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Merged
mkuehbach merged 4 commits into from
Sep 10, 2025
Merged

Fairmat addition pr402 to em #1585

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6974c07
Adding content of fairmat PR402 to complete the discussion from 1423 …
atomprobe-tc Aug 25, 2025
431a50b
Bugfixes detected during implementation of apm examples observed afte…
atomprobe-tc Aug 25, 2025
7236be5
Few more bugfixes that were spotted when using the voted upon NXem fo…
atomprobe-tc Aug 25, 2025
3e3ecf0
Merge branch 'main' into fairmat_addition_pr402_to_em
atomprobe-tc Sep 10, 2025
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25 changes: 15 additions & 10 deletions applications/NXapm.nxdl.xml
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Expand Up @@ -44,7 +44,7 @@
<symbol name="p">
<doc>
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
instance of :ref:`NXapm_event_data`. 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.
</doc>
Expand Down Expand Up @@ -149,7 +149,7 @@
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
instrument parameters. Each individual collection should then though be stored in an own NXapm_event_data
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,
Expand Down Expand Up @@ -203,7 +203,7 @@
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 compaigns with different target detection rate can be stored.
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
Expand Down Expand Up @@ -340,7 +340,7 @@

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.
purpose the :ref:`NXapm_event_data` instance should be used.
</doc>
</field>
<field name="end_time" type="NX_DATE_TIME" recommended="true">
Expand All @@ -361,6 +361,11 @@
</doc>
</field>
<group name="citeID" type="NXcite" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<field name="author" type="NX_CHAR" optional="true">
<doc>
The author(s) of that reference.
</doc>
</field>
<field name="doi" type="NX_CHAR"/>
</group>
<group name="noteID" type="NXnote" minOccurs="0" maxOccurs="unbounded" nameType="partial">
Expand Down Expand Up @@ -673,7 +678,7 @@
</enumeration>
</field>
</group>
<group name="NAMED_reference_frame" type="NXcoordinate_system" minOccurs="1" maxOccurs="unbounded" nameType="partial">
<group name="NAMED_reference_frameID" type="NXcoordinate_system" minOccurs="1" maxOccurs="unbounded" nameType="partial">
<doc>
A coordinate system. Multiple instances require unique names.

