Regenerate nxdls

# Conflicts: # contributed_definitions/NXapm.nxdl.xml # contributed_definitions/NXapm_charge_state_analysis.nxdl.xml # contributed_definitions/NXapm_hit_finding.nxdl.xml # contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml # contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml # contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml # contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml # contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml # contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_tool_results.nxdl.xml # contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml # contributed_definitions/NXapm_ranging.nxdl.xml # contributed_definitions/NXapm_reconstruction.nxdl.xml # contributed_definitions/NXapm_volt_and_bowl.nxdl.xml # contributed_definitions/NXcg_alpha_complex.nxdl.xml # contributed_definitions/NXcg_cylinder_set.nxdl.xml # contributed_definitions/NXcg_face_list_data_structure.nxdl.xml # contributed_definitions/NXcg_grid.nxdl.xml # contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml # contributed_definitions/NXcg_hexahedron_set.nxdl.xml # contributed_definitions/NXcg_parallelogram_set.nxdl.xml # contributed_definitions/NXcg_point_set.nxdl.xml # contributed_definitions/NXcg_polyline_set.nxdl.xml # contributed_definitions/NXcg_sphere_set.nxdl.xml # contributed_definitions/NXcorrector_cs.nxdl.xml # contributed_definitions/NXdelocalization.nxdl.xml # contributed_definitions/NXem_conventions.nxdl.xml # contributed_definitions/NXem_ebsd.nxdl.xml # contributed_definitions/NXem_eds.nxdl.xml # contributed_definitions/NXevent_data_apm.nxdl.xml # contributed_definitions/NXgraph_edge_set.nxdl.xml # contributed_definitions/NXimage_c_set.nxdl.xml # contributed_definitions/NXimage_r_set.nxdl.xml # contributed_definitions/NXion.nxdl.xml # contributed_definitions/NXms_feature_set.nxdl.xml # contributed_definitions/NXoptical_system_em.nxdl.xml # contributed_definitions/NXpulser_apm.nxdl.xml # contributed_definitions/NXrotation_set.nxdl.xml # contributed_definitions/NXscanbox_em.nxdl.xml # contributed_definitions/NXsimilarity_grouping.nxdl.xml # contributed_definitions/NXspectrum_set.nxdl.xml
FAIRmat-NFDI · Dec 11, 2024 · 2cb86dc · 2cb86dc
1 parent a882d73
commit 2cb86dc
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Showing 26 changed files with 128 additions and 102 deletions.
diff --git a/contributed_definitions/NXcg_polygon_set.nxdl.xml b/contributed_definitions/NXcg_polygon_set.nxdl.xml
@@ -46,7 +46,9 @@ descriptors.-->
             </doc>
         </symbol>
     </symbols>
-    <!--somewhat redundant as there is NXoff_geometry but easier to understand-->
+    <!--
+somewhat redundant as there is NXoff_geometry but easier to understand
+-->
     <doc>
          Computational geometry description of a set of polygons in Euclidean space.
 
@@ -121,7 +123,7 @@ properties of the polygon primitives-->
         <doc>
              The accumulated length of the polygon edge.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
@@ -132,7 +134,7 @@ properties of the polygon primitives-->
              edges of the vertex according to the sequence in the polygons array.
              Usually, the winding_order field is required to interpret the value.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_total"/>
         </dimensions>
     </field>
@@ -144,7 +146,7 @@ properties of the polygon primitives-->
              * 1 - convex,
              * 2 - concave
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>

diff --git a/contributed_definitions/NXcg_primitive_set.nxdl.xml b/contributed_definitions/NXcg_primitive_set.nxdl.xml
@@ -109,15 +109,15 @@ to enable an instantiation of the actual geometric primitives-->
         <doc>
              Identifier of each member for explicit indexing.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
     <field name="center" type="NX_NUMBER" units="NX_ANY">
         <doc>
              The center of mass position of each primitive.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="d"/>
         </dimensions>
@@ -127,15 +127,15 @@ to enable an instantiation of the actual geometric primitives-->
         <doc>
              True if the center is a center of mass.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
     <field name="shape" type="NX_NUMBER" units="NX_LENGTH">
         <doc>
              A qualitative description of the shape of each primitive.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="d"/>
         </dimensions>
@@ -147,7 +147,7 @@ to enable an instantiation of the actual geometric primitives-->
              Often the term length is associated with the assumption that one
              edge is parallel to an axis of the coordinate system.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
@@ -156,15 +156,15 @@ to enable an instantiation of the actual geometric primitives-->
              Qualifier often used to describe the length of one characteristic edge
              within the coordinate system.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
     <field name="is_closed" type="NX_BOOLEAN">
         <doc>
              True if primitive is closed such that it has properties like area or volume.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
@@ -174,7 +174,7 @@ to enable an instantiation of the actual geometric primitives-->
 
