distance_cut(NX_NUMBER): + # doc: | + # TODO + # units: NX_ANY + # normal_end_length(NX_NUMBER): + # doc: | + # TODO + # units: NX_ANY # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 7fddc5781400cffe09b044d5429d7fe0b455304de680629ca951870bcac17348 -# +# ca8663cc1ce83dc2b909222722579b297373777ad01ebda5c5fa954862339b06 +# # # # # # @@ -182,65 +190,63 @@ NXapm_compositionspace_config(NXobject): # # # -# -# -# +# +# +# +# Specification of the tomographic reconstruction used for this analysis. +# Typically, reconstructions in the field of atom probe tomography are communicated via +# files which store at least reconstructed ion positions and mass-to-charge-state-ratio +# values. Container files like HDF5 though can store multiple reconstructions. +# Therefore, the position and mass_to_charge concepts point to specific instances +# to use for this analysis. +# +# +# +# +# +# # -# Specification of the tomographic reconstruction used for this analysis. -# Typically, reconstructions in the field of atom probe tomography are communicated via -# files which store at least reconstructed ion positions and mass-to-charge-state-ratio -# values. Container files like HDF5 though can store multiple reconstructions. -# Therefore, the position and mass_to_charge concepts point to specific instances -# to use for this analysis. +# Name of the node which resolves the reconstructed +# ion position values to use for this analysis. # -# -# -# -# -# -# -# Name of the node which resolves the reconstructed -# ion position values to use for this analysis. -# -# -# -# -# Name of the node which resolves the mass-to-charge-state ratio -# values for each reconstructed ion to use for this analysis. -# -# -# -# +# +# # -# Specification of the ranging definitions used for this analysis. -# -# Indices start from 1. The value 0 is reserved for the null model of unranged positions whose -# iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. +# Name of the node which resolves the mass-to-charge-state ratio +# values for each reconstructed ion to use for this analysis. # -# -# -# -# -# -# -# Name of the (parent) node directly below which the ranging definitions for -# (molecular) ions are stored. -# -# -# -# +# +# +# +# +# Specification of the ranging definitions used for this analysis. +# +# Indices start from 1. The value 0 is reserved for the null model of unranged positions whose +# iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. +# +# +# +# +# +# # -# Step during which the point cloud is discretized to compute element-specific composition fields. -# Iontypes are atomically decomposed to correctly account for the multiplicity of each element that -# was ranged for each ion. +# Name of the (parent) node directly below which the ranging definitions for +# (molecular) ions are stored. # -# -# -# Edge length of cubic voxels building the 3D grid that is used for discretizing -# the point cloud. -# -# -# +# +# +# +# +# Step during which the point cloud is discretized to compute element-specific composition fields. +# Iontypes are atomically decomposed to correctly account for the multiplicity of each element that +# was ranged for each ion. +# +# +# +# Edge length of cubic voxels building the 3D grid that is used for discretizing +# the point cloud. +# +# # # # Optional step during which the subsequent segmentation step is prepared with the aim to eventually @@ -274,60 +280,71 @@ NXapm_compositionspace_config(NXobject): # # # -# +# +# +# +# Step during which the voxel set is segmented into voxel sets with different +# chemical composition. +# +# # -# Step during which the voxel set is segmented into voxel sets with different -# chemical composition. +# A principal component analysis of the chemical space to guide a decision into how many sets of voxels +# with different chemical composition the machine learning algorithm suggests to split the voxel set. # -# +# +# +# +# The decision is guided through the evaluation of the information criterion +# minimization. +# +# # -# A principal component analysis of the chemical space to guide a decision into how many sets of voxels -# with different chemical composition the machine learning algorithm suggests to split the voxel set. +# The maximum number of chemical classes to probe with the Gaussian mixture model +# with which the voxel set is segmented into a mixture of voxels with that many different +# chemical compositions. # -# -# +# +# # -# The decision is guided through the evaluation of the information criterion -# minimization. +# Configuration for the Gaussian mixture model that is used in the segmentation +# step. # -# -# -# The maximum number of chemical classes to probe with the Gaussian mixture model -# with which the voxel set is segmented into a mixture of voxels with that many different -# chemical compositions. -# -# -# -# -# Configuration for the Gaussian mixture model that is used in the segmentation -# step. -# -# # # -# +# +# +# +# Step during which the chemically segmented voxel sets are analyzed for their +# spatial organization. +# +# # -# Step during which the chemically segmented voxel sets are analyzed for their -# spatial organization. +# Configuration for the DBScan algorithm that is used in the clustering step. # -# +# # -# Configuration for the DBScan algorithm that is used in the clustering step. +# The maximum distance between voxel pairs in a neighborhood to be considered +# connected. # -# -# -# The maximum distance between voxel pairs in a neighborhood to be considered -# connected. -# -# -# -# -# The number of voxels in a neighborhood for a voxel to be considered as a core -# point. -# -# -# +# +# +# +# The number of voxels in a neighborhood for a voxel to be considered as a core +# point. +# +# # # # +# # diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml index da22d39d28..8e65f89089 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml @@ -18,23 +18,35 @@ symbols: Total number of ions in the reconstructed dataset. type: group NXapm_compositionspace_results(NXobject): - - # by default for application definitions the value of the exists keyword is required unless it is explicitly specified differently (NXentry): exists: ['min', '1', 'max', '1'] definition(NX_CHAR): \@version(NX_CHAR): exists: optional enumeration: [NXapm_compositionspace_results] - - # can be used for the name of the tool and version but also - # for if desired all the dependencies and libraries - (NXprogram): + identifier_analysis(NX_UINT): + exists: recommended + profiling(NXcs_profiling): + exists: optional + current_working_directory(NX_CHAR): + exists: recommended + start_time(NX_DATE_TIME): + exists: recommended + end_time(NX_DATE_TIME): + exists: recommended + total_elapsed_time(NX_NUMBER): + program1(NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): - identifier_analysis(NX_UINT): + environment(NXcollection): exists: recommended + doc: | + Programs and libraries representing the computational environment + (NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + program(NX_CHAR): + \@version(NX_CHAR): # config config(NXnote): @@ -52,14 +64,17 @@ NXapm_compositionspace_results(NXobject): (NXuser): exists: optional specimen(NXsample): + exists: recommended doc: | Contextualize back to the specimen from which the dataset was collected that was here analyzed with CompositionSpace tool. - type(NX_CHAR): + is_simulation(NX_BOOLEAN): doc: | - A qualifier whether the specimen is a real one or a virtual one. - enumeration: [experiment, simulation] + True, if the specimen that the reconstructed dataset + describes is a simulated one. + False, if the specimen that the reconstructed dataset + describes is a real one. atom_types(NX_CHAR): doc: | List of comma-separated elements from the periodic table that are @@ -98,7 +113,7 @@ NXapm_compositionspace_results(NXobject): extent(NX_POSINT): dimensions: dim: (grid_dim,) - identifier_offset(NX_INT): + index_offset(NX_INT): unit: NX_UNITLESS position(NX_NUMBER): unit: NX_LENGTH @@ -114,7 +129,7 @@ NXapm_compositionspace_results(NXobject): dim: (n_voxels, grid_dim) # bounding box if needed - identifier_voxel(NX_UINT): + indices_voxel(NX_INT): unit: NX_UNITLESS doc: | For each ion, the identifier of the voxel into which the ion binned. @@ -127,7 +142,7 @@ NXapm_compositionspace_results(NXobject): for the occupancy of each voxel with atoms. dimensions: dim: (n_voxels,) - (NXion): + (NXatom): exists: ['min', '1', 'max', 'unbounded'] name(NX_CHAR): doc: | @@ -153,7 +168,7 @@ NXapm_compositionspace_results(NXobject): nameType: partial title(NX_CHAR): exists: recommended - identifier_axis_feature(NX_UINT): + axis_feature_indices(NX_UINT): unit: NX_DIMENSIONLESS doc: | Element identifier stored sorted in descending order of feature importance. @@ -208,12 +223,10 @@ NXapm_compositionspace_results(NXobject): Information criterion minimization. sequence_index(NX_POSINT): enumeration: [3, 4] - CLUSTER_ANALYSIS(NXprocess): - nameType: any + cluster_analysisID(NXprocess): + nameType: partial doc: | Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. - - Instances should use cluster_analysis as a name prefix. n_ic_cluster(NX_UINT): unit: NX_UNITLESS doc: | @@ -260,24 +273,20 @@ NXapm_compositionspace_results(NXobject): not-necessarily watertight or topologically closed objects built from individual voxels. sequence_index(NX_POSINT): enumeration: [4, 5] - ic_opt(NXobject): + ic_opt(NXprocess): doc: | Respective DBScan clustering result for each segmentation/ic_opt case. - CLUSTER_ANALYSIS(NXprocess): + cluster_analysisID(NXprocess): exists: ['min', '0', 'max', 'unbounded'] - nameType: any - doc: | - Instances should use cluster_analysis as a name prefix. - DBSCAN(NXprocess): + nameType: partial + dbscanID(NXprocess): exists: ['min', '1', 'max', 'unbounded'] - nameType: any + nameType: partial epsilon(NX_FLOAT): unit: NX_LENGTH doc: | The maximum distance between voxel pairs in a neighborhood to be considered connected. - - Instances should use dbscan as a name prefix. min_samples(NX_UINT): unit: NX_UNITLESS doc: | @@ -298,28 +307,15 @@ NXapm_compositionspace_results(NXobject): specifies for which voxel in the grid clusters from this process were found. dimensions: dim: (n_voxels,) - profiling(NXcs_profiling): - exists: optional - current_working_directory(NX_CHAR): - exists: recommended - start_time(NX_DATE_TIME): - exists: recommended - end_time(NX_DATE_TIME): - exists: recommended - total_elapsed_time(NX_NUMBER): - - # number_of_processes(NX_POSINT): - # number_of_threads(NX_POSINT): - # number_of_gpus(NX_POSINT): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 72b1a2247b9862efa2ba693260918f404055a5d15e305d07c90c9bcbe1f0f60f -# +# 735b187b1429dbf082283a98acd44503f05d26cfbd5ccad861338be7411fa7ac +# # # # # # @@ -375,14 +370,28 @@ NXapm_compositionspace_results(NXobject): # # # -# -# +# +# +# +# +# +# +# +# # # # # -# +# +# +# Programs and libraries representing the computational environment +# +# +# +# +# +# +# # # # @@ -395,20 +404,19 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # Contextualize back to the specimen from which the # dataset was collected that was here analyzed with # CompositionSpace tool. # -# +# # -# A qualifier whether the specimen is a real one or a virtual one. +# True, if the specimen that the reconstructed dataset +# describes is a simulated one. +# False, if the specimen that the reconstructed dataset +# describes is a real one. # -# -# -# -# # # # @@ -466,7 +474,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # # Position of each cell in Euclidean space. @@ -486,7 +494,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # For each ion, the identifier of the voxel into which the ion binned. # @@ -504,7 +512,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # # Chemical symbol of the element from the periodic table. @@ -536,7 +544,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # Element identifier stored sorted in descending order of feature importance. # @@ -614,11 +622,9 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. -# -# Instances should use cluster_analysis as a name prefix. # # # @@ -681,21 +687,16 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # Respective DBScan clustering result for each segmentation/ic_opt case. # -# -# -# Instances should use cluster_analysis as a name prefix. -# -# +# +# # # # The maximum distance between voxel pairs in a neighborhood # to be considered connected. -# -# Instances should use dbscan as a name prefix. # # # @@ -727,14 +728,5 @@ NXapm_compositionspace_results(NXobject): # # # -# -# -# -# -# -# # -# # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml index 0e973c29c5..14b23a39f3 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml @@ -7,8 +7,7 @@ symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. - # n_positions: Number of position values. - # n_disjoint_clusters: Number of disjoint cluster. + # n_positions, n_disjoint_clusters n_ivec_max: | Maximum number of atoms per molecular ion. Should be 32 for paraprobe. n_clust_algos: | @@ -65,17 +64,16 @@ NXapm_paraprobe_clusterer_config(NXobject): # recover_bitmask(NX_BOOLEAN): # doc: | # Specifies if the tool should try to recover, after a recovery of the - # evaporation IDs a bitmask which identifies which of the positions + # evaporation_id a bitmask which identifies which of the positions # in dataset/dataset/dataset_name_reconstruction where covered # by the IVAS/APSuite cluster analysis. This can be useful to recover # the region of interest. - CLUSTER_ANALYSIS(NXapm_paraprobe_tool_config): + cluster_analysisID(NXapm_paraprobe_tool_config): + nameType: partial exists: ['min', '0', 'max', 'unbounded'] doc: | This process performs a cluster analysis on a reconstructed dataset or a ROI within it. - - Instances should use cluster_analysis as a name prefix. reconstruction(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -104,14 +102,14 @@ NXapm_paraprobe_clusterer_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -119,7 +117,7 @@ NXapm_paraprobe_clusterer_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -132,10 +130,6 @@ NXapm_paraprobe_clusterer_config(NXobject): number_of_objects(NX_UINT): bitdepth(NX_UINT): mask(NX_UINT): - - # leave open if scalar or matrix - # dim: (i,) - # identifier(NX_UINT): evaporation_id_filter(NXsubsampling_filter): exists: optional min_incr_max(NX_INT): @@ -317,8 +311,8 @@ NXapm_paraprobe_clusterer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f986e00c983c27fa7f7121a25902d457ce5ef89a366de044e4141f68a3f268f1 -# +# a2cf168bee2387ccb8f0c8cd2ba8610829d582cd9429a5ee6797c0e1eedb1022 +# # # +# # # # Maximum number of atoms per molecular ion. Should be 32 for paraprobe. @@ -425,16 +418,14 @@ NXapm_paraprobe_clusterer_config(NXobject): # -# +# # # This process performs a cluster analysis on a # reconstructed dataset or a ROI within it. -# -# Instances should use cluster_analysis as a name prefix. # # # @@ -466,7 +457,7 @@ NXapm_paraprobe_clusterer_config(NXobject): # # # -# +# # # # @@ -474,7 +465,7 @@ NXapm_paraprobe_clusterer_config(NXobject): # # # -# +# # # # @@ -482,7 +473,7 @@ NXapm_paraprobe_clusterer_config(NXobject): # # # -# +# # # # @@ -495,9 +486,6 @@ NXapm_paraprobe_clusterer_config(NXobject): # # # -# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml index d9f46e7df3..61aec9b38a 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml @@ -36,12 +36,11 @@ NXapm_paraprobe_clusterer_results(NXobject): mask(NX_UINT): # results - DBSCAN(NXsimilarity_grouping): + dbscanID(NXsimilarity_grouping): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial doc: | Results of a DBScan clustering analysis. - - Instances should use dbscan as a name prefix. eps(NX_FLOAT): unit: NX_LENGTH doc: | @@ -50,28 +49,29 @@ NXapm_paraprobe_clusterer_results(NXobject): unit: NX_UNITLESS doc: | The minimum points (min_pts) parameter used. - cardinality(NX_UINT): + cardinality(NX_POSINT): unit: NX_UNITLESS doc: | Number of members in the set which is partitioned into features. Specifically, this is the total number of targets filtered from the dataset, i.e. typically the number of clusters which is usually not and for sure not necessarily the total number of ions in the dataset. - identifier_offset(NX_INT): + index_offset(NX_INT): + unit: NX_UNITLESS doc: | Which identifier is the first to be used to label a cluster. The value should be chosen in such a way that special values can be resolved: - * identifier_offset - 1 indicates an object belongs to no cluster. - * identifier_offset - 2 indicates an object belongs to the noise category. + * index_offset - 1 indicates an object belongs to no cluster. + * index_offset - 2 indicates an object belongs to the noise category. - Setting for instance identifier_offset to 1 recovers the commonly used + Setting for instance index_offset to 1 recovers the commonly used case that objects of the noise category get the value of -1 and points of the unassigned category get the value 0. targets(NX_UINT): unit: NX_UNITLESS doc: | - The evaporation (sequence) identifier (aka identifier_evaporation) to figure out + The evaporation (sequence) id (aka evaporation_id) to figure out which ions from the reconstruction were considered targets. The length of this array is not necessarily n_ions. Instead, it is the value of cardinality. @@ -142,10 +142,6 @@ NXapm_paraprobe_clusterer_results(NXobject): dimensions: rank: 1 dim: (k,) - - # number_of_objects(NX_UINT): - # bitdepth(NX_UINT): - # mask(NX_UINT): is_noise(NX_BOOLEAN): exists: optional doc: | @@ -153,10 +149,6 @@ NXapm_paraprobe_clusterer_results(NXobject): dimensions: rank: 1 dim: (k,) - - # number_of_objects(NX_UINT): - # bitdepth(NX_UINT): - # mask(NX_UINT): is_core(NX_BOOLEAN): exists: optional doc: | @@ -173,14 +165,15 @@ NXapm_paraprobe_clusterer_results(NXobject): # at the level of the set of targets number_of_targets(NX_UINT): + unit: NX_UNITLESS doc: | Total number of targets in the set, i.e. ions that were filtered and considered in this cluster analysis. - number_of_noise(NX_UINT): + number_of_noise_members(NX_UINT): unit: NX_UNITLESS doc: | Total number of members in the set which are categorized as noise. - number_of_core(NX_UINT): + number_of_core_members(NX_UINT): unit: NX_UNITLESS doc: | Total number of members in the set which are categorized as a core point. @@ -190,14 +183,14 @@ NXapm_paraprobe_clusterer_results(NXobject): Total number of clusters (excluding noise and unassigned). # at the level of the feature set - identifier_feature(NX_UINT): + indices_feature(NX_INT): unit: NX_UNITLESS doc: | - Numerical identifier of each feature aka identifier_cluster. + Numerical identifier of each feature aka cluster_id. dimensions: rank: 1 dim: (n_feat,) - feature_member_count(NX_UINT): + number_of_members(NX_UINT): unit: NX_UNITLESS doc: | Number of members for each feature. @@ -218,38 +211,36 @@ NXapm_paraprobe_clusterer_results(NXobject): end_time(NX_DATE_TIME): total_elapsed_time(NX_FLOAT): current_working_directory(NX_CHAR): - number_of_processes(NX_POSINT): - number_of_threads(NX_POSINT): - number_of_gpus(NX_POSINT): + number_of_processes(NX_UINT): + number_of_threads(NX_UINT): + number_of_gpus(NX_UINT): (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. name(NX_CHAR): - coordinate_system_set(NXcoordinate_system_set): - exists: ['min', '1', 'max', '1'] - paraprobe(NXcoordinate_system): - type(NX_CHAR): - handedness(NX_CHAR): - x(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - y(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - z(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) + paraprobe(NXcoordinate_system): + type(NX_CHAR): + handedness(NX_CHAR): + x(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + y(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + z(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0f3236fc7f667546b711f80a9e964b3f8ada5ef723619dde316e539efd4fabdb -# +# b549210ac96c1a0b9159ec25b304a47b9e93907c4e4653712ce7d31e1df44001 +# # # -# +# # -# Results of a DBScan clustering analysis. -# -# Instances should use dbscan as a name prefix. +# Results of a DBScan clustering analysis. # # # -# The epsilon (eps) parameter used. +# The epsilon (eps) parameter used. # # # # -# The minimum points (min_pts) parameter used. +# The minimum points (min_pts) parameter used. # # -# +# # -# Number of members in the set which is partitioned into features. -# Specifically, this is the total number of targets filtered from the -# dataset, i.e. typically the number of clusters which is usually not and -# for sure not necessarily the total number of ions in the dataset. +# Number of members in the set which is partitioned into features. +# Specifically, this is the total number of targets filtered from the +# dataset, i.e. typically the number of clusters which is usually not and +# for sure not necessarily the total number of ions in the dataset. # # -# +# # -# Which identifier is the first to be used to label a cluster. -# -# The value should be chosen in such a way that special values can be resolved: -# * identifier_offset - 1 indicates an object belongs to no cluster. -# * identifier_offset - 2 indicates an object belongs to the noise category. -# -# Setting for instance identifier_offset to 1 recovers the commonly used -# case that objects of the noise category get the value of -1 and points of the -# unassigned category get the value 0. +# Which identifier is the first to be used to label a cluster. +# +# The value should be chosen in such a way that special values can be resolved: +# * index_offset - 1 indicates an object belongs to no cluster. +# * index_offset - 2 indicates an object belongs to the noise category. +# +# Setting for instance index_offset to 1 recovers the commonly used +# case that objects of the noise category get the value of -1 and points of the +# unassigned category get the value 0. # # # # -# The evaporation (sequence) identifier (aka identifier_evaporation) to figure out -# which ions from the reconstruction were considered targets. The length -# of this array is not necessarily n_ions. -# Instead, it is the value of cardinality. +# The evaporation (sequence) id (aka evaporation_id) to figure out +# which ions from the reconstruction were considered targets. The length +# of this array is not necessarily n_ions. +# Instead, it is the value of cardinality. # # # @@ -367,11 +356,11 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# The number of solutions found for each target. Typically, -# this value is 1 in which case the field can be omitted. -# Otherwise, this array is the concatenated set of values of solution -# tuples for each target that can be used to decode model_labels, -# core_sample_indices, and weight. +# The number of solutions found for each target. Typically, +# this value is 1 in which case the field can be omitted. +# Otherwise, this array is the concatenated set of values of solution +# tuples for each target that can be used to decode model_labels, +# core_sample_indices, and weight. # # # @@ -379,12 +368,12 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# The raw labels from the DBScan clustering backend process. -# The length of this array is not necessarily n_ions. -# Instead, it is typically the value of cardinality provided that each -# target has only one associated cluster. If targets are assigned to -# multiple cluster this array is as long as the total number of solutions -# found and +# The raw labels from the DBScan clustering backend process. +# The length of this array is not necessarily n_ions. +# Instead, it is typically the value of cardinality provided that each +# target has only one associated cluster. If targets are assigned to +# multiple cluster this array is as long as the total number of solutions +# found and # # # @@ -392,8 +381,8 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# The raw array of core sample indices which specify which of the -# targets are core points. +# The raw array of core sample indices which specify which of the +# targets are core points. # # # @@ -401,7 +390,7 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# Numerical label for each target (member in the set) aka cluster identifier. +# Numerical label for each target (member in the set) aka cluster identifier. # # # @@ -409,7 +398,7 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# Categorical label(s) for each target (member in the set) aka cluster name(s). +# Categorical label(s) for each target (member in the set) aka cluster name(s). # # # @@ -417,39 +406,29 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# Weights for each target that specifies how probable the target is assigned to -# a specific cluster. -# -# For the DBScan algorithm and atom probe tomography this value is the -# multiplicity of each ion with respect to the cluster. That is how many times -# should the position of the ion be accounted for because the ion is e.g. a -# molecular ion with several elements or nuclides of requested type. +# Weights for each target that specifies how probable the target is assigned to +# a specific cluster. +# +# For the DBScan algorithm and atom probe tomography this value is the +# multiplicity of each ion with respect to the cluster. That is how many times +# should the position of the ion be accounted for because the ion is e.g. a +# molecular ion with several elements or nuclides of requested type. # # # # # -# # # -# Are targets assigned to the noise category or not. +# Are targets assigned to the noise category or not. # # # # # -# # # -# Are targets assumed a core point. +# Are targets assumed a core point. # # # @@ -457,44 +436,44 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# In addition to the detailed storage which members were grouped to which -# feature here summary statistics are stored that communicate e.g. how many -# cluster were found. +# In addition to the detailed storage which members were grouped to which +# feature here summary statistics are stored that communicate e.g. how many +# cluster were found. # # -# +# # -# Total number of targets in the set, i.e. ions that were filtered -# and considered in this cluster analysis. +# Total number of targets in the set, i.e. ions that were filtered +# and considered in this cluster analysis. # # -# +# # -# Total number of members in the set which are categorized as noise. +# Total number of members in the set which are categorized as noise. # # -# +# # -# Total number of members in the set which are categorized as a core point. +# Total number of members in the set which are categorized as a core point. # # # # -# Total number of clusters (excluding noise and unassigned). +# Total number of clusters (excluding noise and unassigned). # # # -# +# # -# Numerical identifier of each feature aka identifier_cluster. +# Numerical identifier of each feature aka cluster_id. # # # # # -# +# # -# Number of members for each feature. +# Number of members for each feature. # # # @@ -516,36 +495,34 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# -# -# +# +# +# # # # -# If used, metadata of at least the person who performed this analysis. +# If used, metadata of at least the person who performed this analysis. # # # -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml index 4b7d52752d..50a272e9d4 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml @@ -38,14 +38,14 @@ NXapm_paraprobe_distancer_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -53,7 +53,7 @@ NXapm_paraprobe_distancer_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -66,10 +66,8 @@ NXapm_paraprobe_distancer_config(NXobject): number_of_objects(NX_UINT): bitdepth(NX_UINT): mask(NX_UINT): - - # leave open if scalar or matrix - # dim: (i,) - identifier(NX_UINT): + + # evaporation_id_filter(NXsubsampling_filter): exists: optional min_incr_max(NX_INT): @@ -106,17 +104,15 @@ NXapm_paraprobe_distancer_config(NXobject): How many triangle sets to consider. Multiple triangle sets can be defined which are composed into one joint triangle set for the analysis. - TRIANGLE_SET(NXnote): - nameType: any + triangle_setID(NXnote): + nameType: partial exists: ['min', '1', 'max', 'unbounded'] doc: | Each triangle_set that is referred to here should be a face_list_data_structure, i.e. an array of (n_vertices, 3) of NX_FLOAT for vertex coordinates, an (n_facets, 3) array of NX_UINT incident vertices of each facet. Vertex indices are assumed to - start at zero and must not exceed n_vertices - 1, i.e. the identifier_offset is 0. + start at zero and must not exceed n_vertices - 1, i.e. the index_offset is 0. Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. - - Instances should use triangle_set as a name prefix. type(NX_CHAR): algorithm(NX_CHAR): checksum(NX_CHAR): @@ -139,7 +135,7 @@ NXapm_paraprobe_distancer_config(NXobject): doc: | Absolute path in the (HDF5) file that points to the array of facet normal vectors for the triangles in that triangle_set. - identifier_patch(NX_CHAR): + indices_patch(NX_CHAR): exists: optional doc: | Absolute path in the (HDF5) file that points to the array @@ -164,8 +160,8 @@ NXapm_paraprobe_distancer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 156d418f0810f31078f74822927ab70cbc2bbc8b2d0bf91bb2d29c2a0eb828af -# +# 75d8113fdf1f793aa6755135eb9817d5625b71bd094724914fdc685e36ec2d99 +# # # -# # # +# # # # @@ -275,12 +269,12 @@ NXapm_paraprobe_distancer_config(NXobject): # # # -# Specifies for which point the tool will compute distances. -# -# The value *default* configures that distances are computed for all points. -# The value *skin* configures that distances are computed only for those -# points which are not farther away located to a triangle than -# threshold_distance. +# Specifies for which point the tool will compute distances. +# +# The value *default* configures that distances are computed for all points. +# The value *skin* configures that distances are computed only for those +# points which are not farther away located to a triangle than +# threshold_distance. # # # @@ -289,27 +283,25 @@ NXapm_paraprobe_distancer_config(NXobject): # # # -# Maximum distance for which distances are -# computed when *method* is *skin*. +# Maximum distance for which distances are +# computed when *method* is *skin*. # # # # # -# How many triangle sets to consider. -# Multiple triangle sets can be defined which are -# composed into one joint triangle set for the analysis. +# How many triangle sets to consider. +# Multiple triangle sets can be defined which are +# composed into one joint triangle set for the analysis. # # -# +# # -# Each triangle_set that is referred to here should be a face_list_data_structure, -# i.e. an array of (n_vertices, 3) of NX_FLOAT for vertex coordinates, an (n_facets, 3) -# array of NX_UINT incident vertices of each facet. Vertex indices are assumed to -# start at zero and must not exceed n_vertices - 1, i.e. the identifier_offset is 0. -# Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. -# -# Instances should use triangle_set as a name prefix. +# Each triangle_set that is referred to here should be a face_list_data_structure, +# i.e. an array of (n_vertices, 3) of NX_FLOAT for vertex coordinates, an (n_facets, 3) +# array of NX_UINT incident vertices of each facet. Vertex indices are assumed to +# start at zero and must not exceed n_vertices - 1, i.e. the index_offset is 0. +# Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. # # # @@ -317,32 +309,32 @@ NXapm_paraprobe_distancer_config(NXobject): # # # -# Absolute path in the (HDF5) file that points to the array -# of vertex positions for the triangles in that triangle_set. +# Absolute path in the (HDF5) file that points to the array +# of vertex positions for the triangles in that triangle_set. # # # # -# Absolute path in the (HDF5) file that points to the array -# of vertex indices for the triangles in that triangle_set. +# Absolute path in the (HDF5) file that points to the array +# of vertex indices for the triangles in that triangle_set. # # # # -# Absolute path in the (HDF5) file that points to the array -# of vertex normal vectors for the triangles in that triangle_set. +# Absolute path in the (HDF5) file that points to the array +# of vertex normal vectors for the triangles in that triangle_set. # # # # -# Absolute path in the (HDF5) file that points to the array -# of facet normal vectors for the triangles in that triangle_set. +# Absolute path in the (HDF5) file that points to the array +# of facet normal vectors for the triangles in that triangle_set. # # -# +# # -# Absolute path in the (HDF5) file that points to the array -# of identifier for the triangles in that triangle_set. +# Absolute path in the (HDF5) file that points to the array +# of identifier for the triangles in that triangle_set. # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml index 6836186551..995efebb35 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml @@ -52,16 +52,16 @@ NXapm_paraprobe_distancer_results(NXobject): dimensions: rank: 1 dim: (n_ions,) - identifier_triangle(NX_UINT): + indices_triangle(NX_INT): exists: optional unit: NX_UNITLESS doc: | For each point the identifier of the triangle for which the - shortest distance was found + shortest distance was found. dimensions: rank: 1 dim: (n_ions,) - identifier_point(NX_UINT): + indices_point(NX_INT): exists: optional unit: NX_UNITLESS doc: | @@ -128,38 +128,36 @@ NXapm_paraprobe_distancer_results(NXobject): end_time(NX_DATE_TIME): total_elapsed_time(NX_FLOAT): current_working_directory(NX_CHAR): - number_of_processes(NX_POSINT): - number_of_threads(NX_POSINT): - number_of_gpus(NX_POSINT): + number_of_processes(NX_UINT): + number_of_threads(NX_UINT): + number_of_gpus(NX_UINT): (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. name(NX_CHAR): - coordinate_system_set(NXcoordinate_system_set): - exists: ['min', '1', 'max', '1'] - paraprobe(NXcoordinate_system): - type(NX_CHAR): - handedness(NX_CHAR): - x(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - y(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - z(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) + paraprobe(NXcoordinate_system): + type(NX_CHAR): + handedness(NX_CHAR): + x(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + y(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + z(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 215366866eee513ec55b3569917e5355f9b9cb96cfbbb1042d9f6087c368a7cc -# +# 951432cc2ac4d93cafff1dde53c40f83d0f5b24cb915eca1fdf65fc2fe9fc79c +# # # # @@ -333,14 +331,14 @@ NXapm_paraprobe_intersector_config(NXobject): # next_set to nodes representing members of the current_set. # # -# +# # # Current set stores a set of members, meshes of volumetric features, # which will be checked for proximity and/or volumetric intersection, # to members of the current_set. # The meshes were generated as a result of some other meshing process. # -# +# # # This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k`) # step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). @@ -364,7 +362,7 @@ NXapm_paraprobe_intersector_config(NXobject): # current_set. # # -# +# # # Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the # members of the set as instances of NXcg_polyhedron. @@ -392,7 +390,7 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# +# # # Array of identifier whereby the path to the geometry data can be inferred # automatically. @@ -403,14 +401,14 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# +# # # Next set stores a set of members, meshes of volumetric features, # which will be checked for proximity and/or volumetric intersection, # to members of the next_set. # The meshes were generated as a result of some other meshing process. # -# +# # # This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k + 1`) # step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). @@ -434,7 +432,7 @@ NXapm_paraprobe_intersector_config(NXobject): # next_set. # # -# +# # # # Descriptive category explaining what these features are. @@ -457,7 +455,7 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# +# # # Array of identifier whereby the path to the geometry data can be inferred # automatically. diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml index a0a9916484..58bdd4bc46 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml @@ -36,7 +36,7 @@ NXapm_paraprobe_intersector_results(NXobject): current_to_next_link(NX_UINT): unit: NX_UNITLESS doc: | - A matrix of identifier_feature that specifies which named features + A matrix of indices_feature that specifies which named features from the current_set have directed link(s) pointing to which named feature(s) from the next_set. dimensions: @@ -55,7 +55,7 @@ NXapm_paraprobe_intersector_results(NXobject): exists: optional unit: NX_UNITLESS doc: | - A matrix of identifier_feature which specifies which named feature(s) + A matrix of indices_feature which specifies which named feature(s) from the next_set have directed link(s) pointing to which named feature(s) from the current_set. Only if the mapping whereby the links are defined is symmetric it holds that next_to_current maps @@ -95,7 +95,7 @@ NXapm_paraprobe_intersector_results(NXobject): The third comparison is the current_set against the next_set. Once the (forward) links for these comparisons are ready, pair relations - are analyzed with respect to which objects with identifier_feature + are analyzed with respect to which objects with indices_feature cluster in identifier space. Thereby, a logical connection (link) is established between the features in the current_set and the next_set. Recall that these two sets typically represent different features @@ -113,8 +113,8 @@ NXapm_paraprobe_intersector_results(NXobject): current_set_feature_to_cluster(NX_UINT): unit: NX_UNITLESS doc: | - Matrix of identifier_feature and identifier_cluster pairs which - encodes the cluster to which each identifier_feature was assigned. + Matrix