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Bring NXapm back that has been accepted now by the NIAC #396

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a9404c4
Whitespace changes on NXcg that were relevant for syncing with the NIAC
atomprobe-tc Jul 14, 2025
973f272
Brought back changes for atom probe proposal and a few fixes where ap…
atomprobe-tc Jul 14, 2025
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1,597 changes: 1,597 additions & 0 deletions applications/NXapm.nxdl.xml
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3,131 changes: 3,131 additions & 0 deletions applications/nyaml/NXapm.yaml
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2 changes: 1 addition & 1 deletion base_classes/NXactuator.nxdl.xml
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<?xml version='1.0' encoding='UTF-8'?>
<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
<!--
# NeXus - Neutron and X-ray Common Data Format
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155 changes: 155 additions & 0 deletions base_classes/NXapm_charge_state_analysis.nxdl.xml
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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2024-2025 NeXus International Advisory Committee (NIAC)
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# 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="NXapm_charge_state_analysis" extends="NXprocess" 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.
</doc>
<symbol name="n_cand">
<doc>
The number of ion candidates.
</doc>
</symbol>
<symbol name="n_ivec_max">
<doc>
Maximum number of allowed atoms per ion.
</doc>
</symbol>
<symbol name="n_variable">
<doc>
Number of entries
</doc>
</symbol>
</symbols>
<doc>
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.
</doc>
<group name="config" type="NXparameters">
<doc>
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.
</doc>
<field name="nuclides" type="NX_UINT" units="NX_UNITLESS">
<doc>
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.
</doc>
<dimensions rank="1">
<dim index="1" value="n_variable"/>
</dimensions>
</field>
<field name="mass_to_charge_range" type="NX_FLOAT" units="NX_ANY">
<doc>
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.
</doc>
<dimensions rank="1">
<dim index="1" value="2"/>
</dimensions>
</field>
<field name="min_half_life" type="NX_FLOAT" units="NX_TIME">
<doc>
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.
</doc>
</field>
<field name="min_abundance" type="NX_FLOAT" units="NX_DIMENSIONLESS">
<doc>
Parameter that defines the minimum natural abundance of each nuclide of each
ion such that the ion qualifies as a candidate.
</doc>
</field>
<field name="sacrifice_isotopic_uniqueness" type="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.
</doc>
</field>
</group>
<field name="charge_state" type="NX_INT" units="NX_UNITLESS">
<doc>
Signed charge, i.e. integer multiple of the elementary
charge of each candidate.
</doc>
<dimensions rank="1">
<dim index="1" value="n_cand"/>
</dimensions>
</field>
<field name="nuclide_hash" type="NX_UINT" units="NX_UNITLESS">
<doc>
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`.
</doc>
<dimensions rank="2">
<dim index="1" value="n_cand"/>
<dim index="2" value="n_ivec_max"/>
</dimensions>
</field>
<field name="mass" type="NX_FLOAT" units="NX_MASS">
<doc>
Accumulated mass of the nuclides in each candidate.
Not corrected for quantum effects.
</doc>
<dimensions rank="1">
<dim index="1" value="n_cand"/>
</dimensions>
</field>
<field name="natural_abundance_product" type="NX_FLOAT" units="NX_DIMENSIONLESS">
<doc>
The product of the natural abundances of the nuclides for each candidate.
</doc>
<dimensions rank="1">
<dim index="1" value="n_cand"/>
</dimensions>
</field>
<field name="shortest_half_life" type="NX_FLOAT" units="NX_TIME">
<doc>
For each candidate the half life of the nuclide that has the
shortest half life.
</doc>
<dimensions rank="1">
<dim index="1" value="n_cand"/>
</dimensions>
</field>
</definition>
70 changes: 70 additions & 0 deletions base_classes/NXapm_measurement.nxdl.xml
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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2025-2025 NeXus International Advisory Committee (NIAC)
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# 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="NXapm_measurement" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<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. &lt;https://doi.org/10.1017/S1431927620022205&gt;`_
* `C. Fleischmann et al. &lt;https://doi.org/10.1016/j.ultramic.2018.08.010&gt;`_
* `W. Windl et al. &lt;https://doi.org/10.1093/micmic/ozad067.294&gt;`_
* `C. Freysoldt et al. &lt;https://doi.org/10.1103/PhysRevLett.124.176801&gt;`_
* `G. da Costa et al. &lt;https://doi.org/10.1038/s41467-024-54169-2&gt;`_

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. &lt;https://doi.org/10.1017/S1431927622003397&gt;`_
* `P. Stender et al. &lt;https://doi.org/10.1017/S1431927621013982&gt;`_
* `I. Dimkou et al. &lt;https://doi.org/10.1093/micmic/ozac051&gt;`_

to name but a few.
</doc>
<field name="status" type="NX_CHAR">
<doc>
A statement whether the measurement completed successfully, or was aborted.
</doc>
<enumeration>
<item value="success"/>
<item value="aborted"/>
</enumeration>
</field>
<field name="quality" type="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.
</doc>
</field>
<group type="NXinstrument_apm"/>
<group type="NXevent_data_apm"/>
</definition>
118 changes: 118 additions & 0 deletions base_classes/NXapm_ranging.nxdl.xml
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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2024-2025 NeXus International Advisory Committee (NIAC)
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# 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="NXapm_ranging" extends="NXprocess" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<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 &lt;https://doi.org/10.1002/sia.1719&gt;`_
* `D. Haley et al. &lt;https://doi.org/10.1017/S1431927620024290&gt;`_
* `M. Kühbach et al. &lt;https://doi.org/10.1017/S1431927621012241&gt;`_
</doc>
<group type="NXprogram"/>
<group type="NXnote"/>
<group name="mass_to_charge_distribution" type="NXprocess">
<doc>
Specifies the mass-to-charge-state ratio histogram.
</doc>
<group type="NXprogram"/>
<field name="min_mass_to_charge" type="NX_FLOAT" units="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}]`.
</doc>
</field>
<field name="max_mass_to_charge" type="NX_FLOAT" units="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}]`.
</doc>
</field>
<field name="n_mass_to_charge" type="NX_POSINT" units="NX_UNITLESS">
<doc>
The number of bins on the interval :math:`[{\frac{m}{q}}_{min}`,
{\frac{m}{q}}_{max}]`.
</doc>
</field>
<group name="mass_spectrum" type="NXdata">
<doc>
A default histogram aka mass spectrum of
the mass-to-charge-state ratio values.
</doc>
</group>
</group>
<group name="background_quantification" type="NXprocess">
<doc>
Details of the background model that was used to
correct the total counts per bin into counts.
</doc>
<group type="NXprogram"/>
<field name="description" type="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.
</doc>
</field>
</group>
<group name="peak_search_and_deconvolution" type="NXprocess">
<doc>
How were peaks in the mass-to-charge-state ratio histogram identified.
</doc>
<group type="NXprogram"/>
<group type="NXpeak"/>
</group>
<group name="peak_identification" type="NXprocess">
<doc>
Details about how peaks, with taking into account
error models, were interpreted as ion types or not.
</doc>
<group type="NXprogram"/>
<field name="number_of_ion_types" type="NX_UINT" units="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.
</doc>
</field>
<field name="maximum_number_of_atoms_per_molecular_ion" type="NX_UINT" units="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. &lt;https://doi.org/10.1017/S1431927621012241&gt;`_).
</doc>
</field>
<group type="NXatom"/>
</group>
</definition>
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