              Set to NaN if does not apply for primitives for which is_closed is False.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
@@ -184,7 +184,7 @@ to enable an instantiation of the actual geometric primitives-->
 
              Set to NaN if does not apply for primitives for which is_closed is False.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>
@@ -196,7 +196,7 @@ to enable an instantiation of the actual geometric primitives-->
              Use the depends_on attribute to specify in which coordinate system
              these direction unit vectors are defined.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="d"/>
         </dimensions>

diff --git a/contributed_definitions/NXcg_tetrahedron_set.nxdl.xml b/contributed_definitions/NXcg_tetrahedron_set.nxdl.xml
@@ -93,7 +93,7 @@ from MarDI, for now let's assume we do not need polytopes for d > 3-->
         <doc>
              Area of each of the four triangular faces of each tetrahedron.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="4"/>
         </dimensions>
@@ -102,7 +102,7 @@ from MarDI, for now let's assume we do not need polytopes for d > 3-->
         <doc>
              Length of each edge of each tetrahedron.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="6"/>
         </dimensions>

diff --git a/contributed_definitions/NXcg_triangle_set.nxdl.xml b/contributed_definitions/NXcg_triangle_set.nxdl.xml
@@ -99,7 +99,7 @@ properties of triangles-->
              reported for the edges traversed according to the sequence
              in which vertices are indexed in triangles.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="3"/>
         </dimensions>
@@ -110,7 +110,7 @@ properties of triangles-->
              reported for the angle opposite to the edges which are traversed
              according to the sequence in which vertices are indexed in triangles.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="3"/>
         </dimensions>

diff --git a/contributed_definitions/NXcg_unit_normal_set.nxdl.xml b/contributed_definitions/NXcg_unit_normal_set.nxdl.xml
@@ -49,7 +49,7 @@ rather make this a set of vectors, irrespective whether these are unit or not-->
         <doc>
              Direction of each normal
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="c"/>
             <dim index="2" value="d"/>
         </dimensions>
@@ -63,7 +63,7 @@ rather make this a set of vectors, irrespective whether these are unit or not-->
              * 1 - outer
              * 2 - inner
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="c"/>
         </dimensions>
     </field>

diff --git a/contributed_definitions/NXcoordinate_system.nxdl.xml b/contributed_definitions/NXcoordinate_system.nxdl.xml
@@ -88,7 +88,7 @@ https://www.zenodo.org/record/3526738/files/lyso009a_0087.JF07T32V01_master.h5?d
              This axis is frequently referred to as the x-axis in real space and
              the i-axis in reciprocal space.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="3"/>
         </dimensions>
     </field>
@@ -112,7 +112,7 @@ https://www.zenodo.org/record/3526738/files/lyso009a_0087.JF07T32V01_master.h5?d
              This axis is frequently referred to as the y-axis in real space and
              the j-axis in reciprocal space.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="3"/>
         </dimensions>
     </field>
@@ -136,7 +136,7 @@ https://www.zenodo.org/record/3526738/files/lyso009a_0087.JF07T32V01_master.h5?d
              This axis is frequently referred to as the z-axis in real space and
              the k-axis in reciprocal space.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="3"/>
         </dimensions>
     </field>

diff --git a/contributed_definitions/NXcrystal_structure.nxdl.xml b/contributed_definitions/NXcrystal_structure.nxdl.xml
@@ -81,7 +81,7 @@ used algorithm. Dictionary-based alternatives are emerging.-->
         <doc>
              Crystallography unit cell parameters a, b, and c.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="d"/>
         </dimensions>
     </field>
@@ -90,7 +90,7 @@ used algorithm. Dictionary-based alternatives are emerging.-->
         <doc>
              Crystallography unit cell parameters alpha, beta, and gamma.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="d"/>
         </dimensions>
     </field>
@@ -186,7 +186,7 @@ used algorithm. Dictionary-based alternatives are emerging.-->
         <doc>
              Label for each atom position.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_pos"/>
         </dimensions>
     </field>
@@ -197,7 +197,7 @@ used algorithm. Dictionary-based alternatives are emerging.-->
              of each isotope respectively. Z and N have to be 8-bit unsigned integers.
              For the rationale behind this `M. Kühbach et al. (2021) &lt;https://doi.org/10.1017/S1431927621012241&gt;`_
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_pos"/>
         </dimensions>
     </field>
@@ -206,7 +206,7 @@ used algorithm. Dictionary-based alternatives are emerging.-->
         <doc>
              Atom positions.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="n_pos"/>
             <dim index="2" value="d"/>
         </dimensions>
@@ -223,7 +223,7 @@ to describe the simulated Kikuchi pattern generated from such a model-->
         <doc>
              Relative occupancy of the atom position.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_pos"/>
         </dimensions>
     </field>
@@ -243,7 +243,7 @@ to describe the simulated Kikuchi pattern generated from such a model-->
              Miller indices refer to the Cartesian right-handed coordinate system
              of the unit cell.
         </doc>
-        <dimensions>
+        <dimensions rank="2">
             <dim index="1" value="n_hkl"/>
             <dim index="2" value="6"/>
         </dimensions>
@@ -252,15 +252,15 @@ to describe the simulated Kikuchi pattern generated from such a model-->
         <doc>
              Spacing between crystallographic planes as defined by field miller.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_hkl"/>
         </dimensions>
     </field>
     <field name="relative_intensity" type="NX_NUMBER" units="NX_DIMENSIONLESS">
         <doc>
              Relative intensity of the signal for the plane.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_hkl"/>
         </dimensions>
     </field>