of indices_feature and cluster_id pairs which + encodes the cluster to which each indices_feature was assigned. Here for features of the current_set. dimensions: rank: 2 @@ -122,13 +122,13 @@ NXapm_paraprobe_intersector_results(NXobject): next_set_feature_to_cluster(NX_UINT): unit: NX_UNITLESS doc: | - Matrix of identifier_feature and identifier_cluster pairs which - encodes the cluster to which each identifier_feature was assigned. + Matrix of indices_feature and cluster_id pairs which + encodes the cluster to which each indices_feature was assigned. Here for features of the next_set. dimensions: rank: 2 dim: (n_features_next, 2) - identifier_cluster(NX_UINT): + cluster_id(NX_UINT): unit: NX_UNITLESS doc: | The identifier (names) of the cluster. @@ -180,38 +180,36 @@ NXapm_paraprobe_intersector_results(NXobject): end_time(NX_DATE_TIME): total_elapsed_time(NX_FLOAT): current_working_directory(NX_CHAR): - number_of_processes(NX_POSINT): - number_of_threads(NX_POSINT): - number_of_gpus(NX_POSINT): + number_of_processes(NX_UINT): + number_of_threads(NX_UINT): + number_of_gpus(NX_UINT): (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. name(NX_CHAR): - coordinate_system_set(NXcoordinate_system_set): - exists: ['min', '1', 'max', '1'] - paraprobe(NXcoordinate_system): - type(NX_CHAR): - handedness(NX_CHAR): - x(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - y(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - z(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) + paraprobe(NXcoordinate_system): + type(NX_CHAR): + handedness(NX_CHAR): + x(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + y(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + z(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 9ae3964e8fb32d3c3ded86f695523c44b46639ee4a4f01528fe7b8d62a8f9579 -# +# fc5d07680b423f6c20340b57ce4a43d41ff2530f0859529046003134ccc85e49 +# # # # # -# A matrix of identifier_feature that specifies which named features +# A matrix of indices_feature that specifies which named features # from the current_set have directed link(s) pointing to which named # feature(s) from the next_set. # @@ -311,7 +309,7 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# A matrix of identifier_feature which specifies which named feature(s) +# A matrix of indices_feature which specifies which named feature(s) # from the next_set have directed link(s) pointing to which named # feature(s) from the current_set. Only if the mapping whereby the # links are defined is symmetric it holds that next_to_current maps @@ -353,7 +351,7 @@ NXapm_paraprobe_intersector_results(NXobject): # The third comparison is the current_set against the next_set. # # Once the (forward) links for these comparisons are ready, pair relations -# are analyzed with respect to which objects with identifier_feature +# are analyzed with respect to which objects with indices_feature # cluster in identifier space. Thereby, a logical connection (link) is # established between the features in the current_set and the next_set. # Recall that these two sets typically represent different features @@ -371,8 +369,8 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# Matrix of identifier_feature and identifier_cluster pairs which -# encodes the cluster to which each identifier_feature was assigned. +# Matrix of indices_feature and cluster_id pairs which +# encodes the cluster to which each indices_feature was assigned. # Here for features of the current_set. # # @@ -382,8 +380,8 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# Matrix of identifier_feature and identifier_cluster pairs which -# encodes the cluster to which each identifier_feature was assigned. +# Matrix of indices_feature and cluster_id pairs which +# encodes the cluster to which each indices_feature was assigned. # Here for features of the next_set. # # @@ -391,7 +389,7 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# +# # # The identifier (names) of the cluster. # @@ -451,9 +449,9 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# -# -# +# +# +# # # # @@ -461,26 +459,24 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml index 7a712677c1..70b945a6e9 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml @@ -94,14 +94,14 @@ NXapm_paraprobe_nanochem_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -109,7 +109,7 @@ NXapm_paraprobe_nanochem_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -205,7 +205,7 @@ NXapm_paraprobe_nanochem_config(NXobject): accuracy of reconstruction protocols and their parameterization. Unused values in each row of the matrix are nullified. - Nuclides are identified as hashed nuclide (see :ref:`NXion`) for further details. + Nuclides are identified as hashed nuclide (see :ref:`NXatom`) for further details. dimensions: dim: (n_ityp_deloc_cand, n_ivec_max) grid_resolution(NX_FLOAT): @@ -501,14 +501,14 @@ NXapm_paraprobe_nanochem_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -516,7 +516,7 @@ NXapm_paraprobe_nanochem_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -761,14 +761,14 @@ NXapm_paraprobe_nanochem_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -776,7 +776,7 @@ NXapm_paraprobe_nanochem_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -818,7 +818,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # dimensionality(NX_POSINT): # cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): dimensions: dim: (n_rois, 3) @@ -865,8 +865,8 @@ NXapm_paraprobe_nanochem_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 95a4157cdfb19b51ef5f05049aee77ec233f87b43d74fd9466432d05c1a1fdc4 -# +# 0eadf37c02da9fc5aaff69a50b81be1b98894002216c103a2c3d89ab270fb2ee +# # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml index 43d21b5ce8..3c66696b24 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml @@ -40,10 +40,9 @@ NXapm_paraprobe_nanochem_results(NXobject): enumeration: [NXapm_paraprobe_nanochem_results] # tasks - (NXdelocalization): + delocalizationID(NXdelocalization): exists: ['min', '0', 'max', 'unbounded'] - doc: | - Instances should use delocalization as a name prefix. + nameType: partial window(NXcs_filter_boolean_mask): number_of_ions(NX_UINT): bitdepth(NX_UINT): @@ -66,10 +65,8 @@ NXapm_paraprobe_nanochem_results(NXobject): doc: | The discretized domain/grid on which the delocalization is applied. dimensionality(NX_POSINT): - unit: NX_UNITLESS enumeration: [1, 2, 3] cardinality(NX_POSINT): - unit: NX_UNITLESS doc: | The total number of cells/voxels of the grid. origin(NX_NUMBER): @@ -101,7 +98,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dim: (d,) # coordinate_system implicit - identifier_offset(NX_INT): + index_offset(NX_INT): unit: NX_UNITLESS doc: | Integer which specifies the first index to be used for distinguishing identifiers for cells. @@ -143,7 +140,7 @@ NXapm_paraprobe_nanochem_results(NXobject): is_axis_aligned(NX_BOOLEAN): doc: | For atom probe should be set to true. - identifier_offset(NX_INT): + index_offset(NX_INT): unit: NX_UNITLESS doc: | Integer which specifies the first index to be used for distinguishing @@ -152,7 +149,7 @@ NXapm_paraprobe_nanochem_results(NXobject): :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array has to be defined. hexahedron(NXcg_face_list_data_structure): - vertex_identifier_offset(NX_INT): + vertex_index_offset(NX_INT): unit: NX_UNITLESS doc: | Integer which specifies the first index to be used for distinguishing @@ -160,7 +157,7 @@ NXapm_paraprobe_nanochem_results(NXobject): For implicit indexing the identifiers are defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array has to be defined. - face_identifier_offset(NX_INT): + face_index_offset(NX_INT): unit: NX_UNITLESS doc: | Integer which specifies the first index to be used for distinguishing @@ -384,13 +381,12 @@ NXapm_paraprobe_nanochem_results(NXobject): dim: (i,) # MK:: - (NXisocontour): + iso_surfaceID(NXisocontour): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial doc: | An iso-surface is the boundary between two regions across which the magnitude of a scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. - - Instances should iso_surface as a name prefix. For applications in atom probe microscopy, the location and shape of such a boundary (set) is typically approximated by discretization - triangulation to be specific. @@ -414,15 +410,8 @@ NXapm_paraprobe_nanochem_results(NXobject): doc: | The resulting triangle soup computed via marching cubes. dimensionality(NX_POSINT): - unit: NX_UNITLESS cardinality(NX_POSINT): - unit: NX_UNITLESS - identifier_offset(NX_INT): - unit: NX_UNITLESS - doc: | - Integer which specifies the first index to be used for distinguishing triangles. - Identifiers are defined either implicitly or explicitly. For implicit indexing the - identifiers are defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. + index_offset(NX_INT): triangles(NXcg_face_list_data_structure): number_of_vertices(NX_POSINT): number_of_faces(NX_POSINT): @@ -642,7 +631,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (n_v_feat,) - identifier_feature(NX_UINT): + indices_feature(NX_INT): unit: NX_UNITLESS doc: | The explicit identifier of features. @@ -662,10 +651,10 @@ NXapm_paraprobe_nanochem_results(NXobject): * proxies, proxies, irrespective their distance to the surface * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface - identifier_feature(NX_UINT): + indices_feature(NX_INT): unit: NX_UNITLESS doc: | - Explicit identifier of the feature a sub-set of the identifier_feature in the + Explicit identifier of the feature a sub-set of the indices_feature in the parent group. dimensions: rank: 1 @@ -721,34 +710,26 @@ NXapm_paraprobe_nanochem_results(NXobject): # MK::again we have no effective way to pinpoint the n_rows # MK::namely k != i each OBB has eight vertices - xdmf_topology(NX_UINT): + xdmf_topology(NX_INT): unit: NX_UNITLESS dimensions: rank: 1 dim: (k,) - identifier_feature_xdmf(NX_UINT): + indices_feature_xdmf(NX_INT): unit: NX_UNITLESS dimensions: rank: 1 dim: (k,) - OBJECT(NXcg_polyhedron): - nameType: any + objectID(NXcg_polyhedron): + nameType: partial exists: ['min', '0', 'max', 'unbounded'] - doc: | - Instances should use object as a name prefix. polyhedron(NXcg_face_list_data_structure): - - # number_of_vertices(NX_POSINT): - # number_of_faces(NX_POSINT): - # identifier_vertex_offset(NX_UINT): - # identifier_face_offset(NX_UINT): vertices(NX_FLOAT): unit: NX_LENGTH dimensions: rank: 2 dim: (n_v, 3) faces(NX_UINT): - unit: NX_UNITLESS dimensions: rank: 2 dim: (n_f, 3) @@ -757,23 +738,23 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 2 dim: (n_f, 3) - xdmf_topology(NX_UINT): + xdmf_topology(NX_INT): exists: recommended unit: NX_UNITLESS dimensions: rank: 1 dim: (k,) - identifier_feature_xdmf(NX_UINT): - exists: recommended + indices_feature_xdmf(NX_INT): unit: NX_UNITLESS + exists: recommended dimensions: rank: 1 dim: (k,) - identifier_ion(NX_UINT): + ion_id(NX_UINT): exists: optional unit: NX_UNITLESS doc: | - Array of identifier_evaporation / identifier_ion which details which ions + Array of evaporation_id / identifier_ion which details which ions lie inside or on the surface of the feature. dimensions: rank: 1 @@ -788,7 +769,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (i,) - (NXion): + (NXatom): exists: ['min', '0', 'max', 'unbounded'] charge_state(NX_INT): @@ -848,39 +829,27 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (4,) - MESH_STATE(NXcg_triangle): - nameType: any + mesh_stateID(NXcg_triangle): + nameType: partial exists: ['min', '0', 'max', 'unbounded'] doc: | The triangle surface mesh representing the interface model. Exported at state before or after the next DCOM step. - - Instances should use mesh_state as a name prefix. state(NX_CHAR): doc: | Was this state exported before or after the next DCOM step. enumeration: [before, after] dimensionality(NX_POSINT): - unit: NX_UNITLESS cardinality(NX_POSINT): - unit: NX_UNITLESS - identifier_offset(NX_INT): - unit: NX_UNITLESS + index_offset(NX_INT): triangles(NXcg_face_list_data_structure): dimensionality(NX_POSINT): - unit: NX_UNITLESS - number_of_vertices(NX_POSINT): - unit: NX_UNITLESS - number_of_faces(NX_POSINT): - unit: NX_UNITLESS - identifier_vertex_offset(NX_INT): - unit: NX_UNITLESS - identifier_edge_offset(NX_INT): - unit: NX_UNITLESS - identifier_face_offset(NX_INT): - unit: NX_UNITLESS - identifier_face(NX_UINT): - unit: NX_UNITLESS + number_of_vertices(NX_UINT): + number_of_faces(NX_UINT): + index_offset_vertex(NX_INT): + index_offset_edge(NX_INT): + index_offset_face(NX_INT): + indices_face(NX_INT): dimensions: rank: 1 dim: (j,) @@ -909,7 +878,6 @@ NXapm_paraprobe_nanochem_results(NXobject): rank: 1 dim: (i,) faces(NX_UINT): - unit: NX_UNITLESS dimensions: rank: 2 dim: (j, 3) @@ -976,9 +944,7 @@ NXapm_paraprobe_nanochem_results(NXobject): resolves the lateral surface of each cylinder such that their renditions are smooth in visualization software like Paraview. dimensionality(NX_POSINT): - unit: NX_UNITLESS cardinality(NX_POSINT): - unit: NX_UNITLESS center(NX_NUMBER): unit: NX_LENGTH doc: | @@ -997,7 +963,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dim: (i, 3) # XDMF support - identifier(NX_UINT): + roi_id(NX_UINT): exists: optional unit: NX_UNITLESS doc: | @@ -1041,11 +1007,9 @@ NXapm_paraprobe_nanochem_results(NXobject): Therefore, the XDMF support fields number_of_atoms and number_of_ions are only expected to display pairwise the same values respectively, if all ions are built from a single atom only. - ROI(NXcg_roi): - nameType: any + roiID(NXcg_roi): + nameType: partial exists: ['min', '0', 'max', 'unbounded'] - doc: | - Instances should use roi as a name prefix. signed_distance(NX_FLOAT): unit: NX_LENGTH doc: | @@ -1057,7 +1021,7 @@ NXapm_paraprobe_nanochem_results(NXobject): nuclide_hash(NX_UINT): unit: NX_UNITLESS doc: | - Hashvalue as defined in :ref:`NXion`. + Hashvalue as defined in :ref:`NXatom`. dimensions: rank: 1 dim: (k,) @@ -1079,38 +1043,36 @@ NXapm_paraprobe_nanochem_results(NXobject): end_time(NX_DATE_TIME): total_elapsed_time(NX_FLOAT): current_working_directory(NX_CHAR): - number_of_processes(NX_POSINT): - number_of_threads(NX_POSINT): - number_of_gpus(NX_POSINT): + number_of_processes(NX_UINT): + number_of_threads(NX_UINT): + number_of_gpus(NX_UINT): (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. name(NX_CHAR): - coordinate_system_set(NXcoordinate_system_set): - exists: ['min', '1', 'max', '1'] - paraprobe(NXcoordinate_system): - type(NX_CHAR): - handedness(NX_CHAR): - x(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - y(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) - z(NX_NUMBER): - unit: NX_LENGTH - dimensions: - rank: 1 - dim: (3,) + paraprobe(NXcoordinate_system): + type(NX_CHAR): + handedness(NX_CHAR): + x(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + y(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) + z(NX_NUMBER): + unit: NX_LENGTH + dimensions: + rank: 1 + dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# a0d301b2cab1f2815ae71b77a932d1bb68048bbb0a6645d5821f07728a9fa1e5 -# +# ab5376dff2ae43576d83832ec5264dc440f876465506bf0bf83869c39a1b2fb3 +# # # -# -# -# Instances should use delocalization as a name prefix. -# +# # # # @@ -1243,14 +1202,14 @@ NXapm_paraprobe_nanochem_results(NXobject): # # The discretized domain/grid on which the delocalization is applied. # -# +# # # # # # # -# +# # # The total number of cells/voxels of the grid. # @@ -1291,7 +1250,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # Integer which specifies the first index to be used for distinguishing identifiers for cells. # Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are @@ -1344,7 +1303,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # For atom probe should be set to true. # # -# +# # # Integer which specifies the first index to be used for distinguishing # hexahedra. Identifiers are defined either implicitly or explicitly. @@ -1354,7 +1313,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # Integer which specifies the first index to be used for distinguishing # identifiers for vertices. Identifiers are defined either implicitly or explicitly. @@ -1363,7 +1322,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # has to be defined. # # -# +# # # Integer which specifies the first index to be used for distinguishing # identifiers for faces. Identifiers are defined either implicitly or explicitly. @@ -1610,12 +1569,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # An iso-surface is the boundary between two regions across which the magnitude of a # scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. -# -# Instances should iso_surface as a name prefix. # # For applications in atom probe microscopy, the location and shape of such a boundary (set) # is typically approximated by discretization - triangulation to be specific. @@ -1642,15 +1599,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # # The resulting triangle soup computed via marching cubes. # -# -# -# -# -# Integer which specifies the first index to be used for distinguishing triangles. -# Identifiers are defined either implicitly or explicitly. For implicit indexing the -# identifiers are defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. -# -# +# +# +# # # # @@ -1883,7 +1834,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # The explicit identifier of features. # @@ -1904,9 +1855,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface # * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface # -# +# # -# Explicit identifier of the feature a sub-set of the identifier_feature in the +# Explicit identifier of the feature a sub-set of the indices_feature in the # parent group. # # @@ -1968,34 +1919,27 @@ NXapm_paraprobe_nanochem_results(NXobject): # # -# +# # # # # -# +# # # # # # # -# -# -# Instances should use object as a name prefix. -# +# # -# # # # # # # -# +# # # # @@ -2007,19 +1951,19 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # # -# +# # # # # -# +# # -# Array of identifier_evaporation / identifier_ion which details which ions +# Array of evaporation_id / identifier_ion which details which ions # lie inside or on the surface of the feature. # # @@ -2038,7 +1982,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # @@ -2107,12 +2051,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # The triangle surface mesh representing the interface model. # Exported at state before or after the next DCOM step. -# -# Instances should use mesh_state as a name prefix. # # # @@ -2123,17 +2065,17 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# -# -# +# +# +# # -# -# -# -# -# -# -# +# +# +# +# +# +# +# # # # @@ -2166,7 +2108,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # @@ -2243,8 +2185,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # resolves the lateral surface of each cylinder such that their renditions are smooth in # visualization software like Paraview. # -# -# +# +# # # # Position of the geometric center, which often is but not @@ -2266,7 +2208,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # XDMF support to enable coloring each ROI by its identifier. # @@ -2311,10 +2253,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # are only expected to display pairwise the same values respectively, # if all ions are built from a single atom only. # -# -# -# Instances should use roi as a name prefix. -# +# # # # Sorted in increasing order projected along the positive direction @@ -2326,7 +2265,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Hashvalue as defined in :ref:`NXion`. +# Hashvalue as defined in :ref:`NXatom`. # # # @@ -2355,9 +2294,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# -# -# +# +# +# # # # @@ -2365,26 +2304,24 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml index 00af839544..24f30a2d08 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml @@ -45,14 +45,14 @@ NXapm_paraprobe_ranger_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -60,7 +60,7 @@ NXapm_paraprobe_ranger_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -102,8 +102,8 @@ NXapm_paraprobe_ranger_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4c1f72db076800eedafc2113e0e44097edf7568c111c5f1c8e4e23cf8c978785 -# +# d6bd7ff3c66c1daf0e13df6fa1ad7a2edecf9560c6755c02105c25ea1a718706 +# # # # # -# Paraprobe-ranger loads the iontypes and evaluates for each -# ion on which iontype it matches. If it matches on None, the -# ion is considered of the default *unknown_type*. This iontype -# is marked with a 0 in the iontypes array. +# Paraprobe-ranger loads the iontypes and evaluates for each +# ion on which iontype it matches. If it matches on None, the +# ion is considered of the default *unknown_type*. This iontype +# is marked with a 0 in the iontypes array. # -# # # # # # # -# +# # # # @@ -179,12 +172,12 @@ NXapm_paraprobe_ranger_results(NXobject): # # # -# The iontype (identifier) for each ion that was best matching, stored -# in the order of the evaporation sequence ID. The here computed iontypes -# do not take into account the charge state of the ion which is -# equivalent to interpreting a RNG and RRNG range files for each -# ion in such a way that only the those elements are considered of which -# a (molecular) ion is assumed composed according to the NXion instances. +# The iontype (identifier) for each ion that was best matching, stored +# in the order of the evaporation sequence ID. The here computed iontypes +# do not take into account the charge state of the ion which is +# equivalent to interpreting a RNG and RRNG range files for each +# ion in such a way that only the those elements are considered of which +# a (molecular) ion is assumed composed according to the NXatom instances. # # # @@ -210,36 +203,34 @@ NXapm_paraprobe_ranger_results(NXobject): # # # -# -# -# +# +# +# # # # -# If used, metadata of at least the person who performed this analysis. +# If used, metadata of at least the person who performed this analysis. # # # -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml index 93528189bf..9d0a8207f5 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml @@ -38,14 +38,14 @@ NXapm_paraprobe_selector_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -53,7 +53,7 @@ NXapm_paraprobe_selector_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -94,8 +94,8 @@ NXapm_paraprobe_selector_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# aed13f4eee9d8b16dd22984682ee073162ce868bbb10c5f0cf4600583c1b0e0c -# +# 01287da74ce6fcec4c36e74333ace77dea9cff4541e35e811572ebb2baa1f7cb +# # # -# -# -# Instances should use spatial_statistics as a name prefix. -# +# # # # @@ -223,13 +216,13 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# The iontype ID for each ion that was assigned to each ion during -# the randomization of the ionlabels. Iontype labels are just permuted -# but the total number of values for each iontype remain the same. -# -# The order matches the iontypes array from a given ranging results -# as it is specified in the configuration settings inside the specific -# config_filename that was used for this paraprobe-spatstat analysis. +# The iontype ID for each ion that was assigned to each ion during +# the randomization of the ionlabels. Iontype labels are just permuted +# but the total number of values for each iontype remain the same. +# +# The order matches the iontypes array from a given ranging results +# as it is specified in the configuration settings inside the specific +# config_filename that was used for this paraprobe-spatstat analysis. # # # @@ -237,11 +230,11 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# K-nearest neighbor statistics. +# K-nearest neighbor statistics. # # # -# Right boundary of the binning. +# Right boundary of the binning. # # # @@ -254,7 +247,7 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# Cumulated not normalized by total counts. +# Cumulated not normalized by total counts. # # # @@ -262,7 +255,7 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# Cumulated and normalized by total counts. +# Cumulated and normalized by total counts. # # # @@ -271,11 +264,11 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# Radial distribution statistics. +# Radial distribution statistics. # # # -# Right boundary of the binning. +# Right boundary of the binning. # # # @@ -288,7 +281,7 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# Cumulated not normalized by total counts. +# Cumulated not normalized by total counts. # # # @@ -296,7 +289,7 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# Cumulated and normalized by total counts. +# Cumulated and normalized by total counts. # # # @@ -323,36 +316,34 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# -# -# +# +# +# # # # -# If used, metadata of at least the person who performed this analysis. +# If used, metadata of at least the person who performed this analysis. # # # -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml index 171679bbb2..b350fd483c 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml @@ -42,14 +42,14 @@ NXapm_paraprobe_surfacer_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -57,7 +57,7 @@ NXapm_paraprobe_surfacer_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -177,8 +177,8 @@ NXapm_paraprobe_surfacer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6747c166c776cfe9bd86afdc79f19820c13819dd7328185ad1acfefd8c3f08f5 -# +# 11a18b8cf1777115de590b13a530345e00a0e207e152254e9827057553f8cac2 +# # # -# +# # -# -# Instances should use alpha_complex as a name prefix. -# # # # A bitmask which identifies exactly all those ions whose positions @@ -355,7 +345,7 @@ NXapm_paraprobe_surfacer_results(NXobject): # # # -# +# # # # @@ -383,20 +373,20 @@ NXapm_paraprobe_surfacer_results(NXobject): # The set of triangles in the coordinate system paraprobe # which discretizes the exterior surface of the alpha complex. # -# +# # # -# -# -# -# +# +# +# +# # # # # # # -# +# # # # @@ -430,17 +420,17 @@ NXapm_paraprobe_surfacer_results(NXobject): # The set of tetrahedra which represent the interior volume # of the complex if that is a closed two-manifold. # -# +# # # # The accumulated volume of all interior tetrahedra. # # # -# -# -# -# +# +# +# +# # # # @@ -482,9 +472,9 @@ NXapm_paraprobe_surfacer_results(NXobject): # # # -# -# -# +# +# +# # # # @@ -492,26 +482,24 @@ NXapm_paraprobe_surfacer_results(NXobject): # # # -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml index edd773c668..efa0ceb62a 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml @@ -46,14 +46,14 @@ NXapm_paraprobe_tessellator_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): @@ -61,7 +61,7 @@ NXapm_paraprobe_tessellator_config(NXobject): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): - identifier_offset(NX_INT): + index_offset(NX_INT): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): @@ -137,8 +137,8 @@ NXapm_paraprobe_tessellator_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6de30011e50cffeb26ed0fcd027f35146975a1c614dbb15beeb1be7e9f401006 -# +# 8c84fb2c64d4437434831cbc76b4f49a8e00c1437b715c766c6d5daa0e04d34b +# # # # # -# Base class documenting the information common to tools of the paraprobe-toolbox. -# -# The paraprobe-toolbox is a collection of open-source tools for performing -# efficient analyses of point cloud data where each point can represent atoms or -# (molecular) ions. A key application of the toolbox has been for research in the -# field of Atom Probe Tomography (APT) and related Field Ion Microscopy (FIM): -# -# * `paraprobe-toolbox <https://www.gitlab.com/paraprobe/paraprobe-toolbox>`_ -# * `M. Kühbach et al. <https://paraprobe-toolbox.readthedocs.io/en/main/>`_ -# -# The toolbox does not replace but complements existent software tools in this -# research field. Given its capabilities of handling points as objects with -# properties and enabling analyses of the spatial arrangement of and inter- -# sections between geometric primitives, the software can equally be used -# for analyzing data in Materials Science and Materials Engineering. -# -# The common section can be used as a place to store e.g. organizational -# metadata and contextualization of that analysis in a research data -# management system. +# Base class documenting the information common to tools of the paraprobe-toolbox. +# +# The paraprobe-toolbox is a collection of open-source tools for performing +# efficient analyses of point cloud data where each point can represent atoms or +# (molecular) ions. A key application of the toolbox has been for research in the +# field of Atom Probe Tomography (APT) and related Field Ion Microscopy (FIM): +# +# * `paraprobe-toolbox <https://www.gitlab.com/paraprobe/paraprobe-toolbox>`_ +# * `M. Kühbach et al. <https://paraprobe-toolbox.readthedocs.io/en/main/>`_ +# +# The toolbox does not replace but complements existent software tools in this +# research field. Given its capabilities of handling points as objects with +# properties and enabling analyses of the spatial arrangement of and inter- +# sections between geometric primitives, the software can equally be used +# for analyzing data in Materials Science and Materials Engineering. +# +# The common section can be used as a place to store e.g. organizational +# metadata and contextualization of that analysis in a research data +# management system. # # # -# A statement whether the tool executable managed to process the analysis -# or whether this failed. Status is written to the results file after the -# end_time beyond which point in time the tool must no longer compute -# any further analysis results but exit. -# -# Only when this status message is present and its value is `success`, -# one should consider the results of the tool. In all other cases it might -# be that the tool has terminated prematurely or another error occurred. +# A statement whether the tool executable managed to process the analysis +# or whether this failed. Status is written to the results file after the +# end_time beyond which point in time the tool must no longer compute +# any further analysis results but exit. +# +# Only when this status message is present and its value is `success`, +# one should consider the results of the tool. In all other cases it might +# be that the tool has terminated prematurely or another error occurred. # # # @@ -153,69 +147,64 @@ NXapm_paraprobe_tool_common(NXobject): # # # -# +# # -# Internal identifier used by the tool to refer to an analysis (aka simulation -# id). +# Internal identifier used by the tool to refer to an analysis (aka simulation +# id). # # # # -# The configuration file that was used to parameterize -# the algorithms that this tool has executed. +# The configuration file that was used to parameterize +# the algorithms that this tool has executed. # # # # +# doc: | +# Path where the tool stores tool-specific results. If not specified, +# results will be stored in the current working directory.--> # # -# ISO 8601 formatted time code with local time zone offset to UTC -# information included when the analysis in this results file was started, -# i.e. when the respective executable/tool was started as a process. +# ISO 8601 formatted time code with local time zone offset to UTC +# information included when the analysis in this results file was started, +# i.e. when the respective executable/tool was started as a process. # # # # -# ISO 8601 formatted time code with local time zone offset to UTC -# information included when the analysis in this results file were -# completed and the respective process of the tool exited. +# ISO 8601 formatted time code with local time zone offset to UTC +# information included when the analysis in this results file were +# completed and the respective process of the tool exited. # # # # -# Wall-clock time. +# Wall-clock time. # # # # -# +# # -# Details about coordinate systems (reference frames) used. In atom probe several coordinate -# systems have to be distinguished. Names of instances of such :ref:`NXcoordinate_system` -# should be documented explicitly and doing so by picking from the -# following controlled set of names: -# -# * paraprobe -# * lab -# * specimen -# * laser -# * instrument -# * detector -# * recon -# -# The aim of this convention is to support users with contextualizing which reference frame -# each instance (coordinate system) is. If needed, instances of :ref:`NXtransformations` -# are used to detail the explicit affine transformations whereby one can convert -# representations between different reference frames. -# Inspect :ref:`NXtransformations` for further details. +# Details about coordinate systems (reference frames) used. In atom probe several coordinate +# systems have to be distinguished. Names of instances of such :ref:`NXcoordinate_system` +# should be documented explicitly and doing so by picking from the +# following controlled set of names: +# +# * paraprobe +# * lab +# * specimen +# * laser +# * instrument +# * detector +# * recon +# +# The aim of this convention is to support users with contextualizing which reference frame +# each instance (coordinate system) is. If needed, instances of :ref:`NXtransformations` +# are used to detail the explicit affine transformations whereby one can convert +# representations between different reference frames. +# Inspect :ref:`NXtransformations` for further details. # -# -# -# # -# # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_tool_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_tool_config.yaml index b4b3bfefa8..a41f5a7773 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_tool_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_tool_config.yaml @@ -15,7 +15,7 @@ doc: | properties and enabling analyses of the spatial arrangement of and inter- sections between geometric primitives, the software can equally be used for analyzing data in Materials Science and Materials Engineering. - + The configuration and results of a run of a tool from the toolbox is documented using binary container formats. Currently, paraprobe-toolbox uses the Hierarchical Data Format 5 (HDF5). @@ -98,8 +98,8 @@ NXapm_paraprobe_tool_config(NXobject): (NXmatch_filter): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fe35f744d4a24ba3b10c8201960ca744551b7a6067f968e7262aac712f2bddab -# +# 5b1e870ad6840ca73ed2b481cad11f2db20697da8de53c9e68785f4e7ec21a9e +# # # # +# i be careful n_comb can vary for every instance of (NXatom) !