Fixes on NXms related dependent classes

nexusformat · Mar 20, 2023 · 02a61b5 · 02a61b5
1 parent 11be3ca
commit 02a61b5
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Showing 8 changed files with 16 additions and 32 deletions.
diff --git a/contributed_definitions/NXms.nxdl.xml b/contributed_definitions/NXms.nxdl.xml
@@ -238,7 +238,7 @@
             <group name="grid" type="NXcg_grid" optional="true"/>
             <group name="polyhedron_set" type="NXcg_polyhedron_set" optional="true"/>
             <group name="point_set" type="NXcg_point_set" optional="true"/>
-            <group name="boundary" type="NXcg_hexadedron_set" optional="true">
+            <group name="boundary" type="NXcg_hexahedron_set" optional="true">
                 <doc>
                      A boundary to the volume element.
                      Either an instance of NXcg_hexahedron_set or of NXcg_ellipsoid_set.
@@ -396,7 +396,7 @@
                                     <dim index="1" value="c"/>
                                 </dimensions>
                             </field>
-                            <field name="integration_radius" type="NX_NUMBER" units="NX_DEGREE">
+                            <field name="integration_radius" type="NX_NUMBER" units="NX_ANGLE">
                                 <doc>
                                      The portion of orientation space integrated over
                                      to compute the volume fraction.

diff --git a/contributed_definitions/NXatom_set.nxdl.xml → ...ibuted_definitions/NXms_atom_set.nxdl.xml b/contributed_definitions/NXatom_set.nxdl.xml → ...ibuted_definitions/NXms_atom_set.nxdl.xml
@@ -21,7 +21,7 @@
 #
 # 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="NXatom_set" extends="NXobject" type="group" 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" name="NXms_atom_set" extends="NXobject" type="group" 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.

diff --git a/contributed_definitions/NXms_score_results.nxdl.xml b/contributed_definitions/NXms_score_results.nxdl.xml
@@ -479,7 +479,7 @@
                         <doc>
                              Current grain-related quantities.
                         </doc>
-                        <field name="euler" type="NX_NUMBER" optional="true" units="NX_DEGREE">
+                        <field name="euler" type="NX_NUMBER" optional="true" units="NX_ANGLE">
                             <doc>
                                  Bunge-Euler angle triplets for each grain.
                             </doc>

diff --git a/contributed_definitions/nyaml/NXms.yaml b/contributed_definitions/nyaml/NXms.yaml
@@ -210,7 +210,7 @@ NXms:  # (NXannealing)
         exists: optional
       point_set(NXcg_point_set):  # how to model either or case?
         exists: optional
-      boundary(NXcg_hexadedron_set):  # how to model either or case?
+      boundary(NXcg_hexahedron_set):  # how to model either or case?
         exists: optional
         doc: |
           A boundary to the volume element.
@@ -405,7 +405,7 @@ NXms:  # (NXannealing)
                 doc: |
                   The portion of orientation space integrated over
                   to compute the volume fraction.
-                unit: NX_DEGREE
+                unit: NX_ANGLE
                 dimensions:
                   rank: 1
                   dim: [[1, c]]

diff --git a/...ributed_definitions/nyaml/NXatom_set.yaml → ...uted_definitions/nyaml/NXms_atom_set.yaml b/...ributed_definitions/nyaml/NXatom_set.yaml → ...uted_definitions/nyaml/NXms_atom_set.yaml
@@ -3,7 +3,7 @@ doc: |
   A base class to wrap details about a spatial configuration of atoms.
 symbols:
   doc: The symbols used in the schema to specify e.g. dimensions of arrays.
-NXatom_set:
+NXms_atom_set:
   (NXcg_point_set):
     doc: Atom positions.
     # the application-definition specific NXcg_point_set instance

diff --git a/contributed_definitions/nyaml/NXms_score_results.yaml b/contributed_definitions/nyaml/NXms_score_results.