diff --git a/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml b/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml
@@ -86,7 +86,7 @@
              The unsigned integer array representing the content of the mask.
              If padding is used the padded bits have to be set to 0.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_total"/>
         </dimensions>
     </field>
@@ -97,7 +97,7 @@
              to the first identifier, the second bit in the mask to the second
              identifier and so on and so forth.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_object"/>
         </dimensions>
     </field>

diff --git a/contributed_definitions/NXcs_profiling_event.nxdl.xml b/contributed_definitions/NXcs_profiling_event.nxdl.xml
@@ -80,15 +80,15 @@
         <doc>
              Maximum amount of virtual memory allocated per process during the event.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_processes"/>
         </dimensions>
     </field>
     <field name="max_resident_memory_snapshot" type="NX_NUMBER" units="NX_ANY">
         <doc>
              Maximum amount of resident memory allocated per process during the event.
         </doc>
-        <dimensions>
+        <dimensions rank="1">
             <dim index="1" value="n_processes"/>
         </dimensions>
     </field>

diff --git a/contributed_definitions/NXem.nxdl.xml b/contributed_definitions/NXem.nxdl.xml
@@ -517,12 +517,14 @@ NEW ISSUE: will be added by yaml2nxdl automatically-->
             </field>
         </group>
         <group name="sample" type="NXsample">
-            <!--NEW ISSUE: inject the conclusion from the discussion with Andrea
+            <!--
+NEW ISSUE: inject the conclusion from the discussion with Andrea
 according to SAMPLE.yaml 0f8df14 2022/06/15
 ID: -> maps to name
 name: -> short_title
 user: -> not matched right now
-citation: doi ->why relevant, should be solved by RDMS-->
+citation: doi ->why relevant, should be solved by RDMS
+-->
             <doc>
                  A description of the material characterized in the experiment.
                  Sample and specimen are threaded as de facto synonyms.

diff --git a/contributed_definitions/NXem_adf.nxdl.xml b/contributed_definitions/NXem_adf.nxdl.xml
@@ -55,7 +55,7 @@
             <doc>
                  Annulus inner (first value) and outer (second value) half angle.
             </doc>
-            <dimensions>
+            <dimensions rank="1">
                 <dim index="1" value="2"/>
             </dimensions>
         </field>

diff --git a/contributed_definitions/NXem_conventions_ebsd.nxdl.xml b/contributed_definitions/NXem_conventions_ebsd.nxdl.xml
@@ -22,7 +22,9 @@
 # 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="NXem_conventions_ebsd" extends="NXem_conventions" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
-    <!--symbols:-->
+    <!--
+symbols:
+-->
     <doc>
          Base class for method-specific conventions EBSD.
 

diff --git a/contributed_definitions/NXem_correlation.nxdl.xml b/contributed_definitions/NXem_correlation.nxdl.xml
@@ -181,7 +181,7 @@
                 <doc>
                      Descriptor values displaying the ROI.
                 </doc>
-                <dimensions>
+                <dimensions rank="3">
                     <dim index="1" value="n_z"/>
                     <dim index="2" value="n_y"/>
                     <dim index="3" value="n_x"/>
@@ -199,7 +199,7 @@ while for _indices fastest to fast-->
                 <doc>
                      Calibrated coordinate along the z-axis.
                 </doc>
-                <dimensions>
+                <dimensions rank="1">
                     <dim index="1" value="n_z"/>
                 </dimensions>
                 <attribute name="long_name">
@@ -212,7 +212,7 @@ while for _indices fastest to fast-->
                 <doc>
                      Calibrated coordinate along the y-axis.
                 </doc>
-                <dimensions>
+                <dimensions rank="1">
                     <dim index="1" value="n_y"/>
                 </dimensions>
                 <attribute name="long_name">
@@ -225,7 +225,7 @@ while for _indices fastest to fast-->
                 <doc>
                      Calibrated coordinate along the x-axis.
                 </doc>
-                <dimensions>
+                <dimensions rank="1">
                     <dim index="1" value="n_x"/>
                 </dimensions>
                 <attribute name="long_name">