--> # # # -# The symbols used in the schema to specify e.g. dimensions of arrays. +# The symbols used in the schema to specify e.g. dimensions of arrays. # # # -# The total number of ions in the reconstruction. +# The total number of ions in the reconstruction. # # # # -# Maximum number of allowed atoms per (molecular) ion (fragment). -# Needs to match maximum_number_of_atoms_per_molecular_ion. +# Maximum number of allowed atoms per (molecular) ion (fragment). +# Needs to match maximum_number_of_atoms_per_molecular_ion. # # # # -# Total number of integers in the supplementary XDMF topology array. +# Total number of integers in the supplementary XDMF topology array. # # # # -# Number of entries +# Number of entries # # # # -# Application definition for results files of the paraprobe-transcoder tool. -# -# This tool is part of the paraprobe-toolbox. Inspect the base class :ref:`NXapm_paraprobe_tool_results`. -# The purpose and need of the paraprobe-transcoder tool is to create a standardized representation -# of reconstructed position and mass-to-charge-state-ratio values surplus other pieces of information -# to enable working with atom probe data in reconstruction space in the paraprobe-toolbox. -# This includes ranging definitions which map mass-to-charge-state ratio values onto iontypes. -# -# So far the atom probe community has not yet agreed upon a comprehensive standardization on how to -# exchange information especially when it comes to the communication of configurations and results -# from analyses of atom probe data. Instead, different simplistic file formats are used, such as POS, ePOS, -# APT, or RNG and RRNG. None of these formats, though, are self-descriptive, standardize, or document -# their origin and thus the sequence in which the file was generated during an analysis. -# -# Paraprobe-transcoder solves this limitation by interpreting the information content in such files -# and standardize the representation prior injection into the scientific data analysis tools of the toolbox. -# Therefore, the here proposed set of NeXus base classes and application definitions can be a useful -# starting point for the atom probe community to take advantage of standardized information -# exchange and improve the here proposed classes and concepts to become more inclusive. -# -# Paraprobe-transcoder uses a Python library developed based on efforts by members of the -# global atom probe community `International Field Emission Society (IFES) Atom Probe Technical Committee (APT TC) <https://www.github.com/atomprobe-tc/ifes_apt_tc_data_modeling>`_. This library offers the -# actual low-level I/O operations and respective information interpretation of above-mentioned file formats. +# Application definition for results files of the paraprobe-transcoder tool. +# +# This tool is part of the paraprobe-toolbox. Inspect the base class :ref:`NXapm_paraprobe_tool_results`. +# The purpose and need of the paraprobe-transcoder tool is to create a standardized representation +# of reconstructed position and mass-to-charge-state-ratio values surplus other pieces of information +# to enable working with atom probe data in reconstruction space in the paraprobe-toolbox. +# This includes ranging definitions which map mass-to-charge-state ratio values onto iontypes. +# +# So far the atom probe community has not yet agreed upon a comprehensive standardization on how to +# exchange information especially when it comes to the communication of configurations and results +# from analyses of atom probe data. Instead, different simplistic file formats are used, such as POS, ePOS, +# APT, or RNG and RRNG. None of these formats, though, are self-descriptive, standardize, or document +# their origin and thus the sequence in which the file was generated during an analysis. +# +# Paraprobe-transcoder solves this limitation by interpreting the information content in such files +# and standardize the representation prior injection into the scientific data analysis tools of the toolbox. +# Therefore, the here proposed set of NeXus base classes and application definitions can be a useful +# starting point for the atom probe community to take advantage of standardized information +# exchange and improve the here proposed classes and concepts to become more inclusive. +# +# Paraprobe-transcoder uses a Python library developed based on efforts by members of the +# global atom probe community `International Field Emission Society (IFES) Atom Probe Technical Committee (APT TC) <https://www.github.com/atomprobe-tc/ifes_apt_tc_data_modeling>`_. This library offers the +# actual low-level I/O operations and respective information interpretation of above-mentioned file formats. # # # @@ -262,9 +260,9 @@ NXapm_paraprobe_transcoder_results(NXobject): # # # -# By default the entire reconstructed volume is processed. -# In this case, using window is also equivalent to an -# NXspatial_filter that specified a window *entire_dataset*. +# By default the entire reconstructed volume is processed. +# In this case, using window is also equivalent to an +# NXspatial_filter that specified a window *entire_dataset*. # # # @@ -274,7 +272,7 @@ NXapm_paraprobe_transcoder_results(NXobject): # # # -# Mass-to-charge-state-ratio values. +# Mass-to-charge-state-ratio values. # # # @@ -284,8 +282,8 @@ NXapm_paraprobe_transcoder_results(NXobject): # # # -# Three-dimensional reconstructed positions of the ions. -# Interleaved array of x, y, z positions in the specimen space. +# Three-dimensional reconstructed positions of the ions. +# Interleaved array of x, y, z positions in the specimen space. # # # @@ -293,17 +291,17 @@ NXapm_paraprobe_transcoder_results(NXobject): # # # -# Defines in which reference frame the positions are defined. +# Defines in which reference frame the positions are defined. # # # # # # -# An array of triplets of integers which can serve as a supplementary -# array for Paraview to display the reconstruction. The XDMF datatype -# is here 1, the number of primitives 1 per triplet, the last integer -# in each triplet is the identifier of each point starting from zero. +# An array of triplets of integers which can serve as a supplementary +# array for Paraview to display the reconstruction. The XDMF datatype +# is here 1, the number of primitives 1 per triplet, the last integer +# in each triplet is the identifier of each point starting from zero. # # # @@ -314,9 +312,9 @@ NXapm_paraprobe_transcoder_results(NXobject): # # # -# Details about how peaks are interpreted as ion types or not. +# Details about how peaks are interpreted as ion types or not. # -# +# # # # @@ -350,36 +348,34 @@ NXapm_paraprobe_transcoder_results(NXobject): # # # -# -# -# +# +# +# # # # -# If used, metadata of at least the person who performed this analysis. +# If used, metadata of at least the person who performed this analysis. # # # -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_ranging.yaml b/contributed_definitions/nyaml/NXapm_ranging.yaml deleted file mode 100644 index d1937f3da9..0000000000 --- a/contributed_definitions/nyaml/NXapm_ranging.yaml +++ /dev/null @@ -1,188 +0,0 @@ -category: base -doc: | - Base class for the configuration and results of ranging definitions. - - Ranging is a data post-processing step used in the research field of - atom probe during which elemental, isotopic, and/or molecular identities - are assigned to mass-to-charge-state-ratios within a certain interval. - The documentation of these steps is based on ideas that - have been described in the literature: - - * `M. K. Miller `_ - * `D. Haley et al. `_ - * `M. Kühbach et al. `_ -type: group -NXapm_ranging(NXprocess): - (NXprogram): - (NXnote): - mass_to_charge_distribution(NXprocess): - doc: | - Specifies the mass-to-charge-state-ratio histogram. - (NXprogram): - min_incr_max(NX_FLOAT): - unit: NX_ANY - doc: | - Smallest, increment, and largest mass-to-charge-state ratio value. - dimensions: - rank: 1 - dim: (3,) - mass_spectrum(NXdata): - doc: | - A default histogram aka mass spectrum of - the mass-to-charge-state ratio values. - background_quantification(NXprocess): - doc: | - Details of the background model that was used to - correct the total counts per bin into counts. - (NXprogram): - description(NX_CHAR): - doc: | - To begin with we use a free-text field to learn how - atom probers define a background model. Future versions - of NXapm_ranging can then use this information to parameterize - these models. - - # NEW ISSUE: add parameters of the background model in an e.g. - # NXcollection as these are specific to every background model - # NEW ISSUE: touching upon i.e. research activities by Andrew London et al. - # substantiating the need for a clearer description how peak/signals were - # eventually processed via deconvolution methods - peak_search_and_deconvolution(NXprocess): - doc: | - How where peaks in the background-corrected in the histogram - of mass-to-charge-state ratio values identified? - (NXprogram): - (NXpeak): - peak_identification(NXprocess): - doc: | - Details about how peaks, with taking into account - error models, were interpreted as ion types or not. - (NXprogram): - number_of_ion_types(NX_UINT): - unit: NX_UNITLESS - doc: | - How many ion types are distinguished. If no ranging was performed, each - ion is of the special unknown type. The iontype ID of this unknown type - is 0 representing a reserve value. Consequently, - iontypes start counting from 1. - maximum_number_of_atoms_per_molecular_ion(NX_UINT): - unit: NX_UNITLESS - doc: | - Assumed maximum value that suffices to store all relevant - molecular ions, even the most complicated ones. - Currently, a value of 32 is used (see M. Kühbach et al. `_). - (NXion): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 142cdb67a19fd49f06926b8c3a14834dd93b5dd0fe898929f96c3504e2cccc88 -# -# -# -# -# -# Base class for the configuration and results of ranging definitions. -# -# Ranging is a data post-processing step used in the research field of -# atom probe during which elemental, isotopic, and/or molecular identities -# are assigned to mass-to-charge-state-ratios within a certain interval. -# The documentation of these steps is based on ideas that -# have been described in the literature: -# -# * `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ -# * `D. Haley et al. <https://doi.org/10.1017/S1431927620024290>`_ -# * `M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_ -# -# -# -# -# -# Specifies the mass-to-charge-state-ratio histogram. -# -# -# -# -# Smallest, increment, and largest mass-to-charge-state ratio value. -# -# -# -# -# -# -# -# A default histogram aka mass spectrum of -# the mass-to-charge-state ratio values. -# -# -# -# -# -# Details of the background model that was used to -# correct the total counts per bin into counts. -# -# -# -# -# To begin with we use a free-text field to learn how -# atom probers define a background model. Future versions -# of NXapm_ranging can then use this information to parameterize -# these models. -# -# -# -# -# -# -# How where peaks in the background-corrected in the histogram -# of mass-to-charge-state ratio values identified? -# -# -# -# -# -# -# Details about how peaks, with taking into account -# error models, were interpreted as ion types or not. -# -# -# -# -# How many ion types are distinguished. If no ranging was performed, each -# ion is of the special unknown type. The iontype ID of this unknown type -# is 0 representing a reserve value. Consequently, -# iontypes start counting from 1. -# -# -# -# -# Assumed maximum value that suffices to store all relevant -# molecular ions, even the most complicated ones. -# Currently, a value of 32 is used (see M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_). -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXapm_reconstruction.yaml b/contributed_definitions/nyaml/NXapm_reconstruction.yaml deleted file mode 100644 index 377c3787fc..0000000000 --- a/contributed_definitions/nyaml/NXapm_reconstruction.yaml +++ /dev/null @@ -1,377 +0,0 @@ -category: base -doc: | - Base class for the configuration and results of a (static) reconstruction algorithm. - - Generating a tomographic reconstruction of the specimen uses selected and - calibrated ion hit positions, the evaporation sequence, and voltage curve data. - Very often scientists use own software scripts according to published procedures, - so-called reconstruction protocols. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n: | - Number of ions spatially filtered from results of the hit_finding algorithm - from which an instance of a reconstructed volume has been generated. - These ions get new identifier assigned in the process - the so-called - identifier_evaporation, which must not be confused with the identifier_pulse! -type: group -NXapm_reconstruction(NXprocess): - - # when evolving these ideas further inherit from NXapm_method instead - (NXprogram): - (NXnote): - - # config/input - parameter(NX_CHAR): - doc: | - Different reconstruction protocols exist. Although these approaches - are qualitatively similar, each protocol uses different parameters - (and interprets these differently). The source code to IVAS/APSuite - is not open. For now users should store reconstruction parameter - in this free-text field to guide how to parameterize this better in the - future. For LEAP systems and reconstructions performed with IVAS/APSuite - see `T. Blum et al. `_ (page 371). - primary_element(NX_CHAR): - doc: | - CAnalysis.CSpatial.fPrimaryElement - efficiency(NX_FLOAT): - unit: NX_DIMENSIONLESS - doc: | - CAnalysis.CSpatial.fEfficiency - flight_path(NX_FLOAT): - unit: NX_LENGTH - doc: | - CAnalysis.CSpatial.fFlightPath - evaporation_field(NX_FLOAT): - unit: NX_ANY - doc: | - CAnalysis.CSpatial.fEvaporationField - image_compression(NX_FLOAT): - unit: NX_UNITLESS - doc: | - CAnalysis.CSpatial.fImageCompression - - Image compression factor (ICF) - kfactor(NX_FLOAT): - unit: NX_UNITLESS - doc: | - CAnalysis.CSpatial.fKfactor - - k factor - volume(NX_FLOAT): - unit: NX_VOLUME - doc: | - CAnalysis.CSpatial.fRecoVolume - - Sum of ion volumes - shank_angle(NX_FLOAT): - unit: NX_ANGLE - doc: | - CAnalysis.CSpatial.fShankAngle - - Shank angle - tip_radius(NX_FLOAT): - unit: NX_LENGTH - doc: | - CAnalysis.CSpatial.fTipRadius - tip_radius_zero(NX_FLOAT): - unit: NX_LENGTH - doc: | - CAnalysis.CSpatial.fTipRadius0 - voltage_zero(NX_FLOAT): - unit: NX_VOLTAGE - doc: | - CAnalysis.CSpatial.fVoltage0 - obb(NXobject): - doc: | - Tight, axis-aligned bounding box about the point cloud of the reconstruction. - xmin(NX_FLOAT): - unit: NX_LENGTH - doc: | - TODO - xmax(NX_FLOAT): - unit: NX_LENGTH - doc: | - TODO - ymin(NX_FLOAT): - unit: NX_LENGTH - doc: | - TODO - ymax(NX_FLOAT): - unit: NX_LENGTH - doc: | - TODO - zmin(NX_FLOAT): - unit: NX_LENGTH - doc: | - TODO - zmax(NX_FLOAT): - unit: NX_LENGTH - doc: | - TODO - protocol_name(NX_CHAR): - doc: | - Qualitative statement about which reconstruction protocol was used. - enumeration: - open_enum: true - items: [bas, geiser, gault, cameca] - crystallographic_calibration(NX_CHAR): - doc: | - Different strategies for crystallographic calibration of the - reconstruction are possible. Therefore, we collect first such - feedback before parametrizing this further. - - If no crystallographic calibration was performed, the field - should be filled with the n/a, meaning not applied. - - # results - field_of_view(NX_FLOAT): - unit: NX_LENGTH - - # typically in nm reconstruction space not detector coordinates - doc: | - The nominal diameter of the specimen ROI which is measured in the - experiment. The physical specimen cannot be measured completely - because ions may launch but hit in locations other than the detector. - reconstructed_positions(NX_FLOAT): - unit: NX_LENGTH - doc: | - Three-dimensional reconstructed positions of the ions. - dimensions: - rank: 2 - dim: (n, 3) - \@depends_on(NX_CHAR): - doc: | - The instance of :ref:`NXcoordinate_system` - in which the positions are defined. - naive_discretization(NXprocess): - (NXprogram): - - # config/input - # results - (NXdata): - doc: | - To get a first visual overview of the reconstructed dataset, - here a 3d histogram of the ion is stored. Ion counts are characterized - using one nanometer cubic bins without applying position smoothening - algorithms during the histogram computation. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# ce13067901785fc95c428e78fece576b9c8a8a1342276e5811d5640cae5dfdbd -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Number of ions spatially filtered from results of the hit_finding algorithm -# from which an instance of a reconstructed volume has been generated. -# These ions get new identifier assigned in the process - the so-called -# identifier_evaporation, which must not be confused with the identifier_pulse! -# -# -# -# -# Base class for the configuration and results of a (static) reconstruction algorithm. -# -# Generating a tomographic reconstruction of the specimen uses selected and -# calibrated ion hit positions, the evaporation sequence, and voltage curve data. -# Very often scientists use own software scripts according to published procedures, -# so-called reconstruction protocols. -# -# -# -# -# -# -# -# Different reconstruction protocols exist. Although these approaches -# are qualitatively similar, each protocol uses different parameters -# (and interprets these differently). The source code to IVAS/APSuite -# is not open. For now users should store reconstruction parameter -# in this free-text field to guide how to parameterize this better in the -# future. For LEAP systems and reconstructions performed with IVAS/APSuite -# see `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). -# -# -# -# -# CAnalysis.CSpatial.fPrimaryElement -# -# -# -# -# CAnalysis.CSpatial.fEfficiency -# -# -# -# -# CAnalysis.CSpatial.fFlightPath -# -# -# -# -# CAnalysis.CSpatial.fEvaporationField -# -# -# -# -# CAnalysis.CSpatial.fImageCompression -# -# Image compression factor (ICF) -# -# -# -# -# CAnalysis.CSpatial.fKfactor -# -# k factor -# -# -# -# -# CAnalysis.CSpatial.fRecoVolume -# -# Sum of ion volumes -# -# -# -# -# CAnalysis.CSpatial.fShankAngle -# -# Shank angle -# -# -# -# -# CAnalysis.CSpatial.fTipRadius -# -# -# -# -# CAnalysis.CSpatial.fTipRadius0 -# -# -# -# -# CAnalysis.CSpatial.fVoltage0 -# -# -# -# -# Tight, axis-aligned bounding box about the point cloud of the reconstruction. -# -# -# -# TODO -# -# -# -# -# TODO -# -# -# -# -# TODO -# -# -# -# -# TODO -# -# -# -# -# TODO -# -# -# -# -# TODO -# -# -# -# -# -# Qualitative statement about which reconstruction protocol was used. -# -# -# -# -# -# -# -# -# -# -# Different strategies for crystallographic calibration of the -# reconstruction are possible. Therefore, we collect first such -# feedback before parametrizing this further. -# -# If no crystallographic calibration was performed, the field -# should be filled with the n/a, meaning not applied. -# -# -# -# -# -# -# The nominal diameter of the specimen ROI which is measured in the -# experiment. The physical specimen cannot be measured completely -# because ions may launch but hit in locations other than the detector. -# -# -# -# -# Three-dimensional reconstructed positions of the ions. -# -# -# -# -# -# -# -# The instance of :ref:`NXcoordinate_system` -# in which the positions are defined. -# -# -# -# -# -# -# -# -# To get a first visual overview of the reconstructed dataset, -# here a 3d histogram of the ion is stored. Ion counts are characterized -# using one nanometer cubic bins without applying position smoothening -# algorithms during the histogram computation. -# -# -# -# diff --git a/contributed_definitions/nyaml/NXatom.yaml b/contributed_definitions/nyaml/NXatom.yaml deleted file mode 100644 index 6d3f825d8d..0000000000 --- a/contributed_definitions/nyaml/NXatom.yaml +++ /dev/null @@ -1,230 +0,0 @@ -category: base -doc: | - Base class for documenting a set of atoms. - - Atoms in the set may be bonded. - The set may have a net charge to represent - an ion. Ions can be molecular ions. -type: group -NXatom(NXobject): - name(NX_CHAR): - doc: | - Given name for the set. - - This field could for example be used in the research field - of atom probe tomography for storing a standardized - human-readable name of the element or (molecular) ion - like such as Al +++ or 12C +. - identifier_chemical(NX_CHAR): - doc: | - Identifier used to refer to if the set of atoms represents a substance. - enumeration: [inchi] - charge(NX_NUMBER): - unit: NX_CHARGE - doc: | - Signed net (partial) charge of the (molecular) ion. - - Different methods for computing charge are in use. - Care needs to be exercised with respect to the integration. - `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. - charge_state(NX_NUMBER): - unit: NX_UNITLESS - doc: | - Charge reported in multiples of the charge of an electron. - - For research using atom probe tomography the value should be set to - zero if the charge_state is unknown and irrecoverable. This can happen - when classical ranging definition files in formats like RNG, RRNG are used. - These file formats do not document the charge state explicitly but only - the number of atoms of each element per molecular ion surplus the - respective mass-to-charge-state-ratio interval. - - Details on ranging definition files in the literature are `M. K. Miller `_. - volume(NX_NUMBER): - unit: NX_VOLUME - doc: | - Assumed volume affected by the set of atoms. - - Neither individual atoms nor a set of cluster of these have a volume - that is unique as a some cut-off criterion is required. - - # - identifier(NX_CHAR): - doc: | - Identifier for each atom at locations as detailed by position. - dimensions: - rank: 1 - dim: (n_pos,) - type(NX_UINT): - unit: NX_UNITLESS - doc: | - Nuclide information for each atom at locations as detailed by position. - - One `approach `_ for storing nuclide information efficiently - is via hashing with the following formula - - :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - - the number of protons and :math:`N` the number of neutrons - of each nuclide given as 8-bit unsigned integer values. - dimensions: - rank: 1 - dim: (n_pos,) - position(NX_NUMBER): - unit: NX_ANY - doc: | - Position of each atom. - dimensions: - rank: 2 - dim: (n_pos, d) - \@reference_frame(NX_CHAR): - doc: | - Path to a reference frame in which positions are defined - to resolve ambiguity when the reference frame is different - to the NeXus default reference frame (McStas). - occupancy(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - Relative occupancy of the atom position. - - This field is useful for specifying the atomic motif in - instances of :ref:`NXunit_cell`. - dimensions: - rank: 1 - dim: (n_pos,) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 5f3597e24e3e60049c211819bdbd31a2a4bb64f383b3aeab984f0cc310e1e360 -# -# -# -# -# -# Base class for documenting a set of atoms. -# -# Atoms in the set may be bonded. -# The set may have a net charge to represent -# an ion. Ions can be molecular ions. -# -# -# -# Given name for the set. -# -# This field could for example be used in the research field -# of atom probe tomography for storing a standardized -# human-readable name of the element or (molecular) ion -# like such as Al +++ or 12C +. -# -# -# -# -# Identifier used to refer to if the set of atoms represents a substance. -# -# -# -# -# -# -# -# Signed net (partial) charge of the (molecular) ion. -# -# Different methods for computing charge are in use. -# Care needs to be exercised with respect to the integration. -# `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. -# -# -# -# -# Charge reported in multiples of the charge of an electron. -# -# For research using atom probe tomography the value should be set to -# zero if the charge_state is unknown and irrecoverable. This can happen -# when classical ranging definition files in formats like RNG, RRNG are used. -# These file formats do not document the charge state explicitly but only -# the number of atoms of each element per molecular ion surplus the -# respective mass-to-charge-state-ratio interval. -# -# Details on ranging definition files in the literature are `M. K. Miller <https://doi.org/10.1002/sia.1719>`_. -# -# -# -# -# Assumed volume affected by the set of atoms. -# -# Neither individual atoms nor a set of cluster of these have a volume -# that is unique as a some cut-off criterion is required. -# -# -# -# -# -# Identifier for each atom at locations as detailed by position. -# -# -# -# -# -# -# -# Nuclide information for each atom at locations as detailed by position. -# -# One `approach <https://doi.org/10.1017/S1431927621012241>`_ for storing nuclide information efficiently -# is via hashing with the following formula -# -# :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` -# -# the number of protons and :math:`N` the number of neutrons -# of each nuclide given as 8-bit unsigned integer values. -# -# -# -# -# -# -# -# Position of each atom. -# -# -# -# -# -# -# -# Path to a reference frame in which positions are defined -# to resolve ambiguity when the reference frame is different -# to the NeXus default reference frame (McStas). -# -# -# -# -# -# Relative occupancy of the atom position. -# -# This field is useful for specifying the atomic motif in -# instances of :ref:`NXunit_cell`. -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXbeam_splitter.yaml b/contributed_definitions/nyaml/NXbeam_splitter.yaml index d611e2fdc2..089b6284ea 100644 --- a/contributed_definitions/nyaml/NXbeam_splitter.yaml +++ b/contributed_definitions/nyaml/NXbeam_splitter.yaml @@ -273,7 +273,7 @@ NXbeam_splitter(NXcomponent): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # 77d77ed20b614756dc9c077b9bdba91f86bce9d5eb889fbb5b3a471b83064f92 -# +# # # -# -# -# -# Base class to hold different coordinate systems and representation conversions. -# -# How many nodes of type :ref:`NXcoordinate_system_set` should be used in an application definition? -# -# * 0; if there is no instance of :ref:`NXcoordinate_system_set` and therein or elsewhere across -# the application definition, an instance of NXcoordinate_system is defined, -# the default NeXus `McStas <https://mailman2.mcstas.org/pipermail/mcstas-users/2021q2/001431.html>`_ -# coordinate system is assumed. This makes :ref:`NXcoordinate_system_set` and -# NXcoordinate_system base classes backwards compatible to older -# NeXus conventions and classes. -# * 1; if only one :ref:`NXcoordinate_system_set` is defined, it should be placed -# as high up in the node hierarchy (ideally right below an instance of NXentry) -# of the application definition tree as possible. -# This :ref:`NXcoordinate_system_set` should define at least one NXcoordinate_system -# instance. This shall be named such that it is clear how this coordinate system is -# typically referred to in a community. For the NeXus `McStas coordinate system, it is -# advised to call it mcstas for the sake of improved clarity. -# Additional NXcoordinate_system instances should be specified if possible in that same -# :ref:`NXcoordinate_system_set` instead of cluttering them across the tree. -# -# If this is the case, it is assumed that the NXcoordinate_system_members -# overwrite the NeXus default McStas coordinate system, i.e. users can thereby -# conveniently and explicitly specify the coordinate system(s) that -# they wish to use. -# -# Users are encouraged to write also explicit and clean depends_on fields in -# all groups that encode information about where the interpretation of coordinate -# systems is relevant. If these depends_on hints are not provided, it is -# automatically assumed that all children (to arbitrary depth) -# of that branch and sub-branches below the one in which that -# :ref:`NXcoordinate_system_set` is defined use either the only NXcoordinate_system_set -# instance in that set or the application definition is considered -# underconstrained which should at all costs be avoided and in which case -# again McStas is assumed. -# * 2 and more; as soon as more than one :ref:`NXcoordinate_system_set` is specified -# somewhere in the tree, different interpretations are possible as to which -# of these coordinate system sets and instances apply or take preference. -# We realize that such ambiguities should at all costs be avoided. -# However, the opportunity for multiple sets and their instances enables to -# have branch-specific coordinate system conventions which could especially -# be useful for deep classes where multiple scientific methods are combined or -# cases where having a definition of global translation and conversion tables -# how to convert between representations in different coordinate systems -# is not desired or available for now. -# We argue that having 2 or more :ref:`NXcoordinate_system_set` instances and respective -# NXcoordinate_system instances makes the interpretation eventually unnecessary -# complicated. Instead, developers of application definitions should always try -# to work for clarity and thus use only one top-level coordinate system set. -# -# For these reasons we conclude that the option with one top-level -# :ref:`NXcoordinate_system_set` instance is the preferred choice. -# -# McStas is used if neither an instance of :ref:`NXcoordinate_system_set` nor an instance -# of NXcoordinate_system is specified. However, even in this case it is better -# to be explicit like for every other coordinate system definition to support -# users with interpreting the content and logic behind every instance of the tree. -# -# How to store coordinate systems inside :ref:`NXcoordinate_system_set`? -# Individual coordinate systems should be specified as members of the -# :ref:`NXcoordinate_system_set` instance using instances of NXcoordinate_system. -# -# How many individual instances of NXcoordinate_system to allow within one -# instance of :ref:`NXcoordinate_system_set`? -# -# * 0; This case should be avoided for the sake of clarity but this case could -# mean the authors of the definition meant that McStas is used. We conclude, -# McStas is used in this case. -# * 1; Like above-mentioned this case has the advantage that it is explicit -# and faces no ambiguities. However, in reality typically multiple -# coordinate systems have to be mastered especially for complex -# multi-signal modality experiments. -# * 2 or more; If this case is realized, the best practice is that in every -# case where a coordinate system should be referred to the respective class -# has a depends_on field which resolves the possible ambiguities which specific -# coordinate systems is referred to. The benefit of this explicit and clear -# specifying of the coordinate system used in every case is that especially -# in combination with having coordinate systems inside deeper branches -# makes up for a very versatile, backwards compatible, but powerful system -# to express different types of coordinate systems using NeXus. In the case -# of two or more instances of NXcoordinate_system in one :ref:`NXcoordinate_system_set`, -# it is also advised to specify the relationship between the two coordinate systems by -# using the (NXtransformations) group within NXcoordinate_system. -# -# In effect, 1 should be the preferred choice. However, if more than one coordinate -# system is defined for practical purposes, explicit depends_on fields should -# always guide the user for each group and field which of the coordinate system -# one refers to. -# -# -# -# Convention how a positive rotation angle is defined when viewing -# from the end of the rotation unit vector towards its origin. -# This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# Counter_clockwise is equivalent to a right-handed choice. -# Clockwise is equivalent to a left-handed choice. -# -# -# -# -# -# -# -# -# How are rotations interpreted into an orientation according to convention 3 -# of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# -# How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) -# according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# The most frequently used convention is zxz, which is based on the work of H.-J. Bunge -# but other conventions are possible. Apart from undefined, proper Euler angles -# are distinguished from (improper) Tait-Bryan angles. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# To which angular range is the rotation angle argument of an -# axis-angle pair parameterization constrained according to -# convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# Which sign convention is followed when converting orientations -# between different parametrizations/representations according -# to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# -# -# -# -# Details about eventually relevant named directions that may give reasons for anisotropies. -# The classical example is mechanical processing where one has to specify which directions -# (e.g. rolling, transverse, and normal direction) align how with the direction of the base -# vectors of the sample_reference_frame. -# -# It is assumed that the configuration is inspected by looking towards the sample surface. -# If a detector is involved, it is assumed that the configuration is inspected from a position -# that is located behind this detector. -# -# If any of these assumptions is not met, the user is required to explicitly state this. -# -# Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the -# base vectors of this coordinate system as Xp, Yp, Zp. -# -# -# -# -# Details about the sample_reference_frame that is typically overlaid onto the surface of the sample. -# -# It is assumed that the configuration is inspected by looking towards the sample surface. -# If a detector is involved, it is assumed that the configuration is inspected from a position -# that is located behind this detector. -# -# If any of these assumptions is not met, the user is required to explicitly state this. -# -# Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the -# base vectors of this coordinate system as Xs, Ys, Zs. -# -# -# -# -# Details about the detector_reference_frame for a specific detector. -# -# Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the -# base vectors of this coordinate system as Xd, Yd, Zd. -# -# It is assumed that the configuration is inspected by looking towards the sample surface -# from a position that is located behind the detector. -# -# If any of these assumptions is not met, the user is required to explicitly state this. -# -# Instances should use detector_reference_frame as a name prefix. -# -# -# diff --git a/contributed_definitions/nyaml/NXcs_computer.yaml b/contributed_definitions/nyaml/NXcs_computer.yaml deleted file mode 100644 index d5dba84770..0000000000 --- a/contributed_definitions/nyaml/NXcs_computer.yaml +++ /dev/null @@ -1,230 +0,0 @@ -category: base -doc: | - Base class for reporting the description of a computer -type: group -NXcs_computer(NXobject): - name(NX_CHAR): - doc: | - Given name/alias to the computing system, e.g. MyDesktop. - operating_system(NX_CHAR): - doc: | - Name of the operating system, e.g. Windows, Linux, Mac, Android. - \@version: - doc: | - Version plus build number, commit hash, or description of an ever - persistent resource where the source code of the program and build - instructions can be found so that the program can be configured in - such a manner that the result file is ideally recreatable yielding - the same results. - - # difference e.g. in Win11 between hardware ID, UUID, and device ID - uuid(NX_CHAR): - doc: | - Ideally a (globally) unique persistent identifier of the computer, i.e. - the Universally Unique Identifier (UUID) of the computing node. - - # when it comes to performance monitoring - processing(NXobject): - doc: | - Details about the system of processing units e.g. (classical) processing units (CPUs), - coprocessor, graphic cards, accelerator processing units or a system of these. - (NXcircuit): - doc: | - Granularizing the processing units. Typical examples, a desktop computer - with a single CPU one could describe using one instance of NXcircuit. - A dual-socket server one could describe using two instances NXcircuit - A server with two dual-socket server nodes one could describe with - four instances of NXcircuit surplus a field with their level in the hierarchy. - type(NX_CHAR): - doc: | - General type of the processing unit - enumeration: - open_enum: true - items: [cpu, gpu, fpga] - name(NX_CHAR): - doc: | - Given name - memory(NXobject): - doc: | - Details about the memory system. - (NXcircuit): - doc: | - Granularizing the components of the memory system. - type(NX_CHAR): - doc: | - Qualifier for the type of random access memory. - enumeration: [ddr4, ddr5] - max_physical_capacity(NX_POSINT): - unit: NX_ANY - doc: | - Total amount of data which the medium can hold. - name(NX_CHAR): - doc: | - Given name - storage(NXobject): - doc: | - Details about the I/O system. - (NXcircuit): - doc: | - Granularizing the components of the I/O system. - type(NX_CHAR): - doc: | - Qualifier for the type of storage medium used. - enumeration: [solid_state_disk, hard_disk, tape] - max_physical_capacity(NX_POSINT): - unit: NX_ANY - doc: | - Total amount of data which the medium can hold. - name(NX_CHAR): - doc: | - Given name - - # NXcircuit inherits fabrication from NXcomponent - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# def5b601cc7944d9508ed1a048390db9b67fbacb57891fb83b83252ffda54459 -# -# -# -# -# -# Base class for reporting the description of a computer -# -# -# -# Given name/alias to the computing system, e.g. MyDesktop. -# -# -# -# -# Name of the operating system, e.g. Windows, Linux, Mac, Android. -# -# -# -# Version plus build number, commit hash, or description of an ever -# persistent resource where the source code of the program and build -# instructions can be found so that the program can be configured in -# such a manner that the result file is ideally recreatable yielding -# the same results. -# -# -# -# -# -# -# Ideally a (globally) unique persistent identifier of the computer, i.e. -# the Universally Unique Identifier (UUID) of the computing node. -# -# -# -# -# -# Details about the system of processing units e.g. (classical) processing units (CPUs), -# coprocessor, graphic cards, accelerator processing units or a system of these. -# -# -# -# Granularizing the processing units. Typical examples, a desktop computer -# with a single CPU one could describe using one instance of NXcircuit. -# A dual-socket server one could describe using two instances NXcircuit -# A server with two dual-socket server nodes one could describe with -# four instances of NXcircuit surplus a field with their level in the hierarchy. -# -# -# -# General type of the processing unit -# -# -# -# -# -# -# -# -# -# Given name -# -# -# -# -# -# -# Details about the memory system. -# -# -# -# Granularizing the components of the memory system. -# -# -# -# Qualifier for the type of random access memory. -# -# -# -# -# -# -# -# -# Total amount of data which the medium can hold. -# -# -# -# -# Given name -# -# -# -# -# -# -# Details about the I/O system. -# -# -# -# Granularizing the components of the I/O system. -# -# -# -# Qualifier for the type of storage medium used. -# -# -# -# -# -# -# -# -# -# Total amount of data which the medium can hold. -# -# -# -# -# Given name -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcs_filter_boolean_mask.yaml b/contributed_definitions/nyaml/NXcs_filter_boolean_mask.yaml deleted file mode 100644 index b798994a7c..0000000000 --- a/contributed_definitions/nyaml/NXcs_filter_boolean_mask.yaml +++ /dev/null @@ -1,191 +0,0 @@ -category: base -doc: | - Base class for packing and unpacking booleans. - - This base class bookkeeps metadata to inform software about necessary modulo - operations to decode e.g. set membership of objects in sets which are encoded - as a packed array of boolean values. - - One use case is processing of object sets (e.g. point cloud data). If e.g. a - spatial filter has been applied to a set of points we may wish to store - document efficiently which points were analyzed. Array of boolean values - is one option to achieve this. A value is true if the point is included. - The resulting boolean array will be filled with true and false values - in a manner that is often arbitrary and in general case-dependent. - - Especially when the number of points is large, for instance several thousands - or more, some situations can be more efficiently stored if one does not store - the boolean array but just lists the identifiers of the points taken. - - For example, if within a set of 1000 points only one point is included, it would - take (naively) 4000 bits to store the array but only 32 bits to store e.g. the - ID of the single point that is taken. Of course the 4000 bit field is so - sparse that it could be compressed resulting also in a substantial reduction - of the storage demands. Therefore, boolean masks are useful in that - they store compact representation of set memberships. - - This base class can deal with the situation when the number of objects - is not an integer multiple of the bit depth used for storing the states. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n_objs: | - Number of entries (e.g. number of points or objects). - bitdepth: | - Number of bits assumed for the container datatype used. - n_total: | - Length of mask considering the eventual need for padding. -type: group -NXcs_filter_boolean_mask(NXobject): - depends_on(NX_CHAR): - doc: | - Possibility to refer to which set this mask applies. - - If depends_on is not provided, it is assumed that the mask - applies to its direct parent. - number_of_objects(NX_UINT): - unit: NX_UNITLESS - doc: | - Number of objects represented by the mask. - bitdepth(NX_UINT): - unit: NX_UNITLESS - doc: | - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - mask(NX_UINT): - unit: NX_UNITLESS - doc: | - The content of the mask. If padding is used, - padding bits have to be set to 0. - dimensions: - rank: 1 - dim: (n_total,) - identifier(NX_INT): - unit: NX_UNITLESS - doc: | - Link to/or array of identifiers for the objects. The decoded mask is - interpreted consecutively, i.e. the first bit in the mask matches - to the first identifier, the second bit in the mask to the second - identifier and so on and so forth. Resolving of identifier follows - the conventions made for depends_on, so consult also the description - of th content to which depends_on refers. - dimensions: - rank: 1 - dim: (n_object,) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f2642ba0719a09d89b1b9ccd34d19574d842bfb6aeef78f2b0e2eba6bbe72934 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Number of entries (e.g. number of points or objects). -# -# -# -# -# Number of bits assumed for the container datatype used. -# -# -# -# -# Length of mask considering the eventual need for padding. -# -# -# -# -# Base class for packing and unpacking booleans. -# -# This base class bookkeeps metadata to inform software about necessary modulo -# operations to decode e.g. set membership of objects in sets which are encoded -# as a packed array of boolean values. -# -# One use case is processing of object sets (e.g. point cloud data). If e.g. a -# spatial filter has been applied to a set of points we may wish to store -# document efficiently which points were analyzed. Array of boolean values -# is one option to achieve this. A value is true if the point is included. -# The resulting boolean array will be filled with true and false values -# in a manner that is often arbitrary and in general case-dependent. -# -# Especially when the number of points is large, for instance several thousands -# or more, some situations can be more efficiently stored if one does not store -# the boolean array but just lists the identifiers of the points taken. -# -# For example, if within a set of 1000 points only one point is included, it would -# take (naively) 4000 bits to store the array but only 32 bits to store e.g. the -# ID of the single point that is taken. Of course the 4000 bit field is so -# sparse that it could be compressed resulting also in a substantial reduction -# of the storage demands. Therefore, boolean masks are useful in that -# they store compact representation of set memberships. -# -# This base class can deal with the situation when the number of objects -# is not an integer multiple of the bit depth used for storing the states. -# -# -# -# Possibility to refer to which set this mask applies. -# -# If depends_on is not provided, it is assumed that the mask -# applies to its direct parent. -# -# -# -# -# Number of objects represented by the mask. -# -# -# -# -# Number of bits assumed matching on a default datatype. -# (e.g. 8 bits for a C-style uint8). -# -# -# -# -# The content of the mask. If padding is used, -# padding bits have to be set to 0. -# -# -# -# -# -# -# -# Link to/or array of identifiers for the objects. The decoded mask is -# interpreted consecutively, i.e. the first bit in the mask matches -# to the first identifier, the second bit in the mask to the second -# identifier and so on and so forth. Resolving of identifier follows -# the conventions made for depends_on, so consult also the description -# of th content to which depends_on refers. -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcs_profiling.yaml b/contributed_definitions/nyaml/NXcs_profiling.yaml deleted file mode 100644 index 1991b941a4..0000000000 --- a/contributed_definitions/nyaml/NXcs_profiling.yaml +++ /dev/null @@ -1,263 +0,0 @@ -category: base -doc: | - Computer science description for performance and profiling data of an application. - - Performance monitoring and benchmarking of software is a task where questions - can be asked at various levels of detail. In general, there are three main - contributions to performance: - - * Hardware capabilities and configuration - * Software configuration and capabilities - * Dynamic effects of the system in operation and the system working together - with eventually multiple computers, especially when these have to exchange - information across a network and these are used usually by multiple users. - - At the most basic level users may wish to document how long e.g. a data - analysis with a scientific software (app) took. - A frequent idea is here to answer practical questions like how critical is the - effect on the workflow of the scientists, i.e. is the analysis possible in - a few seconds or would it take days if I were to run this analysis on a - comparable machine? - For this more qualitative performance monitoring, mainly the order of - magnitude is relevant, as well as how this was achieved using parallelization - (i.e. reporting the number of CPU and GPU resources used, the number of - processes and threads configured, and providing basic details about the computer). - - At more advanced levels benchmarks may go as deep as detailed temporal tracking - of individual processor instructions, their relation to other instructions, the - state of call stacks; in short eventually the entire app execution history - and hardware state history. Such analyses are mainly used for performance - optimization, i.e. by software and hardware developers as well as for - tracking bugs. Specialized software exists which documents such performance - data in specifically-formatted event log files or databases. - - This base class cannot and should not replace these specific solutions for now. - Instead, the intention of the base class is to serve scientists at the - basic level to enable simple monitoring of performance data and log profiling - data of key algorithmic steps or parts of computational workflows, so that - these pieces of information can guide users which order of magnitude differences - should be expected or not. - - Developers of application definitions should add additional fields and - references to e.g. more detailed performance data to which they wish to link - the metadata in this base class. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. -type: group -NXcs_profiling(NXobject): - - # details about queuing systems etc - current_working_directory(NX_CHAR): - doc: | - Path to the directory from which the tool was called. - command_line_call(NX_CHAR): - doc: | - Command line call with arguments if applicable. - start_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information - included when the app was started. - end_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information - included when the app terminated or crashed. - total_elapsed_time(NX_NUMBER): - unit: NX_TIME - doc: | - Wall-clock time how long the app execution took. This may be in principle - end_time minus start_time; however usage of eventually more precise timers - may warrant to use a finer temporal discretization, - and thus demands a more precise record of the wall-clock time. - number_of_processes(NX_UINT): - unit: NX_UNITLESS - doc: | - Qualifier which specifies with how many nominal processes the app was - invoked. The main idea behind this field e.g. for apps which use e.g. MPI - (Message Passing Interface) parallelization is to communicate - how many processes were used. - - For sequentially running apps number_of_processes and number_of_threads - is 1. If the app uses exclusively GPU parallelization number_of_gpus - can be larger than 1. If no GPU is used number_of_gpus is 0 even though - the hardware may have GPUs installed, thus indicating these were not - used though. - number_of_threads(NX_UINT): - unit: NX_UNITLESS - doc: | - Qualifier how many nominal threads were used at runtime. - Specifically here the maximum number of threads used for the - high-level threading library used (e.g. OMP_NUM_THREADS), posix. - number_of_gpus(NX_UINT): - unit: NX_UNITLESS - doc: | - Qualifier with how many nominal GPUs the app was invoked at runtime. - - # there are more complicated usage models, where GPUs are activated in - # between runs etc, but here application definition and base class developers - # should feel free to suggest customizations wrt to if and how such more - # complicated models should be captured. - (NXcs_computer): - doc: | - A collection with one or more computing nodes each with own resources. - This can be as simple as a laptop or the nodes of a cluster computer. - (NXcs_profiling_event): - doc: | - A collection of individual profiling event data which detail e.g. how - much time the app took for certain computational steps and/or how much - memory was consumed during these operations. - - # how to retrieve UUID for cloud computing instances - # https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/identify_ec2_instances.html - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0cc01f57e0b4c276a9ee507e7846b5410ffcdfb2656444a03d8aa447e41931a1 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Computer science description for performance and profiling data of an application. -# -# Performance monitoring and benchmarking of software is a task where questions -# can be asked at various levels of detail. In general, there are three main -# contributions to performance: -# -# * Hardware capabilities and configuration -# * Software configuration and capabilities -# * Dynamic effects of the system in operation and the system working together -# with eventually multiple computers, especially when these have to exchange -# information across a network and these are used usually by multiple users. -# -# At the most basic level users may wish to document how long e.g. a data -# analysis with a scientific software (app) took. -# A frequent idea is here to answer practical questions like how critical is the -# effect on the workflow of the scientists, i.e. is the analysis possible in -# a few seconds or would it take days if I were to run this analysis on a -# comparable machine? -# For this more qualitative performance monitoring, mainly the order of -# magnitude is relevant, as well as how this was achieved using parallelization -# (i.e. reporting the number of CPU and GPU resources used, the number of -# processes and threads configured, and providing basic details about the computer). -# -# At more advanced levels benchmarks may go as deep as detailed temporal tracking -# of individual processor instructions, their relation to other instructions, the -# state of call stacks; in short eventually the entire app execution history -# and hardware state history. Such analyses are mainly used for performance -# optimization, i.e. by software and hardware developers as well as for -# tracking bugs. Specialized software exists which documents such performance -# data in specifically-formatted event log files or databases. -# -# This base class cannot and should not replace these specific solutions for now. -# Instead, the intention of the base class is to serve scientists at the -# basic level to enable simple monitoring of performance data and log profiling -# data of key algorithmic steps or parts of computational workflows, so that -# these pieces of information can guide users which order of magnitude differences -# should be expected or not. -# -# Developers of application definitions should add additional fields and -# references to e.g. more detailed performance data to which they wish to link -# the metadata in this base class. -# -# -# -# -# Path to the directory from which the tool was called. -# -# -# -# -# Command line call with arguments if applicable. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information -# included when the app was started. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information -# included when the app terminated or crashed. -# -# -# -# -# Wall-clock time how long the app execution took. This may be in principle -# end_time minus start_time; however usage of eventually more precise timers -# may warrant to use a finer temporal discretization, -# and thus demands a more precise record of the wall-clock time. -# -# -# -# -# Qualifier which specifies with how many nominal processes the app was -# invoked. The main idea behind this field e.g. for apps which use e.g. MPI -# (Message Passing Interface) parallelization is to communicate -# how many processes were used. -# -# For sequentially running apps number_of_processes and number_of_threads -# is 1. If the app uses exclusively GPU parallelization number_of_gpus -# can be larger than 1. If no GPU is used number_of_gpus is 0 even though -# the hardware may have GPUs installed, thus indicating these were not -# used though. -# -# -# -# -# Qualifier how many nominal threads were used at runtime. -# Specifically here the maximum number of threads used for the -# high-level threading library used (e.g. OMP_NUM_THREADS), posix. -# -# -# -# -# Qualifier with how many nominal GPUs the app was invoked at runtime. -# -# -# -# -# -# A collection with one or more computing nodes each with own resources. -# This can be as simple as a laptop or the nodes of a cluster computer. -# -# -# -# -# A collection of individual profiling event data which detail e.g. how -# much time the app took for certain computational steps and/or how much -# memory was consumed during these operations. -# -# -# -# diff --git a/contributed_definitions/nyaml/NXdelocalization.yaml b/contributed_definitions/nyaml/NXdelocalization.yaml index c8a2b8b65f..d2bf07a9fb 100644 --- a/contributed_definitions/nyaml/NXdelocalization.yaml +++ b/contributed_definitions/nyaml/NXdelocalization.yaml @@ -94,7 +94,7 @@ NXdelocalization(NXobject): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # fe4c6145dafe2b74b01475cf3a610aa2b91ac9c88ffbd87f86757010f23289ad -# +# # # -# -# -# Application definition for normalized representation of electron microscopy research. -# -# This application definition is a comprehensive example for a general description -# with which to normalize specific (meta)data collected from the research field -# of electron microscopy -# -# NXem is designed to be used for documenting experiments or computer simulations in which -# controlled electron beams are used for studying electron-beam matter interaction to explore -# physical mechanisms and phenomena or to characterize materials with an electron microscope. -# -# -# -# -# -# -# -# -# -# -# The configuration of the software that was used to generate this NeXus file. -# -# -# -# A collection of all programs and libraries that are considered as relevant -# to understand with which software tools this NeXus file instance was -# generated. Ideally, to enable a binary recreation from the input data. -# -# Examples include the name and version of the libraries used to write the -# instance. Ideally, the software which writes these NXprogram instances -# also includes the version of the set of NeXus classes i.e. the specific set -# of base classes, application definitions, and contributed definitions -# with which the here described concepts can be resolved. -# -# For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ -# which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ -# research data management system, it makes sense to store e.g. the GitHub -# repository commit and respective submodule references used. -# -# Instances can also be used to document the modules and libraries that -# are offered by the computational environment such as those parsed -# from conda or python virtualenv environments. -# -# -# -# -# -# -# -# -# Alias (short name) which scientists can use to refer to this experiment. -# -# -# -# -# Free-text description about the experiment. -# -# Users are strongly advised to parameterize the description of their experiment -# by using respective groups and fields and base classes instead of writing prose -# into the field. The reason is that such free-text field is difficult to machine-interpret. -# The motivation behind keeping this field for now is to learn in how far the -# current base classes need extension based on user feedback. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information included -# when the microscope session started. If the application demands that time -# codes in this section of the application definition should only be used -# for specifying when the experiment was performed - and the exact -# duration is not relevant - use this start_time field. -# -# Often though it is useful to specify a time interval via setting both a start_time -# and an end_time because this enables software tools and users to collect a -# more detailed bookkeeping of the experiment. -# -# Users should be aware though that even using only start_time and end_time -# may not be sufficient to infer how long the experiment took or for how long -# data were acquired. To bookkeep more fine-grained timestamps over the -# course of the experiment is possible with start_time and end_time fields -# of respective :ref:`NXevent_data_em` instances. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC included when -# the microscope session ended. -# -# See docstring of the start_time field to see how to use the -# start_time and end_time together. -# -# -# -# -# -# Collection of serialized resources associated with the experiment. -# -# An example how to use this set is to document from which files in formatting -# of technology partners, the (meta)data in an instance of NXem were filled with -# during parsing to NeXus. -# -# -# -# -# -# -# -# -# Information about persons who performed or were involved in the microscope -# session or simulation run. -# -# Examples could be to put here the principle investigator who performed this -# experiment or students who performed simulations to name but a few. -# Adding multiple users if relevant is recommended. -# -# The protection of personal data by laws is in different stages of development -# and strictness. Therefore, the existence of user data has not been made -# required. -# -# Instances should use user as a name prefix. -# -# -# -# -# -# -# Given (first) name and surname. -# -# -# -# -# Name of the affiliation at the point in time when the experiment was performed. -# -# -# -# -# Postal address of the affiliation. -# -# -# -# -# Email address at the point in time when the experiment was performed. -# -# Writing the most permanently used email is recommended. -# -# -# -# -# Telephone number at the point in time when the experiment was performed. -# -# -# -# -# User role at the point in time when the experiment was performed. -# -# Examples are technician operating the microscope, student, postdoc, -# principle investigator, or guest. -# -# -# -# -# -# A physical entity which contains material intended to be investigated. -# Sample and specimen are treated as de facto synonyms. -# Samples can be real or virtual ones as annotated via is_simulation. -# -# The suggested best practice is to call this group sample. In those cases when -# multiple samples need to be grouped inside one entry, these SAMPLE groups -# should be named using the prefix sample followed an index starting from 1, i.e. -# (sample1, sample2). -# -# There are at least two strategies how to store (meta)data when one analyzes multiple -# samples - not different ROIs on a single sample though - in one session. -# -# One strategy is to store each sample and its results under an own NXem/ENTRY. -# This is one of the most frequent use cases as during most sessions typically only a -# single sample is investigated. In this case the name of this group should be NXem/ENTRY/sample. -# -# If multiple samples are investigated storing each of them in an own ENTRY group eventually will -# demand an unnecessary duplication though of many details about the instrument. -# -# This can be avoided by using another strategy how to store all samples and their results. -# Namely, by using only one instance of NXem/ENTRY. That NXem/ENTRY should then be named, -# like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., -# i.e. instances should use sample as a name prefix. -# -# In this case though the collection of events demands to use identifier_sample to state clearly -# for which of the samples loaded the (characterization) event was detected. -# -# This concept is related to term `Specimen`_ of the EMglossary standard. -# -# .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 -# -# -# -# Qualifier whether the sample is a real (in which case is_simulation should be set to false) -# or a virtual one (in which case is_simulation should be set to true). -# -# -# -# -# -# -# -# -# -# -# -# -# Ideally, (globally) unique persistent identifier which distinguishes this sample from all others -# and especially the predecessor/origin from where that sample was cut. The terms sample -# and specimen are here considered as exact synonyms. -# -# This field must not be used for an alias for the sample! Instead, use name. -# -# In cases where multiple specimens were loaded into the microscope, the identifier has to resolve -# the specific sample, whose results are stored by this :ref:`NXentry` instance because a single -# NXentry should be used for the characterization of a single specimen. -# -# Details about the specimen preparation should be stored in resources referring to identifier_parent. -# -# -# -# -# -# Identifier of the sample from which the sample was cut or the string *None*, -# i.e. the parent to this sample. -# -# The purpose of this field is to support functionalities for tracking -# sample provenance in a research data management system. -# -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information -# when the specimen was prepared. -# -# Ideally, report the end of the preparation, i.e. the last known timestamp when -# the measured specimen surface was actively prepared. Ideally, this matches -# the last timestamp that is mentioned in the digital resource pointed to by -# identifier_parent. -# -# Knowing when the specimen was exposed to e.g. specific atmosphere is especially -# required for material that is sensitive to the environment such as specimens that were -# charged with fast diffusing elements or short-lived radioactive tracers. -# -# Additional time stamps prior to preparation_date should better be placed in resources -# which describe but do not pollute the description here with prose. Resolving these -# connected metadata is considered as within the responsibility of the -# research data management system and not the a NeXus file. -# -# -# -# -# An alias used to refer to the specimen to please readability for humans. -# -# -# -# -# List of comma-separated elements from the periodic table that are contained in the sample. -# If the sample substance has multiple components, all elements from each component -# must be included in atom_types. -# -# The purpose of the field is to offer research data management systems an opportunity -# to parse the relevant elements without having to interpret these from the resources -# pointed to by identifier_parent or walk through eventually deeply nested groups in -# individual data instances. -# -# -# -# -# (Measured) sample thickness. -# -# The information is recorded to qualify if the beam used was likely -# able to shine through the specimen. For scanning electron microscopy, -# in many cases the specimen is typically thicker than what is -# illuminatable by the electron beam. -# -# In this case the value should be set to the actual thickness of the specimen -# viewed for an illumination situation where the nominal surface normal of the -# specimen is parallel to the optical axis. -# -# -# -# -# (Measured) density of the specimen. -# -# For multi-layered specimens this field should only be used to describe -# the density of the excited volume. For scanning electron microscopy -# the usage of this field is discouraged and instead an instance of a region-of-interest within connection to individual :ref:`NXevent_data_em` -# instances can provide a cleaner description of the relevant details -# why one may wish to store the density of the specimen. -# -# -# -# -# Discouraged free-text field to provide further detail. -# -# -# -# -# -# The conventions used when reporting crystal orientations. -# We follow the best practices of the Material Science community -# that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# Convention how a positive rotation angle is defined when viewing -# from the end of the rotation unit vector towards its origin. -# This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# Counter_clockwise is equivalent to a right-handed choice. -# Clockwise is equivalent to a left-handed choice. -# -# -# -# -# -# -# -# -# How are rotations interpreted into an orientation according to convention 3 -# of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# -# How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) -# according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# The most frequently used convention is zxz, which is based on the work of H.-J. Bunge -# but other conventions are possible. Apart from undefined, proper Euler angles -# are distinguished from (improper) Tait-Bryan angles. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# To which angular range is the rotation angle argument of an -# axis-angle pair parameterization constrained according to -# convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# Which sign convention is followed when converting orientations -# between different parametrizations/representations according -# to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Location of the origin of the processing_reference_frame. -# -# It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. -# Edges are interpreted by inspecting the direction of their outer unit normals -# (which point either parallel or antiparallel) along respective base vector direction -# of the reference frame. -# -# If any of these assumptions is not met, the user is required to explicitly state this. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing x-axis base vector of the -# processing_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing y-axis base vector of the -# processing_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing z-axis base vector of the -# processing_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Reference to the specifically named :ref:`NXsample` instance(s) for -# which these conventions apply (e.g. /entry1/sample1). -# -# -# -# -# -# -# -# Location of the origin of the sample_reference_frame. -# -# It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. -# Edges are interpreted by inspecting the direction of their outer unit normals -# (which point either parallel or antiparallel) along respective base vector direction -# of the reference frame. -# -# If any of these assumptions is not met, the user is required to explicitly state this. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing x-axis base vector of the -# sample_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing y-axis base vector of the -# sample_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing z-axis base vector of the -# sample_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use detector_reference_frame as a name prefix. -# -# -# -# Reference to the specifically named :ref:`NXdetector` instance for -# which these conventions apply (e.g. /entry1/instrument/detector1). -# -# Instances should use detector_reference_frame as a name prefix. -# -# -# -# -# -# -# -# Location of the origin of the detector_reference_frame. -# -# If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted -# by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) -# along respective base vector direction of the reference frame. -# -# If any of these assumptions is not met, the user is required to explicitly state this. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing x-axis base vector of the -# detector_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing y-axis base vector of the -# detector_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# Direction of the positively pointing z-axis base vector of the -# detector_reference_frame. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Details about the control program used for operating the microscope. -# -# Instances should use control_software as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use lens as a name prefix. -# -# -# -# -# -# -# -# -# -# -# Instances should use aperture as a name prefix. -# -# -# -# -# -# -# -# -# -# -# Instances should use monochromator as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use biprism as a name prefix. -# -# -# -# -# -# -# -# -# -# Instances should use phaseplate as a name prefix. -# -# -# -# -# -# -# -# -# -# -# Instances should use sensor as a name prefix. -# -# -# -# -# Instances should use actuator as a name prefix. -# -# -# -# -# Instances should use beam as a name prefix. -# -# -# -# -# Instances should use deflector as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use lens as a name prefix. -# -# -# -# -# -# -# -# -# -# -# Instances should use aperture as a name prefix. -# -# -# -# -# -# -# -# -# -# -# Instances should use monochromator as a name prefix. -# -# -# -# -# -# -# -# -# -# -# Instances should use sensor as a name prefix. -# -# -# -# -# Instances should use actuator as a name prefix. -# -# -# -# -# Instances should use beam as a name prefix. -# -# -# -# -# Instances should use deflector as a name prefix. -# -# -# -# -# -# Instances should use detector as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use pump as a name prefix. -# -# -# -# -# -# Instances should use sensor as a name prefix. -# -# -# -# -# Instances should use actuator as a name prefix. -# -# -# -# -# -# -# This group should be used to store all event-related (meta)data, -# which are typically measured datasets like images and spectra. -# To avoid that static instrument-related metadata need to be stored -# repetitively the NXem application definitions splits the storage of the -# dynamic (meta)data that typically change for each image and spectrum -# from the static one. -# -# -# -# Instances should use event as a name prefix. -# -# -# -# -# -# -# -# Instances should use image as a name prefix. -# Each NXimage instance must use only one image or stack instance. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use spectrum as a name prefix. -# Each NXspectrum instance must use only one spectrum or stack instance. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use lens as a name prefix. -# -# -# -# -# -# Instances should use aperture as a name prefix. -# -# -# -# Descriptor for the aperture setting when the exact technical details -# are unknown or not directly controllable as the control software of -# the microscope does not enable or was not configured to display these -# values for users. -# -# -# -# -# -# -# Instances should use monochromator as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# Instances should use tableau as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use sensor as a name prefix. -# -# -# -# -# Instances should use actuator as a name prefix. -# -# -# -# -# Instances should use beam as a name prefix. -# -# -# -# -# Instances should use deflector as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# Instances should use lens as a name prefix. -# -# -# -# -# -# Instances should use aperture as a name prefix. -# -# -# -# Descriptor for the aperture setting when the exact technical details -# are unknown or not directly controllable as the control software of -# the microscope does not enable or was not configured to display these -# values for users. -# -# -# -# -# -# Instances should use monochromator as a name prefix. -# -# -# -# -# -# Instances should use sensor as a name prefix. -# -# -# -# -# Instances should use actuator as a name prefix. -# -# -# -# -# Instances should use beam as a name prefix. -# -# -# -# -# Instances should use deflector as a name prefix. -# -# -# -# -# -# Instances should use detector as a name prefix. -# -# -# -# Operation mode of the detector as displayed by the control software. -# -# -# -# -# -# -# -# -# -# Instances should use sensor as a name prefix. -# -# -# -# -# Instances should use actuator as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# Nominal current of the heater. -# -# -# -# -# Nominal voltage of the heater. -# -# -# -# -# -# -# -# -# -# -# -# -# -# Possibility for documenting a set of simulations of electron beam matter interaction. -# -# Instances should use simulation as a name prefix. -# -# -# -# The program with which the simulation was performed. -# -# -# -# -# -# -# -# Programs and libraries representing the computational environment -# -# -# -# -# -# -# -# -# -# Configuration of the simulation -# -# -# -# -# Results of the simulation -# -# -# -# -# -# Description of the volume of interaction between of particle-matter interaction. -# -# Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam -# interaction simulations can be used to qualify and (or) quantify the shape of -# the interaction volume. Results of such simulations can be summary statistics -# or single-particle-resolved sets of trajectories. -# -# Explicit or implicit descriptions of the geometry of this -# interaction volume are possible: -# -# * An implicit description is via a set of electron/specimen interactions -# represented ideally as trajectory data from the computer simulation. -# * An explicit description is via iso-contour surface using either -# a simulation grid or a triangulated surface mesh of the approximated -# iso-contour surface evaluated at specific threshold values. -# Iso-contours could be computed from electron or particle flux through -# an imaginary control surface (the iso-surface) or energy-levels -# (e.g. the case of X-rays). Details depend on the model. -# * Another explicit description is via theoretical models which may -# be relevant e.g. for X-ray spectroscopy -# -# Further details on how the interaction volume can be quantified -# is available in the literature for example: -# -# * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ -# * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ -# * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ -# -# Instances should use interaction_volume as a name prefix. -# -# -# -# -# -# -# -# -# -# A region-of-interest analyzed either during or after the session for which specific -# processed data are available. Instances should use roi as a name prefix. -# -# This concept is related to term `Region Of Interest`_ of the EMglossary standard. -# -# .. _Region Of Interest: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 -# -# -# -# -# -# Instances should use image as a name prefix. -# Each NXimage instance must use only one image or stack instance. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use phase as a name prefix. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXem_calorimetry.yaml b/contributed_definitions/nyaml/NXem_calorimetry.yaml index c6569756d0..858006afc2 100644 --- a/contributed_definitions/nyaml/NXem_calorimetry.yaml +++ b/contributed_definitions/nyaml/NXem_calorimetry.yaml @@ -29,6 +29,8 @@ NXem_calorimetry(NXobject): exists: ['min', '1', 'max', '1'] definition(NX_CHAR): enumeration: [NXem_calorimetry] + identifier_analysis(NX_CHAR): + exists: optional profiling(NXcs_profiling): exists: optional doc: | @@ -44,7 +46,7 @@ NXem_calorimetry(NXobject): Name of the program whereby this config file was created. program(NX_CHAR): \@version(NX_CHAR): - environment(NXobject): + environment(NXcollection): exists: recommended doc: | Programs and libraries representing the computational environment @@ -56,10 +58,10 @@ NXem_calorimetry(NXobject): exists: ['min', '0', 'max', 'unbounded'] sample(NXsample): exists: recommended - type(NX_CHAR): + is_simulation(NX_BOOLEAN): doc: | - A qualifier whether the sample is a real one or a virtual one. - enumeration: [experiment, simulation] + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). atom_types(NX_CHAR): doc: | List of comma-separated elements from the periodic table that are @@ -69,8 +71,7 @@ NXem_calorimetry(NXobject): The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by identifier_parent or walk through - eventually deeply nested groups in data instances. + these from the resources. (NXcite): exists: ['min', '0', 'max', 'unbounded'] @@ -115,7 +116,7 @@ NXem_calorimetry(NXobject): as diffraction pattern matching with a specific state of the sample (e.g. obtained temperature via the actuator) are reported through delta_time. - identifier_pattern(NX_UINT): + indices_pattern(NX_INT): unit: NX_UNITLESS dimensions: rank: 1 @@ -140,11 +141,11 @@ NXem_calorimetry(NXobject): # obtained from that pattern with associated actuator data. # ISO8601 with local time zone information if possible and as precise as practically # possible. The indices follow the same order as - # used for identifier_pattern. + # used for indices_pattern. # dim: (n_p,) pattern_center(NXprocess): doc: | - Computation of the centre for each pattern using e.g. a Circular Hough + Computation of the center for each pattern using e.g. a Circular Hough Transformation. sequence_index(NX_POSINT): @@ -152,7 +153,7 @@ NXem_calorimetry(NXobject): position(NX_FLOAT): unit: NX_LENGTH doc: | - Computed centre for each pattern. + Computed center for each pattern. dimensions: rank: 2 dim: (n_p, 2) @@ -161,7 +162,7 @@ NXem_calorimetry(NXobject): distortion_correction(NXprocess): exists: optional doc: | - Elliptical distortion correction as a step when computing the centre for + Elliptical distortion correction as a step when computing the center for patterns. sequence_index(NX_POSINT): @@ -170,7 +171,7 @@ NXem_calorimetry(NXobject): center(NX_NUMBER): unit: NX_LENGTH doc: | - Computed centre for each pattern. + Computed center for each pattern. dimensions: rank: 2 dim: (n_p, 2) @@ -178,7 +179,7 @@ NXem_calorimetry(NXobject): # \@units: 1/nm integration(NXprocess): doc: | - Integrated diffraction pattern intensity as a function of radial distance from the centre + Integrated diffraction pattern intensity as a function of radial distance from the center azimuthally integrated as a function of time. sequence_index(NX_POSINT): @@ -200,12 +201,12 @@ NXem_calorimetry(NXobject): unit: NX_UNITLESS doc: | Integrated intensity as a function of time and the radial distance from the - pattern centre. + pattern center. dimensions: rank: 2 dim: (n_p, n_f) \@long_name(NX_CHAR): - identifier_pattern(NX_UINT): + indices_pattern(NX_INT): exists: optional unit: NX_UNITLESS doc: | @@ -240,8 +241,8 @@ NXem_calorimetry(NXobject): sequence_index(NX_POSINT): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 43730eda1d028f9abc84758c1d15a9e8e4e23889aa0df74e32c280bebaee8723 -# +# 4142f89f3701f4bac98d8ae1a748b84cd7cd9e234abf03c755544e7decfa229a +# # # # # -# Computation of the centre for each pattern using e.g. a Circular Hough +# Computation of the center for each pattern using e.g. a Circular Hough # Transformation. # # # # # -# Computed centre for each pattern. +# Computed center for each pattern. # # # @@ -458,7 +456,7 @@ NXem_calorimetry(NXobject): # # # -# Elliptical distortion correction as a step when computing the centre for +# Elliptical distortion correction as a step when computing the center for # patterns. # # @@ -466,7 +464,7 @@ NXem_calorimetry(NXobject): # NXcg_ellipsoid--> # # -# Computed centre for each pattern. +# Computed center for each pattern. # # # @@ -477,7 +475,7 @@ NXem_calorimetry(NXobject): # # # -# Integrated diffraction pattern intensity as a function of radial distance from the centre +# Integrated diffraction pattern intensity as a function of radial distance from the center # azimuthally integrated as a function of time. # # @@ -496,7 +494,7 @@ NXem_calorimetry(NXobject): # # # Integrated intensity as a function of time and the radial distance from the -# pattern centre. +# pattern center. # # # @@ -504,7 +502,7 @@ NXem_calorimetry(NXobject): # # # -# +# # # Identifier for each pattern. # diff --git a/contributed_definitions/nyaml/NXevent_data_apm.yaml b/contributed_definitions/nyaml/NXevent_data_apm.yaml deleted file mode 100644 index aeb47c4793..0000000000 --- a/contributed_definitions/nyaml/NXevent_data_apm.yaml +++ /dev/null @@ -1,284 +0,0 @@ -category: base -doc: | - Base class to store state and (meta)data of events over the course of an atom probe experiment. - - Having at least one instance for an instance of NXapm is recommended. - - This base class applies the concept of the NXevent_data_em base class to the specific needs - of atom probe research. Against static and dynamic quantities are split to avoid a duplication - of information. Specifically, the time interval considered is the entire time - starting at start_time until end_time during which we assume the pulser triggered named pulses. - These pulses are identified via the identifier_pulse field. The point in time when each was issued - is specified via the combination of start_time and delta_time. - - Conceptually and technically NeXus currently stores tensorial information as arrays of values - (with each value of the same datatype). For instance, a field temperature(NX_FLOAT) stores - a set of temperature values but that field when used somewhere is a concept. However, that - concept has no information at which point in time these temperatures were taken. - An existent functional relationship between the two concepts is not defined. - - However, a correct interpretation of the temperature values demands knowledge about what is - the independent quantity on which temperature depends on or according to which frequency - temperature values were sampled. - In NeXus there are two approaches which cope with such correlations: - One is :ref:`NXdata` where the attribute signal specifies the correlation. - The other one is :ref:`NXlog` which, like NXdata, demands to granularize logged_against - (dependent signal) and independent quantities into an own group. - In many cases this additional grouping is not desired though. - - One naive solution typically employed is then to store the independent variable values via a second - vector e.g. time_stamp with the same number of entries (with dimensionality defined through symbols). - However, there is no independent logical connection between these two concepts, i.e. temperature - and time_stamp. - - In the case of atom probe though the time that one would use in NXlog is defined implicitly via identifier_pulse, - which is the independent variable vector against which eventually dozens of channels of data are logged. - Not only are these channels logged they should ideally also be self-descriptive in that these channels have - identifier_pulse as the independent variable but we do not wish to duplicate this information all the time but - reference it. - - Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the - symbol depends_on but this is easily to be confused with depends_on that is used for instances of - :ref:`NXtransformations`. Consequently, if depends_on were to be used extra logic is needed by consuming - applications to understand that the here build correlations are conceptually different ones. - - This issue should be discussed further by the NeXus community. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - p: | - Number of pulses collected in between start_time and end_time. -type: group -NXevent_data_apm(NXobject): - start_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval started. If the user wishes to specify an - interval of time that the snapshot should represent during which the instrument - was stable and configured using specific settings and calibrations, - the start_time is the start (left bound of the time interval) while - the end_time specifies the end (right bound) of the time interval. - end_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval ended. - delta_time(NX_NUMBER): - unit: NX_TIME - doc: | - Delta time array which resolves for each identifier_pulse the time difference - between when that pulse was issued and start_time. - - In summary, using start_time, end_time, delta_time, identifier_pulse_offset, - and identifier_pulse exactly specifies the connection between when a pulse was - issued relative to start and absolute in UTC. - dimensions: - rank: 1 - dim: (p,) - identifier_pulse_offset(NX_INT): - unit: NX_UNITLESS - doc: | - Integer used to name the first pulse to know if there is an - offset of the identifiers to zero. - - Identifiers can be defined either implicitly or explicitly. - For implicit indexing identifiers are defined on the interval - :math:`[identifier\_offset, identifier\_offset + c - 1]`. - - Therefore, implicit identifier are completely defined by the value of - identifier_offset and cardinality. For example if identifier run from - -2 to 3 the value for identifier_offset is -2. - - For explicit indexing the field identifier has to be used. - Fortran-/Matlab- and C-/Python-style indexing have specific implicit - identifier conventions where identifier_offset is 1 and 0 respectively. - identifier_pulse(NX_INT): - unit: NX_UNITLESS - doc: | - Identifier that contextualizes how the detector and pulser of an atom probe - instrument follows a sequence of pulses to trigger field evaporation. - - The identifier_pulse is used to associate thus an information about time - when quantities have been collected via sampling. - - In virtually all cases the pulser is a blackbox. Depending on how the - instrument is configured during a measurement the target - values and thus also the actual values may change. - - Maybe the first part of the experiment is run at a certain pulse fraction but thereafter - the pulse_fraction is changed. In this case the field pulse_fraction is a vector which - collects all measured values of the pulse_fraction, identifier_pulse is then an equally - long vector which stores the set of events (e.g. pulsing events) when that value was - measured. - - This may cause several situations: In the case that e.g. the pulse_fraction is never changed - and also exact details not interesting, one stores the set value for the pulse_fraction - and a single value for the identifier_pulse e.g. 0 to indicate that the pulse_fraction was set - at the beginning and it was maintained constant during the measurement. - If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a - vector with two values one for the first and another one for the value from the 100000-th - pulse onwards. The values of identifier_pulse are then [0, 99999] respectively. - dimensions: - rank: 1 - dim: (p,) - instrument(NXinstrument_apm): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4710a7f12dac9a93c938c8a951dff4466f852d3e6b58591b5af53173ac16ae38 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Number of pulses collected in between start_time and end_time. -# -# -# -# -# Base class to store state and (meta)data of events over the course of an atom probe experiment. -# -# Having at least one instance for an instance of NXapm is recommended. -# -# This base class applies the concept of the NXevent_data_em base class to the specific needs -# of atom probe research. Against static and dynamic quantities are split to avoid a duplication -# of information. Specifically, the time interval considered is the entire time -# starting at start_time until end_time during which we assume the pulser triggered named pulses. -# These pulses are identified via the identifier_pulse field. The point in time when each was issued -# is specified via the combination of start_time and delta_time. -# -# Conceptually and technically NeXus currently stores tensorial information as arrays of values -# (with each value of the same datatype). For instance, a field temperature(NX_FLOAT) stores -# a set of temperature values but that field when used somewhere is a concept. However, that -# concept has no information at which point in time these temperatures were taken. -# An existent functional relationship between the two concepts is not defined. -# -# However, a correct interpretation of the temperature values demands knowledge about what is -# the independent quantity on which temperature depends on or according to which frequency -# temperature values were sampled. -# In NeXus there are two approaches which cope with such correlations: -# One is :ref:`NXdata` where the attribute signal specifies the correlation. -# The other one is :ref:`NXlog` which, like NXdata, demands to granularize logged_against -# (dependent signal) and independent quantities into an own group. -# In many cases this additional grouping is not desired though. -# -# One naive solution typically employed is then to store the independent variable values via a second -# vector e.g. time_stamp with the same number of entries (with dimensionality defined through symbols). -# However, there is no independent logical connection between these two concepts, i.e. temperature -# and time_stamp. -# -# In the case of atom probe though the time that one would use in NXlog is defined implicitly via identifier_pulse, -# which is the independent variable vector against which eventually dozens of channels of data are logged. -# Not only are these channels logged they should ideally also be self-descriptive in that these channels have -# identifier_pulse as the independent variable but we do not wish to duplicate this information all the time but -# reference it. -# -# Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the -# symbol depends_on but this is easily to be confused with depends_on that is used for instances of -# :ref:`NXtransformations`. Consequently, if depends_on were to be used extra logic is needed by consuming -# applications to understand that the here build correlations are conceptually different ones. -# -# This issue should be discussed further by the NeXus community. -# -# -# -# ISO 8601 time code with local time zone offset to UTC information included -# when the snapshot time interval started. If the user wishes to specify an -# interval of time that the snapshot should represent during which the instrument -# was stable and configured using specific settings and calibrations, -# the start_time is the start (left bound of the time interval) while -# the end_time specifies the end (right bound) of the time interval. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information included -# when the snapshot time interval ended. -# -# -# -# -# Delta time array which resolves for each identifier_pulse the time difference -# between when that pulse was issued and start_time. -# -# In summary, using start_time, end_time, delta_time, identifier_pulse_offset, -# and identifier_pulse exactly specifies the connection between when a pulse was -# issued relative to start and absolute in UTC. -# -# -# -# -# -# -# -# Integer used to name the first pulse to know if there is an -# offset of the identifiers to zero. -# -# Identifiers can be defined either implicitly or explicitly. -# For implicit indexing identifiers are defined on the interval -# :math:`[identifier\_offset, identifier\_offset + c - 1]`. -# -# Therefore, implicit identifier are completely defined by the value of -# identifier_offset and cardinality. For example if identifier run from -# -2 to 3 the value for identifier_offset is -2. -# -# For explicit indexing the field identifier has to be used. -# Fortran-/Matlab- and C-/Python-style indexing have specific implicit -# identifier conventions where identifier_offset is 1 and 0 respectively. -# -# -# -# -# Identifier that contextualizes how the detector and pulser of an atom probe -# instrument follows a sequence of pulses to trigger field evaporation. -# -# The identifier_pulse is used to associate thus an information about time -# when quantities have been collected via sampling. -# -# In virtually all cases the pulser is a blackbox. Depending on how the -# instrument is configured during a measurement the target -# values and thus also the actual values may change. -# -# Maybe the first part of the experiment is run at a certain pulse fraction but thereafter -# the pulse_fraction is changed. In this case the field pulse_fraction is a vector which -# collects all measured values of the pulse_fraction, identifier_pulse is then an equally -# long vector which stores the set of events (e.g. pulsing events) when that value was -# measured. -# -# This may cause several situations: In the case that e.g. the pulse_fraction is never changed -# and also exact details not interesting, one stores the set value for the pulse_fraction -# and a single value for the identifier_pulse e.g. 0 to indicate that the pulse_fraction was set -# at the beginning and it was maintained constant during the measurement. -# If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a -# vector with two values one for the first and another one for the value from the 100000-th -# pulse onwards. The values of identifier_pulse are then [0, 99999] respectively. -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXibeam_column.yaml b/contributed_definitions/nyaml/NXibeam_column.yaml deleted file mode 100644 index cf7cd8cb1f..0000000000 --- a/contributed_definitions/nyaml/NXibeam_column.yaml +++ /dev/null @@ -1,230 +0,0 @@ -category: base -doc: | - Base class for a set of components equipping an instrument with FIB capabilities. - - Focused-ion-beam (FIB) capabilities turn especially scanning electron microscopes - into specimen preparation labs. FIB is a material preparation technique whereby - portions of the sample are illuminated with a focused ion beam with controlled - intensity. The beam is intense enough and with sufficient ion momentum to - remove material in a controlled manner. - - The fact that an electron microscope with FIB capabilities has needs a - second gun with own relevant control circuits, focusing lenses, and other - components, warrants the definition of an own base class to group these - components and distinguish them from the lenses and components for creating - and shaping the electron beam. - - For more details about the relevant physics and application examples - consult the literature, for example: - - * `L. A. Giannuzzi et al. `_ - * `E. I. Preiß et al. `_ - * `J. F. Ziegler et al. `_ - * `J. Lili `_ - -# symbols: -# doc: The symbols used in the schema to specify e.g. variables. -type: group -NXibeam_column(NXcomponent): - ion_source(NXsource): - doc: | - The source which creates the ion beam. - name(NX_CHAR): - doc: | - Given name/alias for the ion gun. - emitter_type(NX_CHAR): - doc: | - Emitter type used to create the ion beam. - - If the emitter type is other, give further - details in the description field. - enumeration: [liquid_metal, plasma, gas_field, other] - description(NX_CHAR): - doc: | - Ideally, a (globally) unique persistent identifier, link, - or text to a resource which gives further details. - probe(NXion): - doc: | - Which ionized elements or molecular ions form the beam. - Examples are gallium, helium, neon, argon, krypton, - or xenon, O2+. - flux(NX_NUMBER): - unit: NX_ANY - doc: | - Average/nominal flux - brightness(NX_NUMBER): - unit: NX_ANY - doc: | - Average/nominal brightness - - # \@units: A/cm*sr - # NEW ISSUE: (at which location?). - current(NX_NUMBER): - unit: NX_CURRENT - doc: | - Charge current - voltage(NX_NUMBER): - unit: NX_VOLTAGE - doc: | - Ion acceleration voltage upon source exit and - entering the vacuum flight path. - ion_energy_profile(NX_NUMBER): - unit: NX_ENERGY - doc: | - To be defined more specifically. Community suggestions are welcome. - - # NEW ISSUE: details about the life/up-time of the source relevant from maintenance point of view - (NXlens_em): - (NXaperture): - (NXmonochromator): - (NXcomponent): - (NXsensor): - (NXactuator): - (NXbeam): - doc: | - Individual characterization results for the position, shape, - and characteristics of the ion beam. - - :ref:`NXtransformations` should be used to specify the location or position - at which details about the ion beam are probed. - (NXdeflector): - - # for further ideas and comments inspect version - # https://github.com/FAIRmat-NFDI/nexus_definitions/commit/0682943baaef54d4a6386b5433f9721af6d3d81b - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0a4f5073069eba5f9c0bafd732a6340cf9f4ba89e9be3d114c5dec61ef37b1aa -# -# -# -# -# -# -# Base class for a set of components equipping an instrument with FIB capabilities. -# -# Focused-ion-beam (FIB) capabilities turn especially scanning electron microscopes -# into specimen preparation labs. FIB is a material preparation technique whereby -# portions of the sample are illuminated with a focused ion beam with controlled -# intensity. The beam is intense enough and with sufficient ion momentum to -# remove material in a controlled manner. -# -# The fact that an electron microscope with FIB capabilities has needs a -# second gun with own relevant control circuits, focusing lenses, and other -# components, warrants the definition of an own base class to group these -# components and distinguish them from the lenses and components for creating -# and shaping the electron beam. -# -# For more details about the relevant physics and application examples -# consult the literature, for example: -# -# * `L. A. Giannuzzi et al. <https://doi.org/10.1007/b101190>`_ -# * `E. I. Preiß et al. <https://link.springer.com/content/pdf/10.1557/s43578-020-00045-w.pdf>`_ -# * `J. F. Ziegler et al. <https://www.sciencedirect.com/science/article/pii/S0168583X10001862>`_ -# * `J. Lili <https://www.osti.gov/servlets/purl/924801>`_ -# -# -# -# The source which creates the ion beam. -# -# -# -# Given name/alias for the ion gun. -# -# -# -# -# Emitter type used to create the ion beam. -# -# If the emitter type is other, give further -# details in the description field. -# -# -# -# -# -# -# -# -# -# -# Ideally, a (globally) unique persistent identifier, link, -# or text to a resource which gives further details. -# -# -# -# -# Which ionized elements or molecular ions form the beam. -# Examples are gallium, helium, neon, argon, krypton, -# or xenon, O2+. -# -# -# -# -# Average/nominal flux -# -# -# -# -# Average/nominal brightness -# -# -# -# -# -# Charge current -# -# -# -# -# Ion acceleration voltage upon source exit and -# entering the vacuum flight path. -# -# -# -# -# To be defined more specifically. Community suggestions are welcome. -# -# -# -# -# -# -# -# -# -# -# -# -# Individual characterization results for the position, shape, -# and characteristics of the ion beam. -# -# :ref:`NXtransformations` should be used to specify the location or position -# at which details about the ion beam are probed. -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXion.yaml b/contributed_definitions/nyaml/NXion.yaml deleted file mode 100644 index 3bd3ff33e2..0000000000 --- a/contributed_definitions/nyaml/NXion.yaml +++ /dev/null @@ -1,272 +0,0 @@ -category: base -doc: | - Base class for documenting the set of atoms of a (molecular) ion. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n_ivec_max: | - Maximum number of atoms/isotopes allowed per (molecular) ion (fragment). - n_ranges: | - Number of mass-to-charge-state-ratio range intervals for ion type. -type: group -NXion(NXobject): - identifier(NX_CHAR): - doc: | - A unique identifier whereby such an ion can be referred to - via the service offered as described in identifier_type. - identifier_type(NX_CHAR): - doc: | - How can the identifier be resolved? - enumeration: [inchi] - ion_type(NX_UINT): - unit: NX_UNITLESS - doc: | - Ion type (ion species) identifier. - - The identifier zero is reserved for the special unknown ion type. - nuclide_hash(NX_UINT): - unit: NX_UNITLESS - doc: | - Vector of nuclide hash values. - - Individual hash values :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - encode the number of protons :math:`Z` and the number of neutrons :math:`N` - of each nuclide respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - - The array is sorted in decreasing order. For the rationale behind this see `M. Kühbach et al. (2021) `_ - dimensions: - rank: 1 - dim: (n_ivec_max,) - nuclide_list(NX_UINT): - unit: NX_UNITLESS - doc: | - Table which decodes the entries in nuclide_hash into a human-readable matrix of instances. - The first column specifies the nuclide mass number, i.e. using the hashvalues - from the isotope_vector this is :math:`Z + N` or 0. The value 0 documents that no - isotope-specific information about the element encoded is relevant. - The second row specifies the number of protons :math:`Z` or 0. - The value 0 in this case documents a placeholder or that no element-specific - information is relevant. - Taking a carbon-14 nuclide as an example the mass number is 14. - That is encoded as a value pair (14, 6) as one row of the table. - - Therefore, this notation is the typical superscribed nuclide mass number - and subscripted number of protons element notation e.g. :math:`^{14}C`. - The array is stored matching the order of nuclide_hash. - dimensions: - rank: 2 - dim: (n_ivecmax, 2) - - # color(NX_CHAR): - # doc: | - # Color code used for visualizing such ions. - volume(NX_NUMBER): - unit: NX_VOLUME - doc: | - Assumed volume of the ion. - - In atom probe microscopy this field can be used to store the reconstructed - volume per ion (average) which is typically stored alongside ranging - definitions. - charge(NX_NUMBER): - unit: NX_CHARGE - doc: | - Charge of the ion. - charge_state(NX_INT): - unit: NX_UNITLESS - doc: | - Signed charge state of the ion in multiples of electron charge. - - In the example of atom probe microscopy, only positive values will be measured - as the ions are accelerated by a negatively signed bias electric field. - In the case that the charge state is not explicitly recoverable, the value should - be set to zero. - - In atom probe microscopy this is for example the case when using - classical ranging definition files in formats like RNG, RRNG. - These file formats do not document the charge state explicitly - but the number of atoms of each element per molecular ion - surplus the mass-to-charge-state-ratio interval. - Details on ranging definition files can be found in the literature: - `M. K. Miller `_ - name(NX_CHAR): - doc: | - Human-readable ion type name (e.g. Al +++) - The string should consists of UTF-8 characters, ideally using LaTeX - notation to specify the isotopes, ions, and charge state. - Examples are 12C + or Al +++. - - To ease automated parsing, isotope_vector should be the - preferred machine-readable information used. - mass_to_charge_range(NX_NUMBER): - unit: NX_ANY - doc: | - Associated lower (mqmin) and upper (mqmax) bounds of the - mass-to-charge-state ratio interval(s) [mqmin, mqmax] - (boundaries inclusive). This field is primarily of interest - for documenting :ref:`NXprocess` steps of indexing a - ToF/mass-to-charge state histogram. - dimensions: - rank: 2 - dim: (n_ranges, 2) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f85b51ac7b65250a56c2603c5394d8850c9f9874867d6f5bcf4a4c1b70975726 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Maximum number of atoms/isotopes allowed per (molecular) ion (fragment). -# -# -# -# -# Number of mass-to-charge-state-ratio range intervals for ion type. -# -# -# -# -# Base class for documenting the set of atoms of a (molecular) ion. -# -# -# -# A unique identifier whereby such an ion can be referred to -# via the service offered as described in identifier_type. -# -# -# -# -# How can the identifier be resolved? -# -# -# -# -# -# -# -# Ion type (ion species) identifier. -# -# The identifier zero is reserved for the special unknown ion type. -# -# -# -# -# Vector of nuclide hash values. -# -# Individual hash values :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` -# encode the number of protons :math:`Z` and the number of neutrons :math:`N` -# of each nuclide respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. -# -# The array is sorted in decreasing order. For the rationale behind this see `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ -# -# -# -# -# -# -# -# Table which decodes the entries in nuclide_hash into a human-readable matrix of instances. -# The first column specifies the nuclide mass number, i.e. using the hashvalues -# from the isotope_vector this is :math:`Z + N` or 0. The value 0 documents that no -# isotope-specific information about the element encoded is relevant. -# The second row specifies the number of protons :math:`Z` or 0. -# The value 0 in this case documents a placeholder or that no element-specific -# information is relevant. -# Taking a carbon-14 nuclide as an example the mass number is 14. -# That is encoded as a value pair (14, 6) as one row of the table. -# -# Therefore, this notation is the typical superscribed nuclide mass number -# and subscripted number of protons element notation e.g. :math:`^{14}C`. -# The array is stored matching the order of nuclide_hash. -# -# -# -# -# -# -# -# -# -# Assumed volume of the ion. -# -# In atom probe microscopy this field can be used to store the reconstructed -# volume per ion (average) which is typically stored alongside ranging -# definitions. -# -# -# -# -# Charge of the ion. -# -# -# -# -# Signed charge state of the ion in multiples of electron charge. -# -# In the example of atom probe microscopy, only positive values will be measured -# as the ions are accelerated by a negatively signed bias electric field. -# In the case that the charge state is not explicitly recoverable, the value should -# be set to zero. -# -# In atom probe microscopy this is for example the case when using -# classical ranging definition files in formats like RNG, RRNG. -# These file formats do not document the charge state explicitly -# but the number of atoms of each element per molecular ion -# surplus the mass-to-charge-state-ratio interval. -# Details on ranging definition files can be found in the literature: -# `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ -# -# -# -# -# Human-readable ion type name (e.g. Al +++) -# The string should consists of UTF-8 characters, ideally using LaTeX -# notation to specify the isotopes, ions, and charge state. -# Examples are 12C + or Al +++. -# -# To ease automated parsing, isotope_vector should be the -# preferred machine-readable information used. -# -# -# -# -# Associated lower (mqmin) and upper (mqmax) bounds of the -# mass-to-charge-state ratio interval(s) [mqmin, mqmax] -# (boundaries inclusive). This field is primarily of interest -# for documenting :ref:`NXprocess` steps of indexing a -# ToF/mass-to-charge state histogram. -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXisocontour.yaml b/contributed_definitions/nyaml/NXisocontour.yaml index 2772a65d50..0050e1112a 100644 --- a/contributed_definitions/nyaml/NXisocontour.yaml +++ b/contributed_definitions/nyaml/NXisocontour.yaml @@ -40,7 +40,7 @@ NXisocontour(NXobject): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # 8054eb08c275e495dd56bde256fb59d22d80d9cb74c88779a0edd4fb308a21fe -# +# # # -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Grinding and polishing of a sample using abrasives in a wet lab. -# Manual procedures, electro-chemical, vibropolishing. -# -# -# -# -# -# Version specifier of this application definition. -# -# -# -# -# Official NeXus NXDL schema with which this file was written. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# A preparation step performed by a human or a robot/automated system. -# -# -# -# -# -# -# -# Carrier/plate used on which the abrasive/(lubricant) mixture was applied. -# -# -# -# -# -# Medium on the abrasive_medium_carrier (cloth or grinding plate) -# whereby material is abrasively weared. -# -# -# -# -# -# Lubricant -# -# -# -# -# -# Qualitative statement how the revelation of the machine was configured. -# If the rotation was controlled manually, e.g. by turning knobs -# choose manual and estimate the nominal average rotation. -# If the rotation was controlled via choosing from a fixed set -# of options offered by the machine choose fixed and -# specify the nominal rotation. -# If programmed use rotation_history (e.g. for automated/robot systems). -# -# -# -# -# -# -# -# -# -# -# Qualitative statement how the (piston) force with which the sample -# was pressed into/against the abrasive medium was controlled if at all. -# If the force was controlled manually e.g. by turning knobs -# choose manual and estimate nominal average force. -# If the force was controlled via choosing from a fixed set -# of options offered by the machine choose fixed and -# specify the nominal force. -# If programmed use force_history (e.g. for automated/robot systems). -# -# -# -# -# -# -# -# -# -# -# Qualitative statement for how long (assuming regular uninterrupted) -# preparation at the specified conditions the preparation step was -# applied. -# -# -# -# -# -# -# -# -# -# -# Turns per unit time. -# -# -# -# -# -# Force exerted on the sample to press it into the abrasive. -# -# -# -# -# -# Seconds -# -# -# -# -# Qualitative statement how the material removal was characterized. -# -# -# -# -# -# -# -# -# -# How thick a layer was removed. -# -# -# -# -# -# -# A preparation step performed by a human or a robot/automated system -# with the aim to remove residual abrasive medium from the specimen surface. -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXlab_sample_mounting.yaml b/contributed_definitions/nyaml/NXlab_sample_mounting.yaml deleted file mode 100644 index 470414f85c..0000000000 --- a/contributed_definitions/nyaml/NXlab_sample_mounting.yaml +++ /dev/null @@ -1,151 +0,0 @@ -category: application -doc: | - Embedding of a sample in a medium for easing processability. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. -type: group -NXlab_sample_mounting(NXobject): - (NXentry): - - # by default for application definitions the value of the exists keyword is required unless it is explicitly specified differently - \@version: - doc: | - Version specifier of this application definition. - definition: - doc: | - Official NeXus NXDL schema with which this file was written. - enumeration: [NXlab_sample_mounting] - (NXsample): - exists: ['min', '1', 'max', '1'] - (NXuser): - exists: ['min', '1', 'max', 'unbounded'] - start_time(NX_DATE_TIME): - end_time(NX_DATE_TIME): - - # (NXlab_mounting_machine): - mounting_machine(NXfabrication): - vendor: - model: - identifier: - exists: recommended - mounting_method: - doc: | - Qualitative statement how the sample was mounted. - enumeration: [cold_mounting, hot_mounting] - embedding_medium: - doc: | - Type of material. - enumeration: [resin, epoxy] - electrical_conductivity(NX_FLOAT): - unit: NX_ANY - doc: | - Electrical conductivity of the embedding medium. - - # temperature control of the mounting (e.g. relevant when hot_mounting Al) - # cleaning procedures - # a descriptor of the shape of the specimen - # borrow from NXlab_thermo_mechanical_processing to document the external - # stimuli (eventually) applied during mounting - # temperature, mechanical, magnetic, electro-magnetic, are externally - # applied stimuli on the sample, can we use one master schema? - # e.g. one can even store NXcg_polyhedron and NXcg_face_list_data_structure - # instances to keep track of the geometry of specific instrument and how - # the samples were arranged in these - # key question is which steps has the sample experienced? - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# b9d170c9b46c62975977f356527c80694cffe0dfd43fa54139cb712620ce6882 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Embedding of a sample in a medium for easing processability. -# -# -# -# -# -# Version specifier of this application definition. -# -# -# -# -# Official NeXus NXDL schema with which this file was written. