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/NXatom.nxdl.xml

@@ -0,0 +1,133 @@
+<?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. Ions can be molecular ions.
+    </doc>
+    <field name="name" type="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 +.
+        </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.
+            Care needs to be exercised with respect to the integration.
+            `T. A. Manz &lt;10.1039/c6ra04656h&gt;`_ and `N. G. Limas &lt;10.1039/C6RA05507A&gt;`_ discuss 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. 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 &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 volume
+            that is unique as a some cut-off criterion is required.
+        </doc>
+    </field>
+    <!--<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>

base_classes/NXbeam.nxdl.xml

@@ -184,7 +184,7 @@
             If applicable, the first dimension shall represent the extent
             in the direction parallel to the azimuthal reference plane
             (by default it is [1,0,0]), and the second dimension shall be
-            the normal to the reference plane (by default it is  [0,1,0]).
+            the normal to the reference plane (by default it is [0,1,0]).
         </doc>
         <dimensions rank="2">
             <dim index="1" value="nP"/>
@@ -203,13 +203,49 @@
             <dim index="1" value="nP"/>
             <dim index="2" value="2"/>
         </dimensions>
+        <attribute name="units" type="NX_CHAR">
+            <doc>
+                 The units for this observable are not included in the NIAC list.
+                 Responsibility on correct formatting and parsing is handed to the user
+                 by using `NX_ANY`. Correct parsing can still be implemented by using
+                 this attribute.
+
+                 | Fill with:
+
+                 * The unit unidata symbol if the unit has one (Example: T for the unit of magnetic flux density tesla).
+                 * The unit unidata name if the unit has a name (Example: farad for capacitance).
+                 * A string describing the units according to unidata unit operation notation, if the unit is a complex combination of named units and
+                   does not have a name.
+
+                 Example: for lightsource brilliance (SI) 1/(s.mm2.mrad2).
+                 Here: SI units are V2/m2.
+            </doc>
+        </attribute>
     </field>
     <field name="final_polarization" type="NX_NUMBER" units="NX_ANY">
         <doc>Polarization vector on leaving beamline component</doc>
         <dimensions rank="2">
             <dim index="1" value="nP"/>
             <dim index="2" value="2"/>
         </dimensions>
+        <attribute name="units" type="NX_CHAR">
+            <doc>
+                 The units for this observable are not included in the NIAC list.
+                 Responsibility on correct formatting and parsing is handed to the user
+                 by using `NX_ANY`. Correct parsing can still be implemented by using
+                 this attribute.
+
+                 | Fill with:
+
+                 * The unit unidata symbol if the unit has one (Example: T for the unit of magnetic flux density tesla).
+                 * The unit unidata name if the unit has a name (Example: farad for capacitance).
+                 * A string describing the units according to unidata unit operation notation, if the unit is a complex combination of named units and
+                   does not have a name.
+
+                 Example: for lightsource brilliance (SI) 1/(s.mm2.mrad2).
+                 Here: SI units are V2/m2.
+            </doc>
+        </attribute>
     </field>
     <field name="incident_polarization_stokes" type="NX_NUMBER" units="NX_ANY">
         <doc>

base_classes/NXcalibration.nxdl.xml

@@ -62,7 +62,7 @@
     <group name="calibration_object" type="NXnote">
         <doc>
              A file serialisation of a calibration which may not be publicly available (externally from the NeXus file).
-             
+
              This metadata can be a documentation of the source (file) or database (entry) from which pieces
              of information have been extracted for consumption (e.g. in a research data management system (RDMS)).
              It is also possible to include the actual file by using the `file` field.
@@ -92,10 +92,10 @@
                  The symbol of the axis to be used in the fit_function, e.g., `energy`, `E`.
                  This should comply to the following naming rules (similar to python's naming rules):
 
-                   * A variable name must start with a letter or the underscore character
-                   * A variable name cannot start with a number
-                   * A variable name can only contain alpha-numeric characters and underscores (A-z, 0-9, and _ )
-                   * Variable names are case-sensitive (age, Age and AGE are three different variables)
+                 * A variable name must start with a letter or the underscore character
+                 * A variable name cannot start with a number
+                 * A variable name can only contain alpha-numeric characters and underscores (A-z, 0-9, and _ )
+                 * Variable names are case-sensitive (age, Age and AGE are three different variables)
             </doc>
         </attribute>
         <attribute name="input_path">
@@ -157,7 +157,6 @@
 
              For a more detailed description of scaling factors, see 
              :ref:`/NXdata/FIELDNAME_scaling_factor &lt;/NXdata/FIELDNAME_scaling_factor-field&gt;`.
-
         </doc>
     </field>
     <field name="offset" type="NX_FLOAT" units="NX_ANY">

contributed_definitions/NXadc.nxdl.xml → base_classes/NXcg_ellipsoid_set.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)
-# 
+#
 # 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
@@ -21,18 +21,45 @@
 #
 # 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" name="NXadc" extends="NXobject" type="group" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+<!--
+redundant as there is NXcsg, and NXquadric but easier to understand-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_ellipsoid_set" extends="NXcg_primitive_set" 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="d">
+            <doc>
+                 The dimensionality of the space in which the members are assumed embedded.
+            </doc>
+        </symbol>
+        <symbol name="c">
+            <doc>
+                 The cardinality of the set, i.e. the number of members.
+            </doc>
+        </symbol>
     </symbols>
     <doc>
-         Analog-to-digital converter component/integrated circuit.
+         Computational geometry description of a set of ellipsoids.
     </doc>
-    <field name="value" type="NX_NUMBER" units="NX_UNITLESS">
+    <field name="half_axes_radius" type="NX_NUMBER" units="NX_LENGTH">
+        <doc>
+             Radius of the half axes.
+
+             Use if all ellipsoids in the set have the same half-axes.
+        </doc>
+        <dimensions rank="1">
+            <dim index="1" value="d"/>
+        </dimensions>
+    </field>
+    <field name="half_axes_radii" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
-             TBD.
+             Half-axes radii of each ellipsoid.
         </doc>
+        <dimensions rank="2">
+            <dim index="1" value="c"/>
+            <dim index="2" value="d"/>
+        </dimensions>
     </field>
+    <!--properties of ellipsoids-->
 </definition>