Expand Down Expand Up @@ -740,7 +745,7 @@
<group name="measurement" type="NXapm_measurement" optional="true">
<field name="status" type="NX_CHAR" recommended="true"/>
<field name="quality" type="NX_CHAR" recommended="true"/>
<group name="instrument" type="NXinstrument_apm">
<group name="instrument" type="NXapm_instrument">
<field name="type" type="NX_CHAR" recommended="true"/>
<field name="location" type="NX_CHAR" recommended="true"/>
<field name="flight_path" type="NX_FLOAT" recommended="true"/>
Expand Down Expand Up @@ -832,10 +837,10 @@
</group>
</group>
</group>
<group name="eventID" type="NXevent_data_apm" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="eventID" type="NXapm_event_data" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<field name="start_time" type="NX_DATE_TIME" recommended="true"/>
<field name="end_time" type="NX_DATE_TIME" recommended="true"/>
<group name="instrument" type="NXinstrument_apm" recommended="true">
<group name="instrument" type="NXapm_instrument" recommended="true">
<group name="reflectron" type="NXcomponent" recommended="true">
<field name="voltage" type="NX_FLOAT"/>
</group>
Expand Down Expand Up @@ -1260,7 +1265,7 @@
<field name="checksum" type="NX_CHAR" recommended="true"/>
<field name="algorithm" type="NX_CHAR" recommended="true"/>
</group>
<group name="config" type="NXparameters">
<group name="config" type="NXparameters" recommended="true">
<field name="mass_calibration" type="NX_FLOAT" recommended="true" units="NX_ANY">
<doc>
Mass calibration with unit peaks/interp. as mentioned by `T. Blum et al.
Expand Down Expand Up @@ -1308,7 +1313,7 @@
<field name="name" type="NX_CHAR"/>
</group>
</group>
<field name="mass_to_charge" type="NX_FLOAT">
<field name="mass_to_charge" type="NX_FLOAT" units="NX_ANY">
<dimensions rank="1">
<dim index="1" value="n"/>
</dimensions>
Expand Down
78 changes: 18 additions & 60 deletions applications/NXem.nxdl.xml
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Expand Up @@ -219,7 +219,7 @@
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.
of respective :ref:`NXem_event_data` instances.
</doc>
</field>
<field name="end_time" type="NX_DATE_TIME" recommended="true">
Expand All @@ -231,7 +231,14 @@
start_time and end_time together.
</doc>
</field>
<group name="citeID" type="NXcite" minOccurs="0" maxOccurs="unbounded" nameType="partial"/>
<group name="citeID" type="NXcite" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<field name="author" type="NX_CHAR" optional="true">
<doc>
The author(s) of that reference.
</doc>
</field>
<field name="doi" type="NX_CHAR"/>
</group>
<group name="noteID" type="NXnote" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<doc>
Collection of serialized resources associated with the experiment.
Expand Down Expand Up @@ -422,7 +429,7 @@
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`
region-of-interest connected to individual :ref:`NXem_event_data`
instances can provide a cleaner description of the relevant details.
</doc>
</field>
Expand Down Expand Up @@ -508,7 +515,7 @@
</enumeration>
</field>
</group>
<group name="NAMED_reference_frame" type="NXcoordinate_system" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<group name="NAMED_reference_frameID" type="NXcoordinate_system" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<field name="alias" type="NX_CHAR" optional="true"/>
<field name="type" type="NX_CHAR"/>
<field name="origin" type="NX_CHAR" recommended="true"/>
Expand Down Expand Up @@ -747,8 +754,8 @@
</field>
</group>
<group name="measurement" type="NXem_measurement" optional="true">
<!--voltage like all other dynamic quantities should better be placed in instances of NXevent_data_em-->
<group name="instrument" type="NXinstrument_em">
<!--voltage like all other dynamic quantities should better be placed in instances of NXem_event_data-->
<group name="instrument" type="NXem_instrument">
<field name="name" type="NX_CHAR" recommended="true"/>
<field name="location" type="NX_CHAR" recommended="true"/>
<field name="type" type="NX_CHAR" recommended="true"/>
Expand Down Expand Up @@ -976,7 +983,7 @@
<group name="sensorID" type="NXsensor" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
<group name="actuatorID" type="NXactuator" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
</group>
<group name="eventID" type="NXevent_data_em" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="eventID" type="NXem_event_data" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<field name="start_time" type="NX_DATE_TIME" recommended="true"/>
<field name="end_time" type="NX_DATE_TIME" recommended="true"/>
<field name="identifier_sample" type="NX_CHAR" recommended="true"/>
Expand Down Expand Up @@ -1341,7 +1348,7 @@
</field>
</group>
</group>
<group name="instrument" type="NXinstrument_em" recommended="true">
<group name="instrument" type="NXem_instrument" recommended="true">
<group name="ebeam_column" type="NXebeam_column">
<field name="operation_mode" type="NX_CHAR" recommended="true"/>
<group name="electron_source" type="NXsource" optional="true">
Expand Down Expand Up @@ -1639,8 +1646,6 @@ is required to provide such information in this way!-->
<field name="imaging_mode" type="NX_CHAR"/>
</group>
</group>
<!--(NXmicrostructure):
exists: optional-->
<group name="ebsd" type="NXem_ebsd" optional="true">
<group name="gnomonic_reference_frame" type="NXcoordinate_system" recommended="true">
<field name="alias" type="NX_CHAR" optional="true"/>
Expand Down Expand Up @@ -1687,7 +1692,7 @@ exists: optional-->
<field name="checksum" type="NX_CHAR" recommended="true"/>
<field name="algorithm" type="NX_CHAR" recommended="true"/>
</group>
<!--per scan point quantities (identifier_phase, matching_phase, positions, etc.)
<!--per scan point quantities (phase_id, matching_phase, positions, etc.)
just using the implicit optional, for the database example in NOMAD we do
not wish to duplicate all payload data-->
<group name="phaseID" type="NXphase" nameType="partial" minOccurs="0" maxOccurs="unbounded">
Expand All @@ -1703,51 +1708,6 @@ not wish to duplicate all payload data-->
<field name="space_group" type="NX_CHAR"/>
</group>
</group>
<!--foreseen place for phase-specific texture and microstructure representations and statistics
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
microstructureID(NXmicrostructure):
nameType: partial
exists: optional-->
<group name="roi" type="NXdata" recommended="true">
<attribute name="signal" type="NX_CHAR"/>
<attribute name="axes" type="NX_CHAR"/>
Expand Down Expand Up @@ -1781,7 +1741,7 @@ exists: optional-->
</field>
</group>
<field name="atom_types" type="NX_CHAR"/>
<group name="ELEMENT_SPECIFIC_MAP" type="NXimage" minOccurs="0" maxOccurs="118">
<group name="ELEMENT_SPECIFIC_MAP" type="NXimage" nameType="any" minOccurs="0" maxOccurs="118">
<field name="iupac_line_candidates" type="NX_CHAR" recommended="true"/>
<field name="energy_range" type="NX_NUMBER"/>
<group name="image_2d" type="NXdata">
Expand All @@ -1790,15 +1750,13 @@ exists: optional-->
<attribute name="AXISNAME_indices" type="NX_UINT" nameType="partial"/>
<field name="title" type="NX_CHAR" recommended="true"/>
<field name="intensity" type="NX_NUMBER">
<attribute name="units" type="NX_CHAR" recommended="true"/>
<attribute name="long_name" type="NX_CHAR"/>
</field>
<field name="axis_i" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
<attribute name="units" type="NX_CHAR"/>
</field>
<field name="axis_j" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
<attribute name="units" type="NX_CHAR"/>
</field>
</group>
</group>
Expand Down
4 changes: 3 additions & 1 deletion base_classes/NXaberration.nxdl.xml
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Expand Up @@ -25,12 +25,14 @@
<doc>
Quantified aberration coefficient in an aberration_model.

