Fairmat 2024: proposal on electron microscopy (EM)

contributed_definitions/NXaberration.nxdl.xml → base_classes/NXaberration.nxdl.xml

@@ -1,10 +1,10 @@
-<?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
-# 
-# Copyright (C) 2014-2024 NeXus International Advisory Committee (NIAC)
-# 
+#
+# Copyright (C) 2014-2025 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
@@ -21,35 +21,49 @@
 #
 # 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" extends="NXobject" name="NXaberration" 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="NXaberration" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
          Quantified aberration coefficient in an aberration_model.
     </doc>
-    <field name="magnitude" type="NX_FLOAT" units="NX_LENGTH"/>
-    <field name="uncertainty" type="NX_FLOAT" units="NX_LENGTH">
+    <field name="magnitude" type="NX_NUMBER" units="NX_ANY">
+        <doc>
+             Magnitude of the aberration
+        </doc>
+    </field>
+    <field name="magnitude_errors" type="NX_NUMBER" units="NX_ANY">
         <doc>
-             Confidence
+             Uncertainty of the magnitude of the aberration
         </doc>
     </field>
-    <field name="uncertainty_model">
+    <field name="magnitude_errors_model" type="NX_CHAR">
         <doc>
-             How was the uncertainty quantified e.g. via the 95% confidence interval.
+             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_FLOAT" units="NX_TIME">
+    <field name="delta_time" type="NX_NUMBER" units="NX_TIME">
         <doc>
              Time elapsed since the last measurement.
         </doc>
     </field>
-    <field name="angle" type="NX_FLOAT" units="NX_ANGLE">
+    <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
+             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"/>
-    <field name="alias"/>
+    <field name="name" type="NX_CHAR">
+        <doc>
+             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.
+        </doc>
+    </field>
 </definition>

base_classes/NXactivity.nxdl.xml

@@ -0,0 +1,56 @@
+<?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) 2014-2024 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="NXactivity" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <doc>
+         A planned or unplanned action that has a temporal extension and for some time depends on some entity.
+
+         This class is planned be used in the future as the super class for all other activities if inheritance 
+         in base classes is supported in NeXus.
+    </doc>
+    <field name="start_time" type="NX_DATE_TIME">
+        <doc>
+             ISO 8601 formatted time code (with local time zone offset to UTC information
+             included) when this activity started.
+        </doc>
+    </field>
+    <field name="end_time" type="NX_DATE_TIME">
+        <doc>
+             ISO 8601 formatted time code (with local time zone offset to UTC information
+             included) when this activity ended.
+        </doc>
+    </field>
+    <field name="description">
+        <doc>
+             Short description of the activity.
+        </doc>
+    </field>
+    <group name="notes" type="NXnote">
+        <doc>
+             This can be any data or other descriptor acquired during the activity
+             (NXnote allows to add pictures, audio, movies). Alternatively, a
+             reference to the location or a unique identifier or other metadata file. In the
+             case these are not available, free-text description.
+        </doc>
+    </group>
+</definition>

base_classes/NXatom.nxdl.xml

@@ -0,0 +1,134 @@
+<?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) 2014-2025 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="NXatom" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <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. Such ion can be a molecular ion.
+    </doc>
+    <field name="name" type="NX_CHAR">
+        <doc>
+             Human-readable name for the set.
+
+             To provide an exemplar use case this field could 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 +.
+        </doc>
+    </field>
+    <field name="identifier_chemical" type="NX_CHAR">
+        <doc>
+             Identifier used to refer to if the set of atoms represents a substance.
+        </doc>
+        <enumeration>
+            <item value="inchi"/>
+        </enumeration>
+    </field>
+    <field name="charge" type="NX_NUMBER" units="NX_CHARGE">
+        <doc>
+             Signed net (partial) charge of the (molecular) ion.
+
+             Different methods for computing charge are in use and care
+             needs to be exercised with respect to the integration. See
+             `T. A. Manz &lt;10.1039/c6ra04656h&gt;`_ and `N. G. Limas &lt;10.1039/C6RA05507A&gt;`_ for computational details.
+        </doc>
+    </field>
+    <field name="charge_state" type="NX_NUMBER" units="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, like it 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 mass-to-charge-state-ratio interval. Details on ranging definition
+             files can be found in the literature `M. K. Miller &lt;https://doi.org/10.1002/sia.1719&gt;`_.
+        </doc>
+    </field>
+    <field name="volume" type="NX_NUMBER" units="NX_VOLUME">
+        <doc>
+             Assumed volume affected by the set of atoms.
+
+             Neither individual atoms nor a set of cluster of these have a uniquely defined volume
+             as a computation demands some cut-off criterion.
+        </doc>
+    </field>
+    <!--define NXapm_ion extending NXatom for the specific use case of atom probe
+geometry of the set
+<group type="NXcg_point"/>-->
+    <field name="identifier" type="NX_CHAR">
+        <doc>
+             Identifier for each atom at locations as detailed by position.
+        </doc>
+        <dimensions rank="1">
+            <dim index="1" value="n_pos"/>
+        </dimensions>
+    </field>
+    <field name="type" type="NX_UINT" units="NX_UNITLESS">
+        <doc>
+             Nuclide information for each atom at locations as detailed by position.
+
+             One `approach &lt;https://doi.org/10.1017/S1431927621012241&gt;`_ 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.
+        </doc>
+        <dimensions rank="1">
+            <dim index="1" value="n_pos"/>
+        </dimensions>
+    </field>
+    <field name="position" type="NX_NUMBER" units="NX_ANY">
+        <doc>
+             Position of each atom.
+        </doc>
+        <dimensions rank="2">
+            <dim index="1" value="n_pos"/>
+            <dim index="2" value="d"/>
+        </dimensions>
+        <attribute name="reference_frame" type="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).
+            </doc>
+        </attribute>
+    </field>
+    <field name="occupancy" type="NX_NUMBER" units="NX_DIMENSIONLESS">
+        <doc>
+             Relative occupancy of the atom position.
+
+             This field is useful for specifying the atomic motif in
+             instances of :ref:`NXunit_cell`.
+        </doc>
+        <dimensions rank="1">
+            <dim index="1" value="n_pos"/>
+        </dimensions>
+    </field>
+</definition>