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Qualitative statement how the sample was mounted. -# -# -# -# -# -# -# -# -# Type of material. -# -# -# -# -# -# -# -# -# Electrical conductivity of the embedding medium. -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXlockin.yaml b/contributed_definitions/nyaml/NXlockin.yaml index 33af36c672..3e6c074c3a 100644 --- a/contributed_definitions/nyaml/NXlockin.yaml +++ b/contributed_definitions/nyaml/NXlockin.yaml @@ -128,7 +128,7 @@ NXlockin(NXamplifier): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # 8e417ba414cffd83d18d3ece90b9b7ac762c7ba8c6cdf2bda337026ff6c88192 -# +# # # # # @@ -695,57 +796,83 @@ NXmicrostructure(NXobject): # Whether one uses a continuum or atomic scale description of materials, these are always a model only of # the true internal structure of a material. Such models are useful as they enable a coarse-graining and # categorizing of properties and representational aspects from which measured or simulated descriptions -# can be correlated with properties, i.e. descriptor values. +# can be correlated with properties, i.e. descriptor values. The base class here can be used to describe +# the structural aspect of a region-of-interest for a specimen that was investigated or a computer +# simulation that was performed for a virtual specimen. # -# Keep in mind that most specimens are thermo-chemo-mechanically processed prior characterization. -# Therefore, the characterized microstructure may not have probed the same structure as of the untreated +# Specimens experience thermo-chemo-mechanical processing (steps) before characterization. Therefore, +# the characterized microstructure may not turn out to be the same structure as of the untreated # sample from which the region-of-interests on the specimen were sampled. # # Fields such as time and increment enable a quantification of the spatiotemporal evolution of a materials' # structure by using multiple instances of NXmicrostructure. Both measurements and simulation virtually -# always sample this evolution. Most microscopy techniques support to generate only a two-dimensional -# representation (projection) of the characterized material. Often materials are characterized only for -# specific states or via sampling coarsely in time relative to the timescale at which the -# physical phenomena take place. This is typically a compromise between the research questions at hand and technical surplus practical limitations. +# always sample this evolution. Most microscopy techniques characterize only a two-dimensional representation +# (projection) of the characterized material volume. Often materials are characterized only for specific states +# or via sampling coarsely in time relative to the timescale at which the physical phenomena take place. +# This is typically a compromise between the research questions and technical surplus practical limitations. # -# The term microstructural feature covers here crystals and all sorts of crystal defects within the material. -# A key challenge with the description of representations and properties of microstructural features is that -# features with different dimensionality exist and combinations of features of different dimensionality are -# frequently expected to be documented with intuitive naming conventions using flat property lists. -# For these key-value dictionaries often folksonomies are used. These can be based on ad hoc documentation -# of such dictionaries in the literature and the metadata section of public data repositories. +# The term microstructural feature covers here crystals and all sorts of crystal defects within the material +# (interfaces, triple junctions, dislocations, pores, etc.). +# A key challenge with the description of representations and properties of such microstructural features is that +# they can be represented and view as features with different dimensionality. Furthermore, combinations of features of +# different dimensionality are frequently expected to be documented with intuitive naming conventions when +# flat property lists are used. For these key-value dictionaries often folksonomies are used. These can be based +# on ad hoc documentation of such dictionaries in the literature and the metadata section of public data repositories. # # NXmicrostructure is an attempt to standardize these descriptions stronger. # -# The descriptive variety is large especially for junctions. Like crystals and interfaces, junctions are features in -# three-dimensional Euclidean space even if they are formed maybe only through a monolayer or pearl chain of atoms. -# Either way the local atomic and electronic environment is different compared to the situation of an ideal crystal, -# which gives typically rise to a plethora of configurations of which some yield useful properties. +# For crystals the number of typically used technical terms are smaller than for interfaces or line like defects and +# junctions of different types of crystal defects. The term grain describes a contiguous region of material that is +# delineated by interfaces (phase or grain boundaries). With its origin motivated by light optical microscopy though +# a grain is not necessarily a single crystal but can have an internal structure of defect such as dislocations. +# In this base class we use the term and respective group crystals though for single crystals and grains. +# The reason why this is possible is that when e.g. materials engineers talk about grains they inherently assume +# that the internal structure of these grains can be described with homogenized effective properties. +# If alternatively the individual structural crystalline or features of this grain should be distinguished +# it is useful to instantiate these as individual instances of crystals. +# +# Grain boundaries and phase boundaries are two main categories of interfaces. +# A grain boundary delineates two regions with similar crystal structure and phase but different orientation. +# A grain boundary is thus a homophase interface. By contrast, a heterophase boundary delineates two regions with typically +# but not necessarily dissimilar crystal structure but a different atomic occupation that justifies to distinguish two +# phases. There is a substantial variety of interfaces whose distinction was classically based on geometrical arguments +# but considers that atomic segregation is an equally important structural aspect to consider when classifying grain +# boundaries. A concise overview on theoretical aspect of and the semantics for characterizing interfaces and their properties +# is provided in e.g. `W. Bollmann <https://doi.org/10.1007/978-3-642-49173-3>`_ and A. Sutton and R. W. Baluffi, +# Interfaces in Crystalline Materials, Clarendon Press, ISBN 9780198500612. +# +# Also for junctions between crystal defects there is a considerable variety of terms. Junctions are features in +# three-dimensional Euclidean space even if they are formed maybe only through a monolayer or a pearl chain of atoms. +# Either way their local atomic and electronic environment is different compared to the situation of an ideal crystal, +# or the adjoining defects, which gives typically rise to a plethora of configurations of which some yield useful material +# properties or affect material properties. # # Like crystals and interfaces, junctions are assumed to represent groups of atoms that have specific descriptor values # which are different to other features. Taking an example, a triple junction is practically a three-dimensional defect as its atoms # are arranged in three-dimensional space but the characteristics of that defect can often be reduced to a lower-dimensional -# description such as a triple point or a triple line. Therefore, different representations can be used to describe the location, -# shape, and structure of the defect. As different types of crystal defects can interact, there is a substantial number of -# in principle characterizable and representable objects. Take again a triple line as an example. It is a tubular feature built from three -# adjoining interfaces. However, dislocations as line defects can interact with triple lines. Therefore, one can also argue that -# along a triple line there can be dislocation-line-triple-line junctions, likewise dislocations form own junctions. +# description such as a triple line or a triple point as the projection of a line. Therefore, different representations can +# be used to describe the location, shape, and structure of such defect. +# +# This base class provides definitions for crystals, grains, interfaces, triple junctions, and quadruple junctions thus covering, +# volumetric, patch, line, and point like features that can serve as examples for future extension. # -# It is not the aim of this base class to cover all these cases, rather this base class currently provides examples how the -# typically most relevant types of features can be represented using a combination of base classes in NeXus. Currently, -# these are crystals, interfaces, triple lines, quadruple junctions. +# As different types of crystal defects can interact, there is a substantial number of in principle characterizable and representable +# objects. Take again a triple line as an example. It is a tubular feature built from three adjoining interfaces. However, dislocations +# as line defects can interact with triple lines. Therefore, one can also argue that along a triple line there exist dislocation-line- +# triple-line junctions, likewise dislocations form own junctions. # -# The description attempt here took inspiration from `E. E. Underwood <https://doi.org/10.1111/j.1365-2818.1972.tb03709.x>`_ -# and E. E. Underwood's book on Quantitative Stereology published 1970 to categorize features based on their dimensionality. +# The description took inspiration from `E. E. Underwood <https://doi.org/10.1111/j.1365-2818.1972.tb03709.x>`_ +# and E. E. Underwood's book on Quantitative Stereology published in 1970 to categorize features based on their dimensionality. # -# Identifiers can be defined either implicitly or explicitly. Identifiers for implicit indexing are defined -# on the interval :math:`[identifier\_offset, identifier\_offset + cardinality - 1]`. +# Indices can be defined either implicitly or explicitly. Indices for implicit indexing are defined +# on the interval :math:`[index\_offset, index\_offset + cardinality - 1]`. Indices can be used as identifiers +# for distinguishing instances, i.e. indices are equivalent to instance names of individual crystals. # # # # -# Discouraged free-text field for leaving comments. +# Discouraged free-text field for leaving comments # # # @@ -814,6 +941,9 @@ NXmicrostructure(NXobject): # # # +# # # # @@ -821,18 +951,24 @@ NXmicrostructure(NXobject): # (NXcsg): # (NXcontinuous_function): # examples for specific frequently discussed microstructural features--> -# +# # # The chemical composition of this microstructure (region). # -# -# -# -# -# -# # -# +# +# +# Different (thermodynamic) phases can be distinguished for the region-of- +# interest. +# +# +# +# First identifier whereby to identify phases implicitly. +# +# +# +# +# # # One- or two-dimensional projections, or three-dimensional representations of crystals. # @@ -853,8 +989,7 @@ NXmicrostructure(NXobject): # # * :ref:`NXcg_polyline` for a one-dimensional representation as only a projection is available (like in linear intercept analysis) # * :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) -# * :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions -# (like in computer simulations or 3D experiments) +# * :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) # # which represent the geometrical entities of the discretization. # @@ -873,40 +1008,37 @@ NXmicrostructure(NXobject): # Phases are typically distinguished based on statistical thermodynamics argument and crystal structure. # # -# +# # # First identifier whereby to identify crystals implicitly. # # -# +# # # Identifier whereby to identify each crystal explicitly. # # -# +# # # -# -# -# First identifier whereby to identify phases implicitly. -# -# -# +# # # Identifier whereby to identify phase for each crystal explicitly. # # -# +# # # -# -# +# +# # -# True or false value, one for each crystal, to communicate whether that feature -# makes contact with the edge of the ROI. +# True, if the feature makes contact with the edge of the ROI. +# False, if the feature does not make contact with the edge of the ROI. # # -# +# # # # @@ -916,7 +1048,7 @@ NXmicrostructure(NXobject): # average disorientation of that crystal. # # -# +# # # # @@ -924,7 +1056,7 @@ NXmicrostructure(NXobject): # Length of each crystal # # -# +# # # # @@ -932,7 +1064,7 @@ NXmicrostructure(NXobject): # Area of each crystal. # # -# +# # # # @@ -940,11 +1072,16 @@ NXmicrostructure(NXobject): # Volume of each crystal # # -# +# # # +# +# +# Possibility to store the mean orientation of the grain. +# +# # -# +# # # One- or two-dimensional projections or three-dimensional representation of interfaces # between crystals as topological entities equivalent to dual_junctions. @@ -952,6 +1089,14 @@ NXmicrostructure(NXobject): # An example for a surface defect. Most important are interfaces such as grain and phase boundaries # but factually interfaces also exist between the environment and crystals exposed at the # surface of the specimen or internal surfaces like between crystals, cracks, or pores. +# +# Interfaces are typically reported as discretized features. For interface projections on the 2D plane +# these are most frequently polyline segments. For interface patches in 3D these are most frequently +# triangulations. Descriptions with continuous functions are seldom used unless simplified configurations +# are studied in modeling and theoretical studies. +# +# When using discretizations the individual interface segments need to be distinguished from the interfaces +# themselves. Consequently, there are two sets of indices. # # # @@ -959,7 +1104,7 @@ NXmicrostructure(NXobject): # # * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) # * :ref:`NXcg_polyline` or :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) -# * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks +# * :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) using (boolean) masks # (like in computer simulations or 3D experiments) # # which represent the geometrical entities of the discretization. @@ -970,26 +1115,30 @@ NXmicrostructure(NXobject): # How many interfaces are distinguished. # # -# +# # # First identifier whereby to identify interfaces implicitly. # # -# +# # # Identifier whereby to identify each interface explicitly. +# +# An array with as many entries as interfaces or their projections. # # -# +# # # # -# +# # -# Set of pairs of identifier_crystal for each interface. +# Set of pairs of indices_crystal values, for each interface one value pair. +# +# An array with as many pairs as interfaces or their projections. # # -# +# # # # @@ -998,12 +1147,14 @@ NXmicrostructure(NXobject): # # # -# +# # -# Set of pairs of identifier_phase for each interface. +# Set of pairs of indices_phase values, for each interface one value pair. +# +# An array with as many pairs as interfaces or their projections. # # -# +# # # # @@ -1013,13 +1164,32 @@ NXmicrostructure(NXobject): # # # -# +# # -# Set of pairs of identifier_triple_junction for each interface. +# Interfaces can be the physical three-dimensional surfaces or two- or one-dimensional +# projections. The latter situation applies typically for characterization with electron +# microscopy. +# +# In the case of a two-dimensional projection interfaces are interface traces. These have +# two terminating junctions. In three dimensions though the interface is a surface patch +# that is bounded by multiple triple lines. +# +# Number of triple_junctions adjoining each interface. This array resolves the number of +# values along the second dimension for the field indices_triple_junctions. +# +# +# +# +# +# +# +# Set of pairs of indices_triple_junction for each interface. +# +# An array with as many tuples of pairs to describe +# all junctions about all interfaces. # # # -# # # # @@ -1028,13 +1198,13 @@ NXmicrostructure(NXobject): # # # -# +# # -# True or false value, one for each crystal, to communicate whether that feature -# makes contact with the edge of the ROI. +# True, if the interface makes contact with the edge of the ROI. +# False, if the interface does not make contact with the edge of the ROI. # # -# +# # # # @@ -1042,7 +1212,7 @@ NXmicrostructure(NXobject): # Gibbs free surface energy for each interface. # # -# +# # # # @@ -1050,7 +1220,7 @@ NXmicrostructure(NXobject): # Non-intrinsic mobility of each interface. # # -# +# # # # @@ -1061,7 +1231,7 @@ NXmicrostructure(NXobject): # polyline segments whereby the interface is discretized. # # -# +# # # # @@ -1069,11 +1239,11 @@ NXmicrostructure(NXobject): # The surface area of all interfaces. # # -# +# # # # -# +# # # Projections or representations of junctions at which three interfaces meet. # @@ -1100,17 +1270,17 @@ NXmicrostructure(NXobject): # Number of triple junctions. # # -# +# # # First identifier to identify triple junctions implicitly. # # -# +# # # Identifier to identify each triple junction explicitly. # # -# +# # # # -# +# # # Set of tuples of identifier of interfaces connected to the junction for each # triple junction. # # -# +# # # # @@ -1165,30 +1335,30 @@ NXmicrostructure(NXobject): # # # -# +# # # Set of tuples of identifier for polyline segments connected to the junction for # each triple junction. # # -# +# # # # # -# The specific identifier_polyline whereby to resolve ambiguities. +# The specific indices_polyline whereby to resolve ambiguities. # # # # -# +# # -# True or false value, one for each crystal, to communicate whether that feature -# makes contact with the edge of the ROI. +# True, if the triple line makes contact with the edge of the ROI. +# False, if the triple line does not make contact with the edge of the ROI. # # -# +# # # # @@ -1196,7 +1366,7 @@ NXmicrostructure(NXobject): # Specific line energy of each triple junction # # -# +# # # # @@ -1204,7 +1374,7 @@ NXmicrostructure(NXobject): # Non-intrinsic mobility of each triple junction. # # -# +# # # # @@ -1215,30 +1385,40 @@ NXmicrostructure(NXobject): # polyline segments whereby the junction is discretized. # # -# +# # # # # -# The volume of the each triple junction +# The volume about each triple junction. +# +# Respective cut-off criteria need to be specified. # # -# +# # # # -# +# # # Quadruple junctions as a region where four crystals meet. # -# An example for a point defect. +# An example for a point (like) defect. +# +# Thermodynamically such junctions can be unstable. +# Specifically when discretizations are used in simulations +# that do not address the thermodynamics of and splitting characteristics +# of junctions in cases when more than four crystals meet, it is possible +# that so-called higher-order junctions are observed. # # # # Reference to an instance of: # # * :ref:`NXcg_point` -# * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks +# * :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) using (boolean) masks +# +# which represent the geometrical entities of the discretization. # # # @@ -1246,12 +1426,12 @@ NXmicrostructure(NXobject): # Number of quadruple junctions. # # -# +# # # First identifier to identify quadruple junctions implicitly. # # -# +# # # Identifier to identify each quadruple junction explicitly. # @@ -1267,7 +1447,7 @@ NXmicrostructure(NXobject): # junction. # # -# +# # # # @@ -1275,23 +1455,23 @@ NXmicrostructure(NXobject): # # # -# +# # # Explicit positions. # # -# -# +# +# # # # -# +# # # Set of tuples of identifier of crystals connected to the junction for each # junction. # # -# +# # # # @@ -1301,13 +1481,13 @@ NXmicrostructure(NXobject): # # # -# +# # # Set of tuples of identifier of interfaces connected to the junction for each # junction. # # -# +# # # # @@ -1318,13 +1498,13 @@ NXmicrostructure(NXobject): # # # -# +# # # Set of tuples of identifier for triple junctions connected to the junction for # each quadruple junction. # # -# +# # # # @@ -1335,13 +1515,13 @@ NXmicrostructure(NXobject): # # # -# +# # # Set of tuples of identifier for phases of crystals connected to the junction for # each quadruple junction. # # -# +# # # # @@ -1352,13 +1532,13 @@ NXmicrostructure(NXobject): # # # -# +# # -# True or false value, one for each crystal, to communicate whether that feature -# makes contact with the edge of the ROI. +# True, if the junction makes contact with the edge of the ROI. +# True, if the junction does not make contact with the edge of the ROI. # # -# +# # # # @@ -1366,7 +1546,7 @@ NXmicrostructure(NXobject): # Energy of the quadruple_junction as a defect. # # -# +# # # # @@ -1374,7 +1554,7 @@ NXmicrostructure(NXobject): # Non-intrinsic mobility of each quadruple_junction. # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_feature.yaml b/contributed_definitions/nyaml/NXmicrostructure_feature.yaml new file mode 100644 index 0000000000..6624e96e37 --- /dev/null +++ b/contributed_definitions/nyaml/NXmicrostructure_feature.yaml @@ -0,0 +1,52 @@ +category: base +doc: | + Base class for documenting structuring features of a microstructure. + + Instances of the class enable sub-grouping of microstructural features + as the abstract base class NXobject should not be used for this purpose. +type: group +NXmicrostructure_feature(NXobject): + chemical_composition(NXchemical_composition): + doc: | + The chemical composition of this microstructural feature or this set of + features. + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# ae1fc0ea51acf0cf515d8d19dd52c36005553f4ff8c4926460a6ad3dad9c853c +# +# +# +# +# +# Base class for documenting structuring features of a microstructure. +# +# Instances of the class enable sub-grouping of microstructural features +# as the abstract base class NXobject should not be used for this purpose. +# +# +# +# The chemical composition of this microstructural feature or this set of +# features. +# +# +# diff --git a/contributed_definitions/nyaml/NXmicrostructure_gragles_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_gragles_config.yaml deleted file mode 100644 index c913acb042..0000000000 --- a/contributed_definitions/nyaml/NXmicrostructure_gragles_config.yaml +++ /dev/null @@ -1,656 +0,0 @@ -category: application -doc: | - Application definition for configuring GraGLeS. - - GraGLeS is a continuum-scale model for shared-memory-parallelized simulations - of the isothermal evolution of 2D and 3D grain boundary networks with a level-set approach. - CPU parallelization is achieved with OpenMP. - - The code has been implemented by C. Mießen in the group of G. Gottstein - at the Institute für Metallkunde und Metallphysik, RWTH Aachen University. - - Details of the model are summarized in `C. Mießen `_. - -# symbols: -# type: group -type: group -NXmicrostructure_gragles_config(NXobject): - (NXentry): - definition(NX_CHAR): - enumeration: [NXmicrostructure_gragles_config] - identifier_simulation(NX_UINT): - doc: | - Simulation ID as an alias to refer to this simulation. - description(NX_CHAR): - doc: | - Discouraged free-text field to add further details to the computation. - start_time(NX_DATE_TIME): - end_time(NX_DATE_TIME): - exists: recommended - profiling(NXcs_profiling): - exists: optional - (NXuser): - exists: ['min', '0', 'max', 'unbounded'] - program1(NXprogram): - program_name: - \@version: - \@url: - exists: recommended - environment(NXobject): - exists: optional - doc: | - Programs and libraries representing the computational environment - (NXprogram): - exists: ['min', '1', 'max', 'unbounded'] - program(NX_CHAR): - \@version(NX_CHAR): - discretization(NXmicrostructure): - - # [read_from_file] # poisson_voronoi_tessellation - # 0, E_READ_FROM_FILE, 1, E_GENERATE_WITH_VORONOY, 2, E_READ_VERTEX, // The edges need to be ordered 3, E_GENERATE_TESTCASE, 4, E_READ_VOXELIZED_MICROSTRUCTURE - # read the next three from input file - # Microstructure.SimID.10.GrainIDs.2D.1188.raw all in config file - # Microstructure.SimID.10.uds - # 0 0, E_CUBIC, 1, E_HEXAGONAL fish from config file - grid(NXnote): - doc: | - From which file should the microstructure be instantiated. - type: - identifier: - algorithm: - checksum: - edge_length(NX_FLOAT): - unit: NX_LENGTH - doc: | - The formulation of mean curvature flow in the GraGLeS model is scale invariant. - Therefore, the discretization has to be scaled to the actual physical length - of the simulation domain (ve, ROI). - For GraGLeS the discretization is always a square or cubic axis-aligned - bounding box with a regular tiling into material points - (either squares or cubes respectively). - - Edge_length is the length of the entire domain along its edge not - the length of the Wigner-Seitz cell about each material point! - sampling(NXobject): - doc: | - Configuration when snapshots of the system should be taken. - - Keep in mind that essentially geometry snapshot data store the - polylines and polyhedra of all grains which can take substantial disk - space. - system(NX_UINT): - unit: NX_UNITLESS - doc: | - Generate a snapshot of the properties of the grains to follow - the evolution of the microstructure every :math:`n`-th iteration. - Setting zero causes that no property snapshots are taken. - geometry(NX_UINT): - unit: NX_UNITLESS - doc: | - Generate a snapshot of the geometry of the entire grain boundary network - every :math:`n`-th iteration. Setting zero instructs to store no geometry data. - - # 31 no more sampling - # 1 - simulation_control(NXobject): - doc: | - Configuration when the simulation should be stopped in a controlled manner. - Whichever criterion is fulfilled first triggers the controlled stop of - and termination of GraGLeS. - number_of_grains(NX_UINT): - unit: NX_UNITLESS - doc: | - The simulation stops if the total number of grains - becomes smaller than this criterion. - number_of_iterations(NX_UINT): - unit: NX_UNITLESS - doc: | - The simulation stops if more iterations than this criterion have been computed. - numerics(NXobject): - doc: | - Configuration of numerical details of the solver. - - # use proper environment variable number_of_threads(NX_UINT): # obsolete set 01 16 - convolution_mode(NX_CHAR): - doc: | - Which type of convolution kernel and model is used. - enumeration: [gaussian, laplace, laplace_ritchardson] - time_slope(NX_FLOAT): - unit: NX_ANY - doc: | - Constant to calibrate the real time scaling of the simulation. - - # when taking the E_GAUSSIAN convolution mode set the TimeSlopeFactor explicitly here, default Miessen, Liesenjohann was 0.8359-\-> - # 0 - # 12991 # read from file - # discretization(NX_UINT) # 15 - # 15 - # domain_border_size(NX_UINT): # 7 - # 0 - # 0, Energies defined by misorientation, 1, GB Energies and mobilities clambed to 1.0 but uses sectors and Triplejunction mobilities, - # 2, GB Energies clambed to 0.3 or 0.6 / mobilities clambed to 1.0 - use Texture == false - # 0 # 0, E_NO_PROJECT, 1 E_TRIPLE_JUNCTION_DRAG_SINGLE (fixes outermost tj at, 2 empty) - # 1 # 0, E_ITERATIVE, 1, E_SQUARES - # 0.0 - # - grid_coarsement(NXobject): - doc: | - Configuration of the grid coarsement algorithm whereby the representation - of the system is continuously rediscretized such that on average grains - are discretized with discretization many material points along each - direction. - - Grid coarsement can reduce the computational costs substantially although - it cannot be ruled out completely that the rediscretizing may have an effect - on the system evolution. Without grid coarsement the total number of material - points to consider stays the same throughout the simulation. - discretization(NX_UINT): - unit: NX_UNITLESS - doc: | - Number of material points along each direction to discretize the - average grain. The larger this value is chosen the finer the curvature - details are that can be resolved but also the longer the simulation - takes. - is_active(NX_BOOLEAN): - doc: | - If true grid coarsement is active, otherwise it is not. - gradient(NX_FLOAT): - unit: NX_DIMENSIONLESS - doc: | - Fraction how strongly the number of grains has to reduce - to trigger a grid coarsement step in an iteration. - - # the next only guru i.e. in C++ code configurable options - # 3 - # 2 - # 0 # 0, DEFAULT, 1 skips comparison and let grains shring isolated - grain_boundary_mobility(NXobject): - doc: | - Physically-based model of the assumed mobility of the grain boundaries. - - Grain boundary mobility is not an intrinsic property of a grain boundary but system-dependent - especially as grain boundaries in reality are decorated with defects as a consequence of which - the actual mobility is a combination of the mobility of the individual defects and the attached - boundary patches. Grain boundaries have different degrees of microscopic freedom. - Therefore, their mobility follows a distribution. - - # 0 - # 0 # - model(NX_CHAR): - doc: | - Fundamental model how :math:`m` is assumed a function of the disorientation - angle :math:`\Theta`. - enumeration: [rollett_holm] - - # For rollett_holm :math:`m(\Theta) = m_0 \cdot (1 - c_1 * exp(-c_2 \cdot \frac{\Theta}{15}^{c_3}))`. - m_null(NX_FLOAT): - unit: NX_ANY - doc: | - The assumed mobility :math:`m_0` of the fastest grain boundary in the system at the assumed - temperature. GraGLeS was developed for modelling isothermal annealing. - c_one(NX_FLOAT): - unit: NX_DIMENSIONLESS - doc: | - Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not one. - - # 7.5e-14 - c_two(NX_FLOAT): - unit: NX_UNITLESS - doc: | - Mobility scaling factor :math:`c_2`. Typically 5. - c_three(NX_FLOAT): - unit: NX_UNITLESS - doc: | - Mobility scaling factor :math:`c_3`. Typically 9. - grain_boundary_energy(NXobject): - doc: | - Physically-based model of the assumed grain boundary surface energy. - - Like for the grain boundary mobility, defects cause a distribution of energies for the - patches of which the boundary is composed. In practice a too complicated dependency - of the energy and mobility model is observed as a function of the type and chemical - decoration of the defects. Therefore, simplifying assumptions are typically made. - type(NX_CHAR): - doc: | - Fundamental type of assumption if energies are considered isotropic or not. - enumeration: [isotropic, anisotropic] - model(NX_CHAR): - doc: | - Fundamental model how :math:`\gamma` is assumed a function of the disorientation - angle :math:`\Theta`. - enumeration: [read_shockley] - gamma(NX_FLOAT): - unit: NX_ANY - doc: | - Mean grain boundary surface energy that is assumed a function of the - disorientation angle :math:`\Theta` of the adjoining grains :math:`\gamma(\Theta)`. - This value factorizes the curvature_driving_force model. - - # For GraGLeS :math:`\gamma(\Theta) = \{\begin{array}1 \text{for} \Theta > 1. \\ 0.01 \text{for} \Theta \leq 1.\end{array}`. - # 1.0 - # 0.01 - # - curvature_driving_force(NXobject): - doc: | - A continuum-scale curvature of an interface causes the interface to - migrate towards the center of the curvature radius. - is_active(NX_BOOLEAN): - doc: | - If true the curvature_driving_force is considered, otherwise it is not. - stored_elastic_energy(NXobject): - doc: | - A continuum-scale difference of the stored elastic energy in dislocation - configurations across a grain boundary can exert a driving force on the - grain boundary such that the boundary migrates into the volume with the - higher stored elastic energy. - is_active(NX_BOOLEAN): - doc: | - If true the dislocation_driving_force is considered, otherwise it is not. - line_energy(NX_FLOAT): - unit: NX_ANY - doc: | - Prefactor :math:`0.5Gb^2` that factorizes the average - stored elastic energy per length dislocation line. - magnetic_field(NXobject): - doc: | - In case of an applied magnetic field, a difference of the magnetic - susceptibility can exert a driving force on the grain boundary such that - the boundary migrates into the volume with the higher magnetic energy. - is_active(NX_BOOLEAN): - doc: | - If true the magnetic_driving_force is considered, otherwise it is not. - - # MagneticField.xml - # https://github.com/GraGLeS/GraGLeS2D/blob/master/params/MagneticField.xml - triple_line_mobility(NXobject): - doc: | - A triple line mediates the atomic arrangement differences between three - interface patches. Therefore, the triple line is a defect that may not - have the same mobility as adjoining grain boundaries and thus it may - exert what can be conceptualized as a drag (resistance) to the motion - of the adjoining interface patches. - drag(NX_FLOAT): - unit: NX_ANY - doc: | - Assumed triple junction drag. - - # 1.0e10 - # isotropic, anisotropic - # 1 - # 1 25 - # - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 98d39a09a15b012a1cde431e9a83bfbf35dea5f844294b32b6cdd87826cbb53c -# -# -# -# -# -# -# Application definition for configuring GraGLeS. -# -# GraGLeS is a continuum-scale model for shared-memory-parallelized simulations -# of the isothermal evolution of 2D and 3D grain boundary networks with a level-set approach. -# CPU parallelization is achieved with OpenMP. -# -# The code has been implemented by C. Mießen in the group of G. Gottstein -# at the Institute für Metallkunde und Metallphysik, RWTH Aachen University. -# -# Details of the model are summarized in `C. Mießen <https://publications.rwth-aachen.de/record/709678>`_. -# -# -# -# -# -# -# -# -# -# Simulation ID as an alias to refer to this simulation. -# -# -# -# -# Discouraged free-text field to add further details to the computation. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Programs and libraries representing the computational environment -# -# -# -# -# -# -# -# -# -# -# -# From which file should the microstructure be instantiated. -# -# -# -# -# -# -# -# -# The formulation of mean curvature flow in the GraGLeS model is scale invariant. -# Therefore, the discretization has to be scaled to the actual physical length -# of the simulation domain (ve, ROI). -# For GraGLeS the discretization is always a square or cubic axis-aligned -# bounding box with a regular tiling into material points -# (either squares or cubes respectively). -# -# Edge_length is the length of the entire domain along its edge not -# the length of the Wigner-Seitz cell about each material point! -# -# -# -# -# -# Configuration when snapshots of the system should be taken. -# -# Keep in mind that essentially geometry snapshot data store the -# polylines and polyhedra of all grains which can take substantial disk -# space. -# -# -# -# Generate a snapshot of the properties of the grains to follow -# the evolution of the microstructure every :math:`n`-th iteration. -# Setting zero causes that no property snapshots are taken. -# -# -# -# -# Generate a snapshot of the geometry of the entire grain boundary network -# every :math:`n`-th iteration. Setting zero instructs to store no geometry data. -# -# -# -# -# -# -# Configuration when the simulation should be stopped in a controlled manner. -# Whichever criterion is fulfilled first triggers the controlled stop of -# and termination of GraGLeS. -# -# -# -# The simulation stops if the total number of grains -# becomes smaller than this criterion. -# -# -# -# -# The simulation stops if more iterations than this criterion have been computed. -# -# -# -# -# -# Configuration of numerical details of the solver. -# -# -# -# -# Which type of convolution kernel and model is used. -# -# -# -# -# -# -# -# -# -# Constant to calibrate the real time scaling of the simulation. -# -# -# -# -# -# -# Configuration of the grid coarsement algorithm whereby the representation -# of the system is continuously rediscretized such that on average grains -# are discretized with discretization many material points along each -# direction. -# -# Grid coarsement can reduce the computational costs substantially although -# it cannot be ruled out completely that the rediscretizing may have an effect -# on the system evolution. Without grid coarsement the total number of material -# points to consider stays the same throughout the simulation. -# -# -# -# Number of material points along each direction to discretize the -# average grain. The larger this value is chosen the finer the curvature -# details are that can be resolved but also the longer the simulation -# takes. -# -# -# -# -# If true grid coarsement is active, otherwise it is not. -# -# -# -# -# Fraction how strongly the number of grains has to reduce -# to trigger a grid coarsement step in an iteration. -# -# -# -# -# -# -# Physically-based model of the assumed mobility of the grain boundaries. -# -# Grain boundary mobility is not an intrinsic property of a grain boundary but system-dependent -# especially as grain boundaries in reality are decorated with defects as a consequence of which -# the actual mobility is a combination of the mobility of the individual defects and the attached -# boundary patches. Grain boundaries have different degrees of microscopic freedom. -# Therefore, their mobility follows a distribution. -# -# -# -# -# Fundamental model how :math:`m` is assumed a function of the disorientation -# angle :math:`\Theta`. -# -# -# -# -# -# -# -# -# The assumed mobility :math:`m_0` of the fastest grain boundary in the system at the assumed -# temperature. GraGLeS was developed for modelling isothermal annealing. -# -# -# -# -# Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not one. -# -# -# -# -# -# Mobility scaling factor :math:`c_2`. Typically 5. -# -# -# -# -# Mobility scaling factor :math:`c_3`. Typically 9. -# -# -# -# -# -# Physically-based model of the assumed grain boundary surface energy. -# -# Like for the grain boundary mobility, defects cause a distribution of energies for the -# patches of which the boundary is composed. In practice a too complicated dependency -# of the energy and mobility model is observed as a function of the type and chemical -# decoration of the defects. Therefore, simplifying assumptions are typically made. -# -# -# -# Fundamental type of assumption if energies are considered isotropic or not. -# -# -# -# -# -# -# -# -# Fundamental model how :math:`\gamma` is assumed a function of the disorientation -# angle :math:`\Theta`. -# -# -# -# -# -# -# -# Mean grain boundary surface energy that is assumed a function of the -# disorientation angle :math:`\Theta` of the adjoining grains :math:`\gamma(\Theta)`. -# This value factorizes the curvature_driving_force model. -# -# -# -# -# -# -# A continuum-scale curvature of an interface causes the interface to -# migrate towards the center of the curvature radius. -# -# -# -# If true the curvature_driving_force is considered, otherwise it is not. -# -# -# -# -# -# A continuum-scale difference of the stored elastic energy in dislocation -# configurations across a grain boundary can exert a driving force on the -# grain boundary such that the boundary migrates into the volume with the -# higher stored elastic energy. -# -# -# -# If true the dislocation_driving_force is considered, otherwise it is not. -# -# -# -# -# Prefactor :math:`0.5Gb^2` that factorizes the average -# stored elastic energy per length dislocation line. -# -# -# -# -# -# In case of an applied magnetic field, a difference of the magnetic -# susceptibility can exert a driving force on the grain boundary such that -# the boundary migrates into the volume with the higher magnetic energy. -# -# -# -# If true the magnetic_driving_force is considered, otherwise it is not. -# -# -# -# -# -# -# A triple line mediates the atomic arrangement differences between three -# interface patches. Therefore, the triple line is a defect that may not -# have the same mobility as adjoining grain boundaries and thus it may -# exert what can be conceptualized as a drag (resistance) to the motion -# of the adjoining interface patches. -# -# -# -# Assumed triple junction drag. -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXmicrostructure_gragles_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_gragles_results.yaml deleted file mode 100644 index a7c7270ef1..0000000000 --- a/contributed_definitions/nyaml/NXmicrostructure_gragles_results.yaml +++ /dev/null @@ -1,522 +0,0 @@ -category: application -doc: | - Application definition for documenting results with GraGLeS. