FAIRmat-NFDI · mkuehbach · Jul 28, 2025 · Mar 27, 2025 · Mar 27, 2025 · Mar 27, 2025
diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt
diff --git a/applications/NXapm.nxdl.xml b/applications/NXapm.nxdl.xml
diff --git a/applications/NXem.nxdl.xml b/applications/NXem.nxdl.xml
diff --git a/applications/nyaml/NXapm.yaml b/applications/nyaml/NXapm.yaml
diff --git a/applications/nyaml/NXem.yaml b/applications/nyaml/NXem.yaml
diff --git a/...ributed_definitions/NXaberration.nxdl.xml → base_classes/NXaberration.nxdl.xml b/...ributed_definitions/NXaberration.nxdl.xml → base_classes/NXaberration.nxdl.xml
@@ -1,4 +1,4 @@
-<?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
@@ -23,47 +23,54 @@
 -->
 <definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXaberration" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
-         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. &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.
     </doc>
     <field name="magnitude" type="NX_NUMBER" units="NX_ANY">
         <doc>
-             Magnitude of the aberration
+            Magnitude of the aberration
         </doc>
     </field>
     <field name="magnitude_errors" type="NX_NUMBER" units="NX_ANY">
         <doc>
-             Uncertainty of the magnitude of the aberration
+            Uncertainty of the magnitude of the aberration
         </doc>
     </field>
     <field name="magnitude_errors_model" type="NX_CHAR">
         <doc>
-             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.
         </doc>
     </field>
     <field name="delta_time" type="NX_NUMBER" units="NX_TIME">
         <doc>
-             Time elapsed since the last measurement.
+            Time elapsed since the last measurement.
         </doc>
     </field>
     <field name="angle" type="NX_NUMBER" units="NX_ANGLE">
         <doc>
-             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.
         </doc>
     </field>
     <field name="name" type="NX_CHAR">
         <doc>
-             Given name to this aberration.
+            Given name to this aberration.
         </doc>
     </field>
     <field name="alias" type="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.
         </doc>
     </field>
 </definition>
diff --git a/base_classes/NXactuator.nxdl.xml b/base_classes/NXactuator.nxdl.xml
@@ -1,4 +1,4 @@
-<?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

diff --git a/base_classes/NXapm_charge_state_analysis.nxdl.xml b/base_classes/NXapm_charge_state_analysis.nxdl.xml
@@ -0,0 +1,155 @@
+<?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>
diff --git a/base_classes/NXapm_measurement.nxdl.xml b/base_classes/NXapm_measurement.nxdl.xml
@@ -0,0 +1,70 @@
+<?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>