For an introduction in the aberrations in electron microscopy
For an introduction in the details about aberrations with relevance for electron microscopy
see `R. Dunin-Borkowski et al. &lt;https://doi.org/10.1017/9781316337455.022&gt;`_ and
`S. J. Pennycock and P. D. Nellist &lt;https://doi.org/10.1007/978-1-4419-7200-2&gt;`_ (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 &lt;https://www.globalsino.com/EM/page3740.html&gt;`_ an introduction.

The use of the base class is not restricted to electron microscopy but can also be useful for classical optics.
</doc>
<field name="magnitude" type="NX_NUMBER" units="NX_ANY">
<doc>
Expand Down
6 changes: 3 additions & 3 deletions base_classes/NXevent_data_apm.nxdl.xml → base_classes/NXapm_event_data.nxdl.xml
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Expand Up @@ -21,7 +21,7 @@
#
# For further information, see http://www.nexusformat.org
-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXevent_data_apm" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXapm_event_data" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<symbols>
<doc>
The symbols used in the schema to specify e.g. dimensions of arrays.
Expand All @@ -37,7 +37,7 @@

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
This base class applies the concept of the :ref:`NXem_event_data` 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.
Expand Down Expand Up @@ -110,7 +110,7 @@
<dim index="1" value="p"/>
</dimensions>
</field>
<group name="instrument" type="NXinstrument_apm">
<group name="instrument" type="NXapm_instrument">
<doc>
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.
Expand Down
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