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n_summary_stats: | - The total number of summary statistic log entries. - n_grains: | - Number of grains in the computer simulation. - n_interfaces: | - Number of interfaces in the computer simulation. -type: group -NXmicrostructure_gragles_results(NXobject): - (NXentry): - definition(NX_CHAR): - enumeration: [NXmicrostructure_gragles_results] - - # For rollett_holm :math:`m(\Theta) = m_0 \cdot (1 - c_1 * exp(-c_2 \cdot \frac{\Theta}{15}^{c_3}))`. - identifier_simulation(NX_UINT): - doc: | - Simulation ID as an alias to refer to this simulation. - description(NX_CHAR): - doc: | - Discouraged free-text field to add further details to the computation. - start_time(NX_DATE_TIME): - end_time(NX_DATE_TIME): - exists: recommended - (NXuser): - exists: ['min', '0', 'max', 'unbounded'] - program1(NXprogram): - program_name: - \@version: - \@url: - exists: recommended - environment(NXobject): - exists: optional - doc: | - Programs and libraries representing the computational environment - (NXprogram): - exists: ['min', '1', 'max', 'unbounded'] - program(NX_CHAR): - \@version(NX_CHAR): - coordinate_system_set(NXcoordinate_system_set): - rotation_handedness: - rotation_convention: - euler_angle_convention: - axis_angle_convention: - sign_convention: - sample_reference_frame(NXcoordinate_system): - type: - handedness: - origin: - x_alias: - x_direction: - y_alias: - y_direction: - z_alias: - z_direction: - SPATIOTEMPORAL(NXobject): - nameType: any - doc: | - Documentation of the spatiotemporal evolution - - Instances should use spatiotemporal as a name prefix. - - # static quantities for which no change is modelled - # the typical lean summary statistics flattened - summary_statistics(NXobject): - doc: | - Summary quantities which are the result of some post-processing of the snapshot data - (averaging, integrating, interpolating) happening in for practical reasons though in while - running the simulation. Place used for storing descriptors from continuum mechanics - and thermodynamics at the scale of the entire ROI. - kinetics(NXprocess): - exists: optional - doc: | - Evolution of the recrystallized volume fraction over time. - time(NX_NUMBER): - unit: NX_TIME - doc: | - Evolution of the physical time not to be confused with wall-clock time or - profiling data. - dimensions: - rank: 1 - dim: (n_summary_stats,) - iteration(NX_INT): - unit: NX_UNITLESS - doc: | - Iteration or increment counter. - number_of_crystals(NX_UINT): - unit: NX_UNITLESS - doc: | - How many crystals are distinguished. - Crystals are listed irrespective of the phase to which these are assigned. - dimensions: - rank: 1 - dim: (n_summary_stats,) - stress(NXprocess): - exists: optional - type: - doc: | - Which type of stress. - enumeration: [cauchy] - stress(NX_FLOAT): - unit: NX_ANY - doc: | - Applied external stress tensor on the ROI. - dimensions: - rank: 3 - dim: (n_summary_stats, 3, 3) - strain(NXprocess): - exists: optional - type: - doc: | - Which type of strain. - strain(NX_FLOAT): - unit: NX_ANY - doc: | - Applied external strain tensor on the ROI. - dimensions: - rank: 3 - dim: (n_summary_stats, 3, 3) - deformation_gradient(NXprocess): - exists: optional - type: - doc: | - Which type of deformation gradient. - enumeration: [piola] - value(NX_FLOAT): - unit: NX_ANY - doc: | - Applied deformation gradient tensor on the ROI. - dimensions: - rank: 3 - dim: (n_summary_stats, 3, 3) - magnetic_field(NXprocess): - exists: optional - strength(NX_FLOAT): - unit: NX_ANY - doc: | - Applied external magnetic field on the ROI. - dimensions: - rank: 3 - dim: (n_summary_stats, 3, 3) - electrical_field(NXprocess): - exists: optional - - # specify type of field - strength(NX_FLOAT): - unit: NX_ANY - doc: | - Applied external electrical field on the ROI. - dimensions: - rank: 3 - dim: (n_summary_stats, 3, 3) - - # the typically storage-costlier snapshot data - (NXmicrostructure): - exists: ['min', '1', 'max', 'unbounded'] - doc: | - Instances should use microstructure as a name prefix. - time(NX_NUMBER): - iteration(NX_INT): - temperature(NX_FLOAT): - unit: NX_TEMPERATURE - doc: | - Simulated temperature for this snapshot. - grid(NXcg_grid): - exists: optional - crystal(NXobject): - representation: - exists: recommended - number_of_crystals(NX_UINT): - number_of_phases(NX_UINT): - identifier_crystal_offset(NX_INT): - identifier_crystal(NX_INT): - dimensions: - rank: 1 - dim: (n_grains,) - identifier_phase_offset(NX_INT): - identifier_phase(NX_INT): - dimensions: - rank: 1 - dim: (n_grains,) - area(NX_NUMBER): - dimensions: - rank: 1 - dim: (n_grains,) - volume(NX_NUMBER): - dimensions: - rank: 1 - dim: (n_grains,) - interface(NXobject): - exists: optional - representation(NX_CHAR): - exists: recommended - number_of_interfaces(NX_UINT): - identifier_offset(NX_INT): - identifier_crystal(NX_INT): - unit: NX_UNITLESS - doc: | - Set of pairs of identifier_crystal for each interface. - dimensions: - rank: 2 - dim: (n_interfaces, 2) - \@use_these(NX_CHAR): - relative_mobility(NX_FLOAT): - unit: NX_DIMENSIONLESS - doc: | - Mobility times surface energy density of the interface normalized - to the maximum such product of the interface set. - dimensions: - rank: 1 - dim: (n_interfaces,) - area(NX_NUMBER): - dimensions: - rank: 1 - dim: (n_interfaces,) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 15c14e25a745ce71624cd12288e09a7e24b4635dce98afe72dc7a960e594f7db -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# The total number of summary statistic log entries. -# -# -# -# -# Number of grains in the computer simulation. -# -# -# -# -# Number of interfaces in the computer simulation. -# -# -# -# -# Application definition for documenting results with GraGLeS. -# -# -# -# -# -# -# -# -# -# -# Simulation ID as an alias to refer to this simulation. -# -# -# -# -# Discouraged free-text field to add further details to the computation. -# -# -# -# -# -# -# -# -# -# -# -# -# -# Programs and libraries representing the computational environment -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Documentation of the spatiotemporal evolution -# -# Instances should use spatiotemporal as a name prefix. -# -# -# -# -# Summary quantities which are the result of some post-processing of the snapshot data -# (averaging, integrating, interpolating) happening in for practical reasons though in while -# running the simulation. Place used for storing descriptors from continuum mechanics -# and thermodynamics at the scale of the entire ROI. -# -# -# -# Evolution of the recrystallized volume fraction over time. -# -# -# -# Evolution of the physical time not to be confused with wall-clock time or -# profiling data. -# -# -# -# -# -# -# -# Iteration or increment counter. -# -# -# -# -# How many crystals are distinguished. -# Crystals are listed irrespective of the phase to which these are assigned. -# -# -# -# -# -# -# -# -# -# Which type of stress. -# -# -# -# -# -# -# -# Applied external stress tensor on the ROI. -# -# -# -# -# -# -# -# -# -# -# -# Which type of strain. -# -# -# -# -# Applied external strain tensor on the ROI. -# -# -# -# -# -# -# -# -# -# -# -# Which type of deformation gradient. -# -# -# -# -# -# -# -# Applied deformation gradient tensor on the ROI. -# -# -# -# -# -# -# -# -# -# -# -# Applied external magnetic field on the ROI. -# -# -# -# -# -# -# -# -# -# -# -# -# Applied external electrical field on the ROI. -# -# -# -# -# -# -# -# -# -# -# -# -# Instances should use microstructure as a name prefix. -# -# -# -# -# -# Simulated temperature for this snapshot. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Set of pairs of identifier_crystal for each interface. -# -# -# -# -# -# -# -# -# -# Mobility times surface energy density of the interface normalized -# to the maximum such product of the interface set. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXmicrostructure_imm_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_imm_config.yaml deleted file mode 100644 index 878b314e71..0000000000 --- a/contributed_definitions/nyaml/NXmicrostructure_imm_config.yaml +++ /dev/null @@ -1,421 +0,0 @@ -category: application -doc: | - Application definition for the configuration of the legacy (micro)structure generator - developed by the Institut für Metallkunde und Metallphysik at RWTH Aachen University. - - * `N. Leuning et al. `_ - * `C. Mießen `_ - * `M. Kühbach `_ - * `M. Kühbach et al. `_ - - The tool can be used to instantiate specific configurations for two- and three-dimensional discretized microstructures. - Specifically, single-phase material that is composed of crystals, so-called (parent) grains which are tessellated into so-called sub-grains. - Grains are modelled as elongated crystals to mimic fundamental geometrical constraints of the interface network in deformed material. -symbols: - n_categories: | - How many texture components are distinguished, minimum is 1. - n_components: | - How many special texture components are distinguished if any. - n_ori: | - Number of discrete orientations that are distributed across the grains. -type: group -NXmicrostructure_imm_config(NXobject): - (NXentry): - definition(NX_CHAR): - enumeration: [NXmicrostructure_imm_config] - roi(NXobject): - doc: | - The computational domain will be synthesized either as a square (for dimensionality = 2) - or a cube (for dimensionality = 3) with axis-aligned cuboidal parent grains. The domain is - discretized into material points using either square pixel or cubic voxel as the tessellating - unit cells. - dimensionality(NX_UINT): - doc: | - Two-dimensional or three-dimensional simulation. - enumeration: [2, 3] - discretization(NX_UINT): - unit: NX_UNITLESS - doc: | - Target value for the number of material points per equivalent - discrete diameter of the arithmetic average sub-grain. - crystal_symmetry(NX_CHAR): - doc: | - Assumed space group of the material. - enumeration: [fcc, bcc, hcp] - - # PreferenceOrientations.txt - # 1 # 0, E_HCP, 1 E_FCC, 2 E_BCC, 3 E_DEFAULT_STRUCTURE - number_of_grains(NX_UINT): - unit: NX_UNITLESS - doc: | - Target value for the number of grains. The actual domain size and grid will be configured - based on the choices for discretization, number_of_grains, and shape of these grains. - number_of_subgrains(NX_UINT): - unit: NX_UNITLESS - doc: | - Target value for the average number of sub-grains per grain. - - # 0 is there another one if not remove - # 1 always one - # 1-\-> - # 1 - grain_shape(NX_FLOAT): - exists: optional - unit: NX_DIMENSIONLESS - doc: | - If available used to define the sequence of relative extent of grains along the y (first value) - and z-axis (second value) assuming the relative shape along the x-axis is 1. If not provided, - the relative extent of the grains will be 1 one average along each axis (globulitic structure). - dimensions: - rank: 1 - dim: (2,) - - # 0.05 - # 1.0 - # remove 0 all the time 0.00 - # remove 0 all the time 0.00 - # - component_analysis(NXobject): - exists: optional - doc: | - In texture research component analyses set on the idea that properties - of grains different based on orientation with certain regions in orientation - space show similar trends like a different average dislocation density - or orientation_spread. - component_name(NX_CHAR): - doc: | - The first entry is always the null model None which means that an orientation - is not categorized as a special component. Examples for special components are - Dillamore, Copper, Cube, Y, P and Q. - dimensions: - rank: 1 - dim: (n_categories,) - bunge_euler(NX_FLOAT): - unit: NX_ANGLE - doc: | - Bunge-Euler angle parameterization of the texture components - location in orientation space for which specifically different settings - should be configured. - dimensions: - rank: 2 - dim: (n_components, 3) - theta(NX_FLOAT): - unit: NX_ANGLE - doc: | - Disorientation angle below which an orientation is categorized as one of the - components. - dimensions: - rank: 1 - dim: (n_components,) - dislocation_distribution(NXobject): - doc: | - Dislocations are modelled as Rayleigh-distributed mean-field density that - can differ between but is constant within grains and sub-grains. - min_max_grain(NX_FLOAT): - unit: NX_ANY - doc: | - The minimum and the maximum dislocation density to distribute across grains. - dimensions: - rank: 2 - dim: (n_categories, 2) - min_max_subgrain(NX_FLOAT): - unit: NX_ANY - doc: | - The minimum and the maximum dislocation density to distribute across sub-grains. - dimensions: - rank: 2 - dim: (n_categories, 2) - - # 10.8e14# 10.8e14 - doc: | - The variance of the dislocation density distribution across the grains. - dimensions: - rank: 1 - dim: (n_categories,) - variance_subgrain(NX_FLOAT): - unit: NX_ANY - doc: | - The variance of the dislocation density distribution across the sub-grains. - dimensions: - rank: 1 - dim: (n_categories,) - orientation_distribution(NXprocess): - doc: | - Orientations of the grains are sampled from a set of Bunge-Euler angle triplets. - Orientations of the sub-grains are sampled by scattering the orientation - of the (parent) grain and with optional Rayleigh-distributed scatter. - bunge_euler(NX_FLOAT): - unit: NX_ANGLE - doc: | - Bunge-Euler angle parameterization of the texture components - location in orientation space for which specifically different settings - should be configured. - dimensions: - rank: 2 - dim: (n_ori, 3) - variance_subgrain(NX_FLOAT): - unit: NX_ANGLE - doc: | - The variance of the disorientation of the sub-grain to their parent grain. - dimensions: - rank: 1 - dim: (n_categories,) - - # what is with preference orientations? - # 1 # via OpenMP - # 1 - # 0.00 - # 1.00 - # 0.00 - # 1.00 - # -# -# -# -# -# -# -# How many texture components are distinguished, minimum is 1. -# -# -# -# -# How many special texture components are distinguished if any. -# -# -# -# -# Number of discrete orientations that are distributed across the grains. -# -# -# -# -# Application definition for the configuration of the legacy (micro)structure generator -# developed by the Institut für Metallkunde und Metallphysik at RWTH Aachen University. -# -# * `N. Leuning et al. <https://doi.org/10.3390/ma14216588>`_ -# * `C. Mießen <https://doi.org/10.18154/RWTH-2017-10148>`_ -# * `M. Kühbach <https://doi.org/10.18154/RWTH-2018-00294>`_ -# * `M. Kühbach et al. <https://github.com/mkuehbach/GraGLeS>`_ -# -# The tool can be used to instantiate specific configurations for two- and three-dimensional discretized microstructures. -# Specifically, single-phase material that is composed of crystals, so-called (parent) grains which are tessellated into so-called sub-grains. -# Grains are modelled as elongated crystals to mimic fundamental geometrical constraints of the interface network in deformed material. -# -# -# -# -# -# -# -# -# -# The computational domain will be synthesized either as a square (for dimensionality = 2) -# or a cube (for dimensionality = 3) with axis-aligned cuboidal parent grains. The domain is -# discretized into material points using either square pixel or cubic voxel as the tessellating -# unit cells. -# -# -# -# Two-dimensional or three-dimensional simulation. -# -# -# -# -# -# -# -# -# Target value for the number of material points per equivalent -# discrete diameter of the arithmetic average sub-grain. -# -# -# -# -# Assumed space group of the material. -# -# -# -# -# -# -# -# -# -# -# Target value for the number of grains. The actual domain size and grid will be configured -# based on the choices for discretization, number_of_grains, and shape of these grains. -# -# -# -# -# Target value for the average number of sub-grains per grain. -# -# -# -# -# -# If available used to define the sequence of relative extent of grains along the y (first value) -# and z-axis (second value) assuming the relative shape along the x-axis is 1. If not provided, -# the relative extent of the grains will be 1 one average along each axis (globulitic structure). -# -# -# -# -# -# -# -# -# -# In texture research component analyses set on the idea that properties -# of grains different based on orientation with certain regions in orientation -# space show similar trends like a different average dislocation density -# or orientation_spread. -# -# -# -# The first entry is always the null model None which means that an orientation -# is not categorized as a special component. Examples for special components are -# Dillamore, Copper, Cube, Y, P and Q. -# -# -# -# -# -# -# -# Bunge-Euler angle parameterization of the texture components -# location in orientation space for which specifically different settings -# should be configured. -# -# -# -# -# -# -# -# -# Disorientation angle below which an orientation is categorized as one of the -# components. -# -# -# -# -# -# -# -# -# Dislocations are modelled as Rayleigh-distributed mean-field density that -# can differ between but is constant within grains and sub-grains. -# -# -# -# The minimum and the maximum dislocation density to distribute across grains. -# -# -# -# -# -# -# -# -# The minimum and the maximum dislocation density to distribute across sub-grains. -# -# -# -# -# -# -# -# -# -# -# The variance of the dislocation density distribution across the grains. -# -# -# -# -# -# -# -# The variance of the dislocation density distribution across the sub-grains. -# -# -# -# -# -# -# -# -# Orientations of the grains are sampled from a set of Bunge-Euler angle triplets. -# Orientations of the sub-grains are sampled by scattering the orientation -# of the (parent) grain and with optional Rayleigh-distributed scatter. -# -# -# -# Bunge-Euler angle parameterization of the texture components -# location in orientation space for which specifically different settings -# should be configured. -# -# -# -# -# -# -# -# -# The variance of the disorientation of the sub-grain to their parent grain. -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml deleted file mode 100644 index 0e78491007..0000000000 --- a/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml +++ /dev/null @@ -1,333 +0,0 @@ -category: application -doc: | - Application definition for the results of the legacy (micro)structure generator developed - by the Institut für Metallkunde und Metallphysik at RWTH Aachen University. - - * `N. Leuning et al. `_ - * `C. Mießen `_ - * `M. Kühbach `_ - * `M. Kühbach et al. `_ - - The tool can be used to instantiate specific configurations for two- and three-dimensional discretized microstructures. - Specifically, single-phase material that is composed of crystals, so-called (parent) grains which are tessellated into so-called sub-grains. - Grains are modelled as elongated crystals to mimic fundamental geometrical constraints of the interface network in deformed material. -symbols: - n_edge: | - Number of material points along the edge of the square- or cube-shaped domain. - c: | - Number of crystals. -type: group -NXmicrostructure_imm_results(NXobject): - (NXentry): - definition(NX_CHAR): - enumeration: [NXmicrostructure_imm_results] - description(NX_CHAR): - doc: | - Discouraged free-text field to add further details to the computation. - start_time(NX_DATE_TIME): - end_time(NX_DATE_TIME): - exists: recommended - profiling(NXcs_profiling): - exists: optional - (NXuser): - exists: ['min', '0', 'max', 'unbounded'] - program1(NXprogram): - program(NX_CHAR): - \@version(NX_CHAR): - \@url(NX_CHAR): - exists: recommended - environment(NXobject): - exists: optional - doc: | - Programs and libraries representing the computational environment - (NXprogram): - exists: ['min', '1', 'max', 'unbounded'] - program(NX_CHAR): - \@version(NX_CHAR): - (NXmicrostructure): - doc: | - Instances should use microstructure as a name prefix. - grid(NXcg_grid): - extent(NX_UINT): - cell_dimensions(NX_NUMBER): - structure(NXdata): - doc: | - Default plot showing the grid. - \@signal(NX_CHAR): - \@axes(NX_CHAR): - \@AXISNAME_indices(NX_UINT): - nameType: partial - title(NX_CHAR): - identifier_crystal(NX_NUMBER): - unit: NX_UNITLESS - doc: | - Crystal identifier that was assigned to each material point. - - # either (n_edge, n_edge) or (n_edge, n_edge, n_edge) - z(NX_NUMBER): - exists: optional - unit: NX_LENGTH - doc: | - Material point barycenter coordinate along z direction. - dimensions: - rank: 1 - dim: (n_edge,) - \@long_name(NX_CHAR): - doc: | - Coordinate along z direction. - y(NX_NUMBER): - unit: NX_LENGTH - doc: | - Material point barycenter coordinate along y direction. - dimensions: - rank: 1 - dim: (n_edge,) - \@long_name(NX_CHAR): - doc: | - Coordinate along y direction. - x(NX_NUMBER): - unit: NX_LENGTH - doc: | - Material point barycenter coordinate along x direction. - dimensions: - rank: 1 - dim: (n_edge,) - \@long_name(NX_CHAR): - doc: | - Coordinate along x direction. - crystal(NXobject): - reference(NX_CHAR): - number_of_crystals(NX_UINT): - identifier_crystal(NX_INT): - dimensions: - rank: 1 - dim: (c,) - area(NX_NUMBER): - exists: recommended - dimensions: - rank: 1 - dim: (c,) - volume(NX_NUMBER): - exists: recommended - dimensions: - rank: 1 - dim: (c,) - is_subgrain(NX_BOOLEAN): - exists: recommended - doc: | - True if the crystal is considered a sub-grain. - False if the crystal is considered a grain. - dimensions: - rank: 1 - dim: (c,) - bunge_euler(NX_FLOAT): - unit: NX_ANGLE - doc: | - Bunge-Euler angle orientation of each crystal. - dimensions: - rank: 2 - dim: (c, 3) - dislocation_density(NX_FLOAT): - unit: NX_ANY - doc: | - Mean-field dislocation density as a measure of the stored elastic energy - content that is stored in the dislocation network of this grain and related - defects within each crystal. - dimensions: - rank: 1 - dim: (c,) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 1002d3c0f7c125dd73ccace4e9e47a6d93c9f8d75c273033ec5d0d23468a411d -# -# -# -# -# -# -# -# Number of material points along the edge of the square- or cube-shaped domain. -# -# -# -# -# Number of crystals. -# -# -# -# -# Application definition for the results of the legacy (micro)structure generator developed -# by the Institut für Metallkunde und Metallphysik at RWTH Aachen University. -# -# * `N. Leuning et al. <https://doi.org/10.3390/ma14216588>`_ -# * `C. Mießen <https://doi.org/10.18154/RWTH-2017-10148>`_ -# * `M. Kühbach <https://doi.org/10.18154/RWTH-2018-00294>`_ -# * `M. Kühbach et al. <https://github.com/mkuehbach/GraGLeS>`_ -# -# The tool can be used to instantiate specific configurations for two- and three-dimensional discretized microstructures. -# Specifically, single-phase material that is composed of crystals, so-called (parent) grains which are tessellated into so-called sub-grains. -# Grains are modelled as elongated crystals to mimic fundamental geometrical constraints of the interface network in deformed material. -# -# -# -# -# -# -# -# -# -# Discouraged free-text field to add further details to the computation. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Programs and libraries representing the computational environment -# -# -# -# -# -# -# -# -# -# Instances should use microstructure as a name prefix. -# -# -# -# -# -# -# Default plot showing the grid. -# -# -# -# -# -# -# -# Crystal identifier that was assigned to each material point. -# -# -# -# -# -# Material point barycenter coordinate along z direction. -# -# -# -# -# -# -# Coordinate along z direction. -# -# -# -# -# -# Material point barycenter coordinate along y direction. -# -# -# -# -# -# -# Coordinate along y direction. -# -# -# -# -# -# Material point barycenter coordinate along x direction. -# -# -# -# -# -# -# Coordinate along x direction. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# True if the crystal is considered a sub-grain. -# False if the crystal is considered a grain. -# -# -# -# -# -# -# -# Bunge-Euler angle orientation of each crystal. -# -# -# -# -# -# -# -# -# Mean-field dislocation density as a measure of the stored elastic energy -# content that is stored in the dislocation network of this grain and related -# defects within each crystal. -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml b/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml index eefdc0d493..d469aa0180 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml @@ -2,38 +2,48 @@ category: base doc: | Base class to store an inverse pole figure (IPF) mapping (IPF map). symbols: + v: | + Number of pixel along the slow direction used for the IPF color key. + u: | + Number of pixel along the fast direction used for the IPF color key. n_z: | - Number of pixel along the z slowest direction. + Number of pixel along the slowest direction, typically labeled z or k. n_y: | - Number of pixel along the y slow direction. + Number of pixel along the slow direction, typically labeled y or j. n_x: | - Number of pixel along the x fast direction. + Number of pixel along the fast direction, typically labeled x or i. n_rgb: | Number of RGB values along the fastest direction, always three. type: group NXmicrostructure_ipf(NXprocess): depends_on(NX_CHAR): doc: | - Reference to an :ref:`NXcoordinate_system` in which the projection_direction is defined. - - If the field depends_on is not provided but parents of the instance of this base class or its - specializations define an instance of :ref:`NXcoordinate_system`, projection_direction - is defined in this coordinate system. - - If nothing is provided it is assumed that projection_direction is defined in the McStas coordinate system. + Reference to an instance of :ref:`NXcoordinate_system` in which the axes axis_z, + axis_y, and axis_x are defined. + color_model(NX_CHAR): + doc: | + The algorithm whereby orientations are colored. + enumeration: [tsl, mtex] projection_direction(NX_NUMBER): unit: NX_UNITLESS doc: | - The direction along which orientations are projected. + The direction normal vector along which orientations are projected. dimensions: rank: 1 dim: (3,) + \@depends_on(NX_CHAR): + doc: | + Reference to an instance of :ref:`NXcoordinate_system` in which the projection_direction is defined. + + If the field depends_on is not provided but parents of the instance of this base class or its + specializations define an instance of :ref:`NXcoordinate_system`, projection_direction + is defined in this coordinate system. + + If nothing is provided, it is assumed that projection_direction is defined in the McStas coordinate system. input_grid(NXcg_grid): doc: | - Details about the original grid. - - Here original grid means the grid for which the IPF map was computed when that - IPF map was exported from the tech partner's file format representation. + Details about the original grid, i.e. the grid for which the IPF map was computed + when that IPF map was exported from the tech partner's file format representation. output_grid(NXcg_grid): doc: | Details about the grid onto which the IPF is recomputed. @@ -60,40 +70,37 @@ NXmicrostructure_ipf(NXprocess): The main purpose of this map is to offer a normalized default representation of the IPF map for consumption by a research data management system (RDMS). - This is aligned with the first aim of :ref:`NXmicrostructure_ipf`, to bring colleagues - and users of IPF maps together to discuss which pieces of information need storage. - - We are convinced a step-by-step design and community-driven discussion is a practical - strategy to work towards an interoperable description and data model for exchanging - IPF maps as a specific community-accepted method to convey orientation maps. - - With this design the individual RDMS solutions and tools can still continue - to support specific custom data analyses workflow and routes but at least - there is one common understanding which enables also those users who are - not necessarily experts in all the details of the underlying techniques an - understanding if the dataset is worth to become reused or repurposed. - - # \@signal: data - # \@axes: [axis_y, axis_x] - # \@axis_x_indices: 0 - # \@axis_y_indices: 1 data(NX_NUMBER): unit: NX_UNITLESS - - # assume a mapping with step size 0.5 micron - # we need to distinguish - # pixel position, i.e. 0, 1, 2, 3, unit px - # answers in which pixel on the map but map is disconnected from sample surface context - # calibrated pixel position 0., 0.5, 1.0, 1.5, unit micron - # answers in addition physical dimensions (relevant to get crystal extent etc.) but still disconnected from sample surface context - # calibrated pixel position including the offset of the original coordinate system - # answers everything would enable one to point if still in the microscope where on the sample surface each pixel is located - # tech partners oftentimes do not report to more than calibrated pixel position doc: | Inverse pole figure color code for each map coordinate. - dimensions: - rank: 3 - dim: (n_y, n_x, 3) + + Different types of AXISNAME dimensional scale axes are found in practice. A few examples: + + * No scaling, e.g. pixel position values like 0, 1, 2, 3 pixel. + Pixels on the map can be distinguished but that map is disconnected from + any sample surface context and eventually physical scaling + * Scaling but no offset, e.g. calibrated pixel position 0., 0.5, 1.0, 1.5 micron. + Pixels on the map can be compared for their distance to obtain e.g. size of features + but the position of the map relative to the e.g. the sample surface is unclear. + For IPF maps this is the most frequently reported situation. + * Scaling and offset, which resolves also the absolute position of the map in + relation to the sample surface. This is useful information for stitching multiple + mappings together and other processing where precise and accurate + position data are relevant e.g. for correlative materials characterization. + + Three types of dimensional constraints for maps are possible: + + * (n_x, 3), a one-dimensional map, + typically used for coarse sampling and crystal size statistics. + * (n_y, n_x, 3), a two-dimensional map, + the most frequently found reported + * (n_z, n_y, n_x, 3), a three-dimensional map, + these are commonly generated using computational methods, + or in cases multiple EBSD maps have been stitched/reconstructed + into a three-dimensional map. + + # strictly speaking unit must not be constraint for AXISNAME no scaling axis_z(NX_NUMBER): unit: NX_LENGTH doc: | @@ -101,8 +108,6 @@ NXmicrostructure_ipf(NXprocess): dimensions: rank: 1 dim: (n_z,) - - # \@long_name(NX_CHAR): axis_y(NX_NUMBER): unit: NX_LENGTH doc: | @@ -110,8 +115,6 @@ NXmicrostructure_ipf(NXprocess): dimensions: rank: 1 dim: (n_y,) - - # \@long_name(NX_CHAR): axis_x(NX_NUMBER): unit: NX_LENGTH doc: | @@ -119,12 +122,9 @@ NXmicrostructure_ipf(NXprocess): dimensions: rank: 1 dim: (n_x,) - - # \@long_name(NX_CHAR): - # title: legend(NXdata): doc: | - The color code which maps colors to orientation in the fundamental zone. + The color code which maps color to orientation in the fundamental zone. For each stereographic standard triangle (SST), i.e. a rendering of the fundamental zone of the crystal-symmetry-reduced orientation space @@ -143,56 +143,46 @@ NXmicrostructure_ipf(NXprocess): * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). Details are implementation-specific and not standardized yet. - - Given that the SST has a complicated geometry, it can not yet be - visualized using tools like H5Web, which is why for now the matrix - of a rasterized image which is rendered by the backend tool gets - copied into an RGB matrix to offer a default plot. - # \@signal: data - # \@axes: [axis_y, axis_x] - # \@axis_x_indices: 0 - # \@axis_y_indices: 1 + # Given that the SST has a complicated geometry, it can not yet be + # visualized using tools like H5Web, which is why for now the matrix + # of a rasterized image which is rendered by the backend tool gets + # copied into an RGB matrix to offer a default plot. data(NX_NUMBER): - unit: NX_UNITLESS + unit: NX_ANY - # hehe, but can be larger than one but could also be an NX_DIMENSIONLESS ! + # NX_UNITLESS or NX_DIMENSIONLESS doc: | Inverse pole figure color code for each map coordinate. dimensions: rank: 3 - dim: (n_y, n_x, 3) + dim: (v, u, 3) axis_y(NX_NUMBER): unit: NX_UNITLESS doc: | Pixel along the y-axis. dimensions: rank: 1 - dim: (n_y,) - - # \@long_name(NX_CHAR): + dim: (v,) axis_x(NX_NUMBER): unit: NX_UNITLESS doc: | Pixel along the x-axis. dimensions: rank: 1 - dim: (n_x,) - - # \@long_name(NX_CHAR): - # title: + dim: (u,) # for further contextualization see comments in NXms_ipf.yaml # https://github.com/FAIRmat-NFDI/nexus_definitions/commit/26d4faa5c6950161e48f0672f3fdfd8c9bc907e2 # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 68b5b9282aa6a9fa4f4ba2a926a136b94e337da62952a08d186b7a0bae9c7fc2 -# +# 77a3f07c431a994ce35036efe626a026e4071d506fd0d999d66fcfffdd4ee133 +# # # # # +# +# +# Number of pixel along the slow direction used for the IPF color key. +# +# +# +# +# Number of pixel along the fast direction used for the IPF color key. +# +# # # -# Number of pixel along the z slowest direction. +# Number of pixel along the slowest direction, typically labeled z or k. # # # # -# Number of pixel along the y slow direction. +# Number of pixel along the slow direction, typically labeled y or j. # # # # -# Number of pixel along the x fast direction. +# Number of pixel along the fast direction, typically labeled x or i. # # # # -# Number of RGB values along the fastest direction, always three. +# Number of RGB values along the fastest direction, always three. # # # # -# Base class to store an inverse pole figure (IPF) mapping (IPF map). +# Base class to store an inverse pole figure (IPF) mapping (IPF map). # # # -# Reference to an :ref:`NXcoordinate_system` in which the projection_direction is defined. -# -# If the field depends_on is not provided but parents of the instance of this base class or its -# specializations define an instance of :ref:`NXcoordinate_system`, projection_direction -# is defined in this coordinate system. -# -# If nothing is provided it is assumed that projection_direction is defined in the McStas coordinate system. +# Reference to an instance of :ref:`NXcoordinate_system` in which the axes axis_z, +# axis_y, and axis_x are defined. # # +# +# +# The algorithm whereby orientations are colored. +# +# +# +# +# +# # # -# The direction along which orientations are projected. +# The direction normal vector along which orientations are projected. # # # # +# +# +# Reference to an instance of :ref:`NXcoordinate_system` in which the projection_direction is defined. +# +# If the field depends_on is not provided but parents of the instance of this base class or its +# specializations define an instance of :ref:`NXcoordinate_system`, projection_direction +# is defined in this coordinate system. +# +# If nothing is provided, it is assumed that projection_direction is defined in the McStas coordinate system. +# +# # # # -# Details about the original grid. -# -# Here original grid means the grid for which the IPF map was computed when that -# IPF map was exported from the tech partner's file format representation. +# Details about the original grid, i.e. the grid for which the IPF map was computed +# when that IPF map was exported from the tech partner's file format representation. # # # # -# Details about the grid onto which the IPF is recomputed. -# -# Rescaling the visualization of the IPF map may be needed to enable -# visualization in specific software tools like H5Web. +# Details about the grid onto which the IPF is recomputed. +# +# Rescaling the visualization of the IPF map may be needed to enable +# visualization in specific software tools like H5Web. # # # # -# How where orientation values at positions of input_grid computed to values on output_grid. -# -# Nearest neighbour means the orientation of the closed (Euclidean distance) grid point of the input_grid was taken. +# How where orientation values at positions of input_grid computed to values on output_grid. +# +# Nearest neighbour means the orientation of the closed (Euclidean distance) grid point of the input_grid was taken. # # # @@ -283,149 +296,129 @@ NXmicrostructure_ipf(NXprocess): # # # -# Inverse pole figure mapping. -# -# Instances named phase0 should by definition refer to the null phase notIndexed. -# Inspect the definition of :ref:`NXphase` and its field identifier_phase -# for further details. -# -# Details about possible regridding and associated interpolation -# during the computation of the IPF map visualization can be stored -# using the input_grid, output_grid, and interpolation fields. -# -# The main purpose of this map is to offer a normalized default representation -# of the IPF map for consumption by a research data management system (RDMS). -# This is aligned with the first aim of :ref:`NXmicrostructure_ipf`, to bring colleagues -# and users of IPF maps together to discuss which pieces of information need storage. -# -# We are convinced a step-by-step design and community-driven discussion is a practical -# strategy to work towards an interoperable description and data model for exchanging -# IPF maps as a specific community-accepted method to convey orientation maps. -# -# With this design the individual RDMS solutions and tools can still continue -# to support specific custom data analyses workflow and routes but at least -# there is one common understanding which enables also those users who are -# not necessarily experts in all the details of the underlying techniques an -# understanding if the dataset is worth to become reused or repurposed. +# Inverse pole figure mapping. +# +# Instances named phase0 should by definition refer to the null phase notIndexed. +# Inspect the definition of :ref:`NXphase` and its field identifier_phase +# for further details. +# +# Details about possible regridding and associated interpolation +# during the computation of the IPF map visualization can be stored +# using the input_grid, output_grid, and interpolation fields. +# +# The main purpose of this map is to offer a normalized default representation +# of the IPF map for consumption by a research data management system (RDMS). # -# # -# # -# Inverse pole figure color code for each map coordinate. +# Inverse pole figure color code for each map coordinate. +# +# Different types of AXISNAME dimensional scale axes are found in practice. A few examples: +# +# * No scaling, e.g. pixel position values like 0, 1, 2, 3 pixel. +# Pixels on the map can be distinguished but that map is disconnected from +# any sample surface context and eventually physical scaling +# * Scaling but no offset, e.g. calibrated pixel position 0., 0.5, 1.0, 1.5 micron. +# Pixels on the map can be compared for their distance to obtain e.g. size of features +# but the position of the map relative to the e.g. the sample surface is unclear. +# For IPF maps this is the most frequently reported situation. +# * Scaling and offset, which resolves also the absolute position of the map in +# relation to the sample surface. This is useful information for stitching multiple +# mappings together and other processing where precise and accurate +# position data are relevant e.g. for correlative materials characterization. +# +# Three types of dimensional constraints for maps are possible: +# +# * (n_x, 3), a one-dimensional map, +# typically used for coarse sampling and crystal size statistics. +# * (n_y, n_x, 3), a two-dimensional map, +# the most frequently found reported +# * (n_z, n_y, n_x, 3), a three-dimensional map, +# these are commonly generated using computational methods, +# or in cases multiple EBSD maps have been stitched/reconstructed +# into a three-dimensional map. # -# -# -# -# -# # +# # # -# Pixel center coordinate calibrated for step size along the z axis of the map. +# Pixel center coordinate calibrated for step size along the z axis of the map. # # # # # -# # # -# Pixel center coordinate calibrated for step size along the y axis of the map. +# Pixel center coordinate calibrated for step size along the y axis of the map. # # # # # -# # # -# Pixel center coordinate calibrated for step size along the x axis of the map. +# Pixel center coordinate calibrated for step size along the x axis of the map. # # # # # # -# # # -# The color code which maps colors to orientation in the fundamental zone. -# -# For each stereographic standard triangle (SST), i.e. a rendering of the -# fundamental zone of the crystal-symmetry-reduced orientation space -# SO3, it is possible to define a color model which assigns a color to each -# point in the fundamental zone. -# -# Different mapping models are used. These implement (slightly) different -# scaling relations. Differences exist across representations of tech partners. -# -# Differences are which base colors of the RGB color model are placed in -# which extremal position of the SST and where the white point is located. -# -# For further details see: -# -# * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) -# * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). -# -# Details are implementation-specific and not standardized yet. -# -# Given that the SST has a complicated geometry, it can not yet be -# visualized using tools like H5Web, which is why for now the matrix -# of a rasterized image which is rendered by the backend tool gets -# copied into an RGB matrix to offer a default plot. +# The color code which maps color to orientation in the fundamental zone. +# +# For each stereographic standard triangle (SST), i.e. a rendering of the +# fundamental zone of the crystal-symmetry-reduced orientation space +# SO3, it is possible to define a color model which assigns a color to each +# point in the fundamental zone. +# +# Different mapping models are used. These implement (slightly) different +# scaling relations. Differences exist across representations of tech partners. +# +# Differences are which base colors of the RGB color model are placed in +# which extremal position of the SST and where the white point is located. +# +# For further details see: +# +# * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) +# * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). +# +# Details are implementation-specific and not standardized yet. # -# -# -# +# +# +# # -# Inverse pole figure color code for each map coordinate. +# Inverse pole figure color code for each map coordinate. # # -# -# +# +# # # # # # -# Pixel along the y-axis. +# Pixel along the y-axis. # # -# +# # # -# # # -# Pixel along the x-axis. +# Pixel along the x-axis. # # -# +# # # # -# # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_kanapy_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_kanapy_results.yaml index adf0b88d33..5c173dd488 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_kanapy_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_kanapy_results.yaml @@ -43,7 +43,7 @@ NXmicrostructure_kanapy_results(NXobject): \@version(NX_CHAR): \@url(NX_CHAR): exists: recommended - environment(NXobject): + environment(NXcollection): exists: optional doc: | Programs and libraries representing the computational environment @@ -53,10 +53,9 @@ NXmicrostructure_kanapy_results(NXobject): \@version(NX_CHAR): # no units instead labelled-property graph concepts with units - (NXmicrostructure): + microstructureID(NXmicrostructure): exists: ['min', '1', 'max', 'unbounded'] - doc: | - Instances should use microstructure as a name prefix. + nameType: partial grid(NXcg_grid): extent(NX_UINT): cell_dimensions(NX_NUMBER): @@ -70,7 +69,7 @@ NXmicrostructure_kanapy_results(NXobject): \@AXISNAME_indices(NX_UINT): nameType: partial title(NX_CHAR): - identifier_crystal(NX_NUMBER): + indices_crystal(NX_INT): unit: NX_UNITLESS doc: | Crystal identifier that was assigned to each material point. @@ -109,15 +108,15 @@ NXmicrostructure_kanapy_results(NXobject): Coordinate along x direction. # add nodal positions as suggested in NXmicrostructure - crystal(NXobject): + crystals(NXmicrostructure_feature): reference(NX_CHAR): number_of_crystals(NX_UINT): number_of_phases(NX_UINT): - identifier_crystal(NX_INT): + indices_crystal(NX_INT): dimensions: rank: 1 dim: (c,) - identifier_phase(NX_INT): + indices_phase(NX_INT): dimensions: rank: 1 dim: (c,) @@ -140,8 +139,8 @@ NXmicrostructure_kanapy_results(NXobject): dim: (c, 3) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# b6c7028fe2e383e3b2de83dedda1dffd9e3fbe8ffc0b74d8871628c2ce0f2cb6 -# +# 5ae64c7665dc9fef2170ef9bc002aa61b056d3737550c7df60465e2b82812e90 +# # # -# -# -# Instances should use microstructure as a name prefix. -# +# # # # @@ -252,7 +248,7 @@ NXmicrostructure_kanapy_results(NXobject): # # # -# +# # # Crystal identifier that was assigned to each material point. # @@ -300,16 +296,16 @@ NXmicrostructure_kanapy_results(NXobject): # # # -# +# # # # -# +# # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_mtex_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_mtex_config.yaml index 8459edcee9..363a7e4293 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_mtex_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_mtex_config.yaml @@ -14,7 +14,7 @@ type: group NXmicrostructure_mtex_config(NXobject): conventions(NXcollection): doc: | - Reference frame and orientation conventions. + MTex reference frame and orientation conventions. Consult the `MTex docs `_ for details. x_axis_direction(NX_CHAR): doc: | @@ -65,10 +65,10 @@ NXmicrostructure_mtex_config(NXobject): TODO with MTex developers show_micron_bar(NX_BOOLEAN): doc: | - True if MTex renders a scale bar with figures. + True, if MTex renders a scale bar with figures. show_coordinates(NX_BOOLEAN): doc: | - True if MTex renders a grid with figures. + True, if MTex renders a grid with figures. pf_anno_fun_hdl: doc: | Code for the function handle used for annotating pole figure plots. @@ -128,7 +128,9 @@ NXmicrostructure_mtex_config(NXobject): inside_poly(NX_BOOLEAN): doc: | TODO with MTex developers - text_interpreter: + text_interpreter(NX_CHAR): + doc: | + TODO with MTex developers numerics(NXcollection): doc: | Miscellaneous settings relevant for numerics. @@ -201,13 +203,13 @@ NXmicrostructure_mtex_config(NXobject): # version as an instance of (NXprogram) one for MTex one for Matlab # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 2be867a24501f8d04bb94d529ceb202b9c1e69f62738afaeeceec3097f986c54 -# +# 69087abba8fd927cf17ad7bfd2cc2cd7f5cc4c103a401a1ecd38ca6809b4acf1 +# # # +# doc: | +# TODO with MTex developers +# unit: NX_UNITLESS--> # # # @@ -413,7 +415,11 @@ NXmicrostructure_mtex_config(NXobject): # TODO with MTex developers # # -# +# +# +# TODO with MTex developers +# +# # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_odf.yaml b/contributed_definitions/nyaml/NXmicrostructure_odf.yaml index a11a1d11ea..3502889241 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_odf.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_odf.yaml @@ -6,13 +6,13 @@ doc: | much volume of material has a specific orientation. An ODF is computed from pole figure data in a computational process called `pole figure inversion `_. symbols: - n_varphi_one: | - Number of pixel per varphi section plot along the :math:`\varphi_1` fastest + n_varphi_two: | + Number of pixel per varphi section plot along the :math:`\varphi_2` slow direction. n_capital_phi: | Number of pixel per varphi section plot along the :math:`\Phi` fast direction. - n_varphi_two: | - Number of pixel per varphi section plot along the :math:`\varphi_2` slow + n_varphi_one: | + Number of pixel per varphi section plot along the :math:`\varphi_1` fastest direction. k: | Number of local maxima evaluated in the component analysis. @@ -20,17 +20,18 @@ symbols: Number of sampled positions in orientation space. type: group NXmicrostructure_odf(NXprocess): - configuration(NXobject): + configuration(NXparameters): doc: | Details about the algorithm used for computing the ODF. crystal_symmetry_point_group(NX_CHAR): doc: | - Point group of the crystal structure of the phase for which the here documented phase- - dependent ODF was computed.(following the notation of the International Table of Crystallography). + Point group of the crystal structure of the phase for which the here documented + phase-dependent ODF was computed following the notation of the + International Table of Crystallography. specimen_symmetry_point_group(NX_CHAR): doc: | Point group assumed for additionally considered sample symmetries - following the notation of the International Table of Crystallography). + following the notation of the International Table of Crystallography. kernel_halfwidth(NX_NUMBER): unit: NX_ANGLE doc: | @@ -44,7 +45,7 @@ NXmicrostructure_odf(NXprocess): Resolution of the kernel. # specific values and typical results - kth_extrema(NXobject): + kth_extrema(NXprocess): doc: | Group to store descriptors and summary statistics for extrema of the ODF. extrema(NX_CHAR): @@ -68,22 +69,22 @@ NXmicrostructure_odf(NXprocess): location(NX_NUMBER): unit: NX_ANGLE doc: | - Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the kth-most - maxima in decreasing order of the intensity maximum. + Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the + kth-most maxima in decreasing order of the intensity maximum. dimensions: rank: 2 dim: (k, 3) volume_fraction(NX_NUMBER): unit: NX_ANY doc: | - Integrated ODF intensity within a theta angular region of the orientation space (SO3) + Integrated ODF intensity within a theta angular region of the orientation space :math:`SO3` about each location (obeying symmetries) as specified for each location. dimensions: rank: 1 dim: (k,) - sampling(NXobject): + sampling(NXprocess): doc: | - The ODF intensity values (weights) as sampled with a software + The ODF intensity values (weights) as sampled with a software. resolution(NX_NUMBER): unit: NX_ANGLE doc: | @@ -110,7 +111,7 @@ NXmicrostructure_odf(NXprocess): This is one example of typical default plots used in the texture community in materials engineering. - Mind that when parameterized using Euler angles the orientation space is a distorted space. + Mind that the orientation space is a distorted space when it using an Euler angle parameterization. Therefore, equivalent orientations show intensity contributions in eventually multiple locations. # \@signal: intensity @@ -133,8 +134,6 @@ NXmicrostructure_odf(NXprocess): dimensions: rank: 1 dim: (n_varphi_one,) - - # \@long_name(NX_CHAR): capital_phi(NX_NUMBER): unit: NX_ANGLE doc: | @@ -142,8 +141,6 @@ NXmicrostructure_odf(NXprocess): dimensions: rank: 1 dim: (n_capital_phi,) - - # \@long_name(NX_CHAR): varphi_two(NX_NUMBER): unit: NX_ANGLE doc: | @@ -151,17 +148,15 @@ NXmicrostructure_odf(NXprocess): dimensions: rank: 1 dim: (n_varphi_two,) - - # \@long_name(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# cb4a53053dcf07ad3f1c4a9eb44256a9c03afa2696cc0ab50ee634cc1ddbf088 -# +# 243a65e23623a0bc9a66f1041e4358c0618fc1e7d740eb7fdd81edc48865ada1 +# # # # # -# +# # -# Number of pixel per varphi section plot along the :math:`\varphi_1` fastest +# Number of pixel per varphi section plot along the :math:`\varphi_2` slow # direction. # # @@ -192,9 +187,9 @@ NXmicrostructure_odf(NXprocess): # Number of pixel per varphi section plot along the :math:`\Phi` fast direction. # # -# +# # -# Number of pixel per varphi section plot along the :math:`\varphi_2` slow +# Number of pixel per varphi section plot along the :math:`\varphi_1` fastest # direction. # # @@ -216,20 +211,21 @@ NXmicrostructure_odf(NXprocess): # much volume of material has a specific orientation. An ODF is computed from # pole figure data in a computational process called `pole figure inversion <https://doi.org/10.1107/S0021889808030112>`_. # -# +# # # Details about the algorithm used for computing the ODF. # # # -# Point group of the crystal structure of the phase for which the here documented phase- -# dependent ODF was computed.(following the notation of the International Table of Crystallography). +# Point group of the crystal structure of the phase for which the here documented +# phase-dependent ODF was computed following the notation of the +# International Table of Crystallography. # # # # # Point group assumed for additionally considered sample symmetries -# following the notation of the International Table of Crystallography). +# following the notation of the International Table of Crystallography. # # # @@ -249,7 +245,7 @@ NXmicrostructure_odf(NXprocess): # # # -# +# # # Group to store descriptors and summary statistics for extrema of the ODF. # @@ -279,8 +275,8 @@ NXmicrostructure_odf(NXprocess): # # # -# Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the kth-most -# maxima in decreasing order of the intensity maximum. +# Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the +# kth-most maxima in decreasing order of the intensity maximum. # # # @@ -289,7 +285,7 @@ NXmicrostructure_odf(NXprocess): # # # -# Integrated ODF intensity within a theta angular region of the orientation space (SO3) +# Integrated ODF intensity within a theta angular region of the orientation space :math:`SO3` # about each location (obeying symmetries) as specified for each location. # # @@ -297,9 +293,9 @@ NXmicrostructure_odf(NXprocess): # # # -# +# # -# The ODF intensity values (weights) as sampled with a software +# The ODF intensity values (weights) as sampled with a software. # # # @@ -332,7 +328,7 @@ NXmicrostructure_odf(NXprocess): # # This is one example of typical default plots used in the texture community in materials engineering. # -# Mind that when parameterized using Euler angles the orientation space is a distorted space. +# Mind that the orientation space is a distorted space when it using an Euler angle parameterization. # Therefore, equivalent orientations show intensity contributions in eventually multiple locations. # # # # # Pixel center angular position along the :math:`\Phi` direction. @@ -368,7 +363,6 @@ NXmicrostructure_odf(NXprocess): # # # -# # # # Pixel center angular position along the :math:`\varphi_2` direction. @@ -378,5 +372,4 @@ NXmicrostructure_odf(NXprocess): # # # -# # diff --git a/contributed_definitions/nyaml/NXmicrostructure_pf.yaml b/contributed_definitions/nyaml/NXmicrostructure_pf.yaml index a31ed679c0..06f8d13785 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_pf.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_pf.yaml @@ -11,17 +11,17 @@ symbols: Number of pixel per pole figure in the fast direction. type: group NXmicrostructure_pf(NXprocess): - configuration(NXobject): + configuration(NXparameters): doc: | Details about the algorithm that was used to compute the pole figure. crystal_symmetry_point_group(NX_CHAR): doc: | - Point group of the crystal structure of the phase for which the pole figure - was computed (according to International Table of Crystallography). + Point group of the crystal structure of the phase for which the pole figure was + computed following the notation of the International Table of Crystallography. specimen_symmetry_point_group(NX_CHAR): doc: | - Point group of assumed sample symmetries (according to International Table of - Crystallography). + Point group of assumed sample symmetries following the + notation of the International Table of Crystallography. # integration windows halfwidth(NX_NUMBER): @@ -30,7 +30,8 @@ NXmicrostructure_pf(NXprocess): Halfwidth of the kernel. miller_indices(NX_CHAR): doc: | - Miller indices (:math:`(hkl)[uvw]`) to specify the pole figure. + Miller (:math:`(hkl)[uvw]`) or Miller-Bravais indices used to specify the pole + figure. resolution(NX_NUMBER): unit: NX_ANGLE doc: | @@ -58,8 +59,6 @@ NXmicrostructure_pf(NXprocess): dimensions: rank: 1 dim: (n_y,) - - # \@long_name(NX_CHAR): axis_x(NX_NUMBER): unit: NX_ANY doc: | @@ -68,17 +67,15 @@ NXmicrostructure_pf(NXprocess): dimensions: rank: 1 dim: (n_x,) - - # \@long_name(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 818e0c5d7f28f02fcf8859aa7ec82dcb88acccc968e404319dfd6b7602e7f66b -# +# cde4f0f5bbfd471ca65557093c492d7e6d1c90389f5953076647a62cd6241789 +# # # @@ -139,7 +136,8 @@ NXmicrostructure_pf(NXprocess): # # # -# Miller indices (:math:`(hkl)[uvw]`) to specify the pole figure. +# Miller (:math:`(hkl)[uvw]`) or Miller-Bravais indices used to specify the pole +# figure. # # # @@ -174,7 +172,6 @@ NXmicrostructure_pf(NXprocess): # # # -# # # # Pixel center along x direction in the equatorial plane of @@ -185,5 +182,4 @@ NXmicrostructure_pf(NXprocess): # # # -# # diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml index 07b0c3dc84..7c3c14ba86 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml @@ -49,7 +49,8 @@ NXmicrostructure_score_config(NXobject): exists: ['min', '0', 'max', 'unbounded'] sample(NXsample): exists: recommended - dimensionality(NX_UINT): + dimensionality(NX_POSINT): + unit: NX_UNITLESS doc: | Dimensionality of the simulation. enumeration: [3] @@ -66,15 +67,14 @@ NXmicrostructure_score_config(NXobject): The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by identifier_parent or walk through - eventually deeply nested groups in data instances. + these from other sources. program1(NXprogram): exists: recommended doc: | Name of the program whereby this config file was created. program(NX_CHAR): \@version(NX_CHAR): - environment(NXobject): + environment(NXcollection): exists: recommended doc: | Programs and libraries representing the computational environment @@ -82,7 +82,7 @@ NXmicrostructure_score_config(NXobject): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): - material(NXobject): + material(NXparameters): doc: | (Mechanical) properties of the material which scale the amount of stored (elastic) energy in the system and @@ -104,7 +104,7 @@ NXmicrostructure_score_config(NXobject): unit: NX_TEMPERATURE doc: | Melting temperature - deformation(NXobject): + deformation(NXparameters): doc: | Details about the geometry and properties of the polycrystal that represents the starting configuration (typically a deformed microstructure) for the simulation. @@ -131,7 +131,7 @@ NXmicrostructure_score_config(NXobject): unit: NX_LENGTH doc: | Average spherical diameter when model is poisson_voronoi. - ensemble(NXobject): + ensemble(NXparameters): exists: optional doc: | Settings for instantiating properties of deformed grains when model is cuboidal @@ -182,7 +182,7 @@ NXmicrostructure_score_config(NXobject): algorithm(NX_CHAR): enumeration: [sha256] checksum(NX_CHAR): - nucleation(NXobject): + nucleation(NXparameters): doc: | Phenomenological model according to which recrystallization nuclei are placed into the domain whose growth is studied with the simulation. @@ -206,7 +206,7 @@ NXmicrostructure_score_config(NXobject): * random, picking randomly on the SO3 * damask, picking based on information provided in deformation/damask enumeration: [ensemble, random, damask] - ensemble(NXobject): + ensemble(NXparameters): # required unless custom nucleation model doc: | @@ -227,7 +227,7 @@ NXmicrostructure_score_config(NXobject): dimensions: rank: 1 dim: (n_rx_ori,) - grain_boundary_mobility(NXobject): + grain_boundary_mobility(NXparameters): doc: | Model for the assumed mobility of grain boundaries with different disorientation implemented as parameterized Turnbull's model for thermally-activated @@ -242,7 +242,7 @@ NXmicrostructure_score_config(NXobject): # TODO: add equation for the Sebald-Gottstein model the following equation # TODO: add equation for the Rollett-Holm model the following equation enumeration: [sebald_gottstein, rollett_holm] - sebald_gottstein(NXobject): + sebald_gottstein(NXparameters): exists: optional doc: | Parameter of the Sebald-Gottstein migration model. @@ -283,7 +283,7 @@ NXmicrostructure_score_config(NXobject): Migration activation enthalpy for high-angle grain boundaries which in bicrystal or other tailored experiments showed a particular high mobility. - rollett_holm(NXobject): + rollett_holm(NXparameters): doc: | Parameter of the Rollett-Holm migration model. @@ -308,14 +308,14 @@ NXmicrostructure_score_config(NXobject): unit: NX_UNITLESS doc: | Mobility scaling factor :math:`c_3`. Typically 9. - stored_energy_recovery(NXobject): + stored_energy_recovery(NXparameters): doc: | Time-dependent reduction of the stored energy to account for recovery effects. model(NX_CHAR): doc: | Which type of recovery model. enumeration: [none] - dispersoid_drag(NXobject): + dispersoid_drag(NXparameters): doc: | Reduction of the grain boundary migration speed due to the presence of dispersoids through which the total grain boundary area of the recrystallization front can be reduced @@ -324,7 +324,7 @@ NXmicrostructure_score_config(NXobject): doc: | Which type of drag model. enumeration: [none, zener_smith] - zener_smith(NXobject): + zener_smith(NXparameters): # required when model is zener_smith doc: | @@ -367,7 +367,7 @@ NXmicrostructure_score_config(NXobject): rank: 1 dim: (n_drag,) \@long_name(NX_CHAR): - component_analysis(NXobject): + component_analysis(NXparameters): name(NX_CHAR): doc: | Given name of a texture component. @@ -446,7 +446,7 @@ NXmicrostructure_score_config(NXobject): is discretized via equisized cubic voxels. # dim: (d,) - numerics(NXobject): + numerics(NXparameters): doc: | Criteria which enable to stop the simulation in a controlled manner. Whichever criterion is fulfilled first stops the simulation. @@ -488,7 +488,7 @@ NXmicrostructure_score_config(NXobject): dimensions: rank: 1 dim: (n_snapshot,) - cell_cache(NXobject): + cell_cache(NXparameters): doc: | Parameter which control the memory management of cells in the recrystallization front. @@ -519,7 +519,7 @@ NXmicrostructure_score_config(NXobject): dimensions: rank: 1 dim: (n_defrag,) - solitary_unit(NXobject): + solitary_unit(NXparameters): apply(NX_BOOLEAN): doc: | Perform a statistical analyses of the results as it was proposed @@ -534,17 +534,10 @@ NXmicrostructure_score_config(NXobject): doc: | Into how many time steps should the real time interval be discretized upon during post-processing the results with the solitary unit modeling approach. - - # identifier_domain(NX_UINT): - # doc: | - # List of identifier for those CAs domains which should be sampled. - # Identifier start from 1. - # unit: NX_UNITLESS - # dim: (n_su,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 03ff6c1cc0bd458dd25c5847ee92f44c307e0f1cc54c41ac6f07e702b5ef5d01 -# +# 68eef00573d978ee8505c363acca7f7c1ec47ce1c5c7fc2022fe7b87ae50ddb3 +# # # # # Settings for instantiating properties of nuclei for recrystallizing grains. @@ -893,7 +885,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # Model for the assumed mobility of grain boundaries with different disorientation # implemented as parameterized Turnbull's model for thermally-activated @@ -913,7 +905,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # Parameter of the Sebald-Gottstein migration model. # @@ -960,7 +952,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # Parameter of the Rollett-Holm migration model. # @@ -992,7 +984,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # Time-dependent reduction of the stored energy to account for recovery effects. # @@ -1005,7 +997,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # Reduction of the grain boundary migration speed due to the presence of dispersoids # through which the total grain boundary area of the recrystallization front can be reduced @@ -1020,7 +1012,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # # Parameter of the Zener-Smith drag model when model is zener_smith. @@ -1070,7 +1062,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # # Given name of a texture component. @@ -1163,7 +1155,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # Criteria which enable to stop the simulation in a controlled manner. # Whichever criterion is fulfilled first stops the simulation. @@ -1211,7 +1203,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # Parameter which control the memory management # of cells in the recrystallization front. @@ -1250,7 +1242,7 @@ NXmicrostructure_score_config(NXobject): # # # -# +# # # # Perform a statistical analyses of the results as it was proposed @@ -1271,10 +1263,4 @@ NXmicrostructure_score_config(NXobject): # # # -# # diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml index 0bead2080a..80028a09e3 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml @@ -72,7 +72,7 @@ NXmicrostructure_score_results(NXobject): Name of the program with which the simulation was performed. program(NX_CHAR): \@version: - environment(NXobject): + environment(NXcollection): exists: optional doc: | Programs and libraries representing the computational environment @@ -115,14 +115,14 @@ NXmicrostructure_score_results(NXobject): symmetry(NX_CHAR): cell_dimensions(NX_NUMBER): extent(NX_UINT): - identifier_offset(NX_INT): + index_offset(NX_INT): boundary(NXcg_hexahedron): doc: | A tight bounding box or sphere or bounding primitive about the grid. # a good example for a general bounding box description for such a grids of triclinic cells # https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallelepiped - number_of_boundaries(NX_POSINT): + number_of_boundaries(NX_UINT): unit: NX_UNITLESS doc: | How many distinct boundaries are distinguished? @@ -149,8 +149,8 @@ NXmicrostructure_score_results(NXobject): dimensions: rank: 1 dim: (6,) - SPATIOTEMPORAL(NXobject): - nameType: any + spatiotemporalID(NXprocess): + nameType: partial exists: ['min', '1', 'max', 'unbounded'] doc: | Documentation of the spatiotemporal evolution for each CA domain. @@ -158,8 +158,6 @@ NXmicrostructure_score_results(NXobject): SCORE is a hybrid parallelized code that can evolve multiple replicas in parallel. The set of replicas is distributed across MPI processes. Each such replica is then evolved via OpenMP multi-threading. - - Instances should use spatiotemporal as a name prefix. # the typical lean summary statistics flattened summary_statistics(NXprocess): @@ -265,10 +263,9 @@ NXmicrostructure_score_results(NXobject): # unit: NX_ANY # dim: (n_summary_stats, 3, 3) # the typically storage-costlier snapshot data - (NXmicrostructure): + microstructureID(NXmicrostructure): exists: ['min', '1', 'max', 'unbounded'] - doc: | - Instances should use microstructure as a name prefix. + nameType: partial time(NX_FLOAT): iteration(NX_UINT): unit: NX_UNITLESS @@ -292,39 +289,39 @@ NXmicrostructure_score_results(NXobject): # optional places to store the grid for instance if it changes grid(NXcg_grid): exists: recommended - identifier_crystal(NX_UINT): + indices_crystal(NX_INT): exists: recommended unit: NX_UNITLESS doc: | - Grain identifier for each cell. + Index for each crystal whereby its metadata can be retrieved. dimensions: rank: 3 dim: (n_x, n_y, n_z) - identifier_thread(NX_UINT): + thread_id(NX_UINT): exists: optional unit: NX_UNITLESS doc: | - Identifier of the OpenMP thread which processed this part of the grid. + Identifier of the OpenMP thread that processed this part of the grid. dimensions: rank: 3 dim: (n_x, n_y, n_z) - crystals(NXobject): + crystals(NXmicrostructure_feature): representation(NX_CHAR): exists: recommended number_of_crystals(NX_UINT): exists: recommended number_of_phases(NX_UINT): exists: recommended - identifier_crystal_offset(NX_INT): + index_offset_crystal(NX_INT): exists: recommended - identifier_crystal(NX_INT): + indices_crystal(NX_INT): exists: recommended dimensions: rank: 1 dim: (n_grains,) - identifier_phase_offset(NX_INT): + index_offset_phase(NX_INT): exists: recommended - identifier_phase(NX_INT): + indices_phase(NX_INT): exists: recommended dimensions: rank: 1 @@ -368,7 +365,7 @@ NXmicrostructure_score_results(NXobject): dimensions: rank: 1 dim: (n_grains,) - recrystallization_front(NXobject): + recrystallization_front(NXmicrostructure_feature): exists: recommended doc: | Details about those cells which in this time step represent the discrete @@ -399,7 +396,7 @@ NXmicrostructure_score_results(NXobject): dimensions: rank: 2 dim: (n_front, 3) - identifier_deformed_grain(NX_UINT): + deformed_grain_id(NX_UINT): exists: recommended unit: NX_UNITLESS doc: | @@ -407,7 +404,7 @@ NXmicrostructure_score_results(NXobject): dimensions: rank: 1 dim: (n_front,) - identifier_recrystallized_grain(NX_UINT): + recrystallized_grain_id(NX_UINT): exists: recommended unit: NX_UNITLESS doc: | @@ -416,7 +413,7 @@ NXmicrostructure_score_results(NXobject): dimensions: rank: 1 dim: (n_front,) - identifier_thread(NX_UINT): + thread_id(NX_UINT): exists: optional unit: NX_UNITLESS doc: | @@ -435,8 +432,8 @@ NXmicrostructure_score_results(NXobject): dim: (n_front,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 877d375485ae7b31492b80b0d566d3f88f0068aedcb70825c5bef0802cc1a62a -# +# 609c1c0e42efe23249deed2b570fbab384ac818d1f711cb6f43319b5a4188e93 +# # # +# rotation_handedness(NX_CHAR): +# rotation_convention(NX_CHAR): +# euler_angle_convention(NX_CHAR): +# axis_angle_convention(NX_CHAR): +# sign_convention(NX_CHAR):--> # # # @@ -641,7 +638,7 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # # # @@ -649,7 +646,7 @@ NXmicrostructure_score_results(NXobject): # # -# +# # # How many distinct boundaries are distinguished? # Most grids discretize a cubic or cuboidal region. In this case @@ -682,21 +679,19 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # # Documentation of the spatiotemporal evolution for each CA domain. # # SCORE is a hybrid parallelized code that can evolve multiple replicas # in parallel. The set of replicas is distributed across MPI processes. # Each such replica is then evolved via OpenMP multi-threading. -# -# Instances should use spatiotemporal as a name prefix. # # # # # Summary quantities which are the result of some post-processing of the snapshot data -# (averaging, integrating, interpolating) happening for practical and performance reasons +# (averaging, integrating, interpolating) happening for practical and performance reasons # during the simulation. Place used for storing descriptors from continuum mechanics # and thermodynamics at the scale of the entire ROI. # @@ -804,24 +799,21 @@ NXmicrostructure_score_results(NXobject): # # # -# -# -# Instances should use microstructure as a name prefix. -# +# # # # @@ -847,9 +839,9 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # -# Grain identifier for each cell. +# Index for each crystal whereby its metadata can be retrieved. # # # @@ -857,9 +849,9 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # -# Identifier of the OpenMP thread which processed this part of the grid. +# Identifier of the OpenMP thread that processed this part of the grid. # # # @@ -868,18 +860,18 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # # # -# -# +# +# # # # # -# -# +# +# # # # @@ -928,7 +920,7 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # # Details about those cells which in this time step represent the discrete # recrystallization front. @@ -960,7 +952,7 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # # Grain identifier assigned to each cell in the recrystallization front. # @@ -968,7 +960,7 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # # Grain identifier assigned to each nucleus which affected that cell in the # recrystallization front. @@ -977,7 +969,7 @@ NXmicrostructure_score_results(NXobject): # # # -# +# # # Identifier of the OpenMP thread processing each cell in the recrystallization # front. diff --git a/contributed_definitions/nyaml/NXmicrostructure_slip_system.yaml b/contributed_definitions/nyaml/NXmicrostructure_slip_system.yaml index ad0dc6900d..60c2686f79 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_slip_system.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_slip_system.yaml @@ -6,6 +6,8 @@ symbols: The symbols used in the schema to specify e.g. dimensions of arrays. n: | Number of slip systems. + m: | + Number of indices used for reporting Miller (3) or Miller-Bravais indices (4). type: group NXmicrostructure_slip_system(NXobject): lattice_type(NX_CHAR): @@ -19,27 +21,26 @@ NXmicrostructure_slip_system(NXobject): dimensions: rank: 2 dim: (n, i) - - # fastest changing dimension needs to be i and not 3 because for instance for hexagonal hkil notation is used miller_direction(NX_NUMBER): unit: NX_UNITLESS doc: | - Array of Miller indices which describe the crystallographic direction. + Array of Miller or Miller-Bravais indices that describe the crystallographic + direction. dimensions: rank: 2 - dim: (n, i) + dim: (n, m) is_specific(NX_BOOLEAN): unit: NX_UNITLESS doc: | - For each slip system a marker whether the specified Miller indices refer to - a specific or a crystallographic equivalent set of the slip system. + For each slip system a marker whether the Miller indices refer to a specific slip system + or to a set of equivalent crystallographic slip systems. dimensions: rank: 1 dim: (n,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 8d95502300b03898a97e38b85b397fd790484087064691fd448b15f0d0259b66 -# +# ac1be2e5d31ae8744ee7c60637ccbe064462fe7d6ecce7b0e8ae326b3a25fab3 +# # # # # -# Array of Miller indices which describe the crystallographic direction. +# Array of Miller or Miller-Bravais indices that describe the crystallographic +# direction. # # # -# +# # # # # -# For each slip system a marker whether the specified Miller indices refer to -# a specific or a crystallographic equivalent set of the slip system. +# For each slip system a marker whether the Miller indices refer to a specific slip system +# or to a set of equivalent crystallographic slip systems. # # # diff --git a/contributed_definitions/nyaml/NXpiezo_config_spm.yaml b/contributed_definitions/nyaml/NXpiezo_config_spm.yaml index fe8171b385..c9ac6a4e2f 100644 --- a/contributed_definitions/nyaml/NXpiezo_config_spm.yaml +++ b/contributed_definitions/nyaml/NXpiezo_config_spm.yaml @@ -85,7 +85,7 @@ NXpiezo_config_spm(NXobject): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # c4d63a3b96c8b7339c29f711dcad4108ace41b7495cc6960f9426f3bfbfe324f -# +# # # -# -# -# -# -# number of components -# -# -# -# -# Set of sample components and their configuration. -# -# The idea here is to have a united place for all materials descriptors that are not -# part of the individual sample components, but rather their configuration. -# -# -# -# Array of strings referring to the names of the NXsample_components. -# The order of these components serves as an index (starting at 1). -# -# -# -# -# Concentration of each component -# -# -# -# -# -# -# -# Volume fraction of each component -# -# -# -# -# -# -# -# Scattering length density of each component -# -# -# -# -# -# -# -# Each component set can contain multiple components. -# -# -# -# -# For description of a sub-component set. Can contain multiple components itself. -# -# -# diff --git a/contributed_definitions/nyaml/NXscan_control.yaml b/contributed_definitions/nyaml/NXscan_control.yaml index 84e2c3240e..997b2fec71 100644 --- a/contributed_definitions/nyaml/NXscan_control.yaml +++ b/contributed_definitions/nyaml/NXscan_control.yaml @@ -519,7 +519,7 @@ NXscan_control(NXobject): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # e1d63e6a9fabe8ec4e5a96775fc0ab1e542f86ef3c11fc8348745b7bbd300054 -# +# # # -# +# # -# Which numerical identifier is the first to be used to label a feature. +# Which numerical index is the first to be used to label a feature. # # The value should be chosen in such a way that special values can be resolved: -# * identifier_offset - 1 indicates that an object belongs to no cluster. -# * identifier_offset - 2 indicates that an object belongs to the noise category. -# Setting for instance identifier_offset to 1 recovers the commonly used +# * index_offset - 1 indicates that an object belongs to no cluster. +# * index_offset - 2 indicates that an object belongs to the noise category. +# Setting for instance index_offset to 1 recovers the commonly used # case that objects of the noise category get values to -1 and unassigned # points to 0. Numerical identifier have to be strictly increasing. # @@ -207,7 +207,7 @@ NXsimilarity_grouping(NXobject): # # Matrix of numerical label for each member in the set. # For classical clustering algorithms this can for instance -# encode the identifier_cluster. +# encode the indices_cluster. # # # @@ -247,7 +247,7 @@ NXsimilarity_grouping(NXobject): # # -# +# # # Array of numerical identifier of each feature. # diff --git a/contributed_definitions/nyaml/NXspatial_filter.yaml b/contributed_definitions/nyaml/NXspatial_filter.yaml index cad4a6973c..aa7d5f1bad 100644 --- a/contributed_definitions/nyaml/NXspatial_filter.yaml +++ b/contributed_definitions/nyaml/NXspatial_filter.yaml @@ -48,7 +48,7 @@ NXspatial_filter(NXobject): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ # 32bfaf73b5c1cf3a3f45a5634089df0c0eee85f614dbf7bbf0aaea64c8876300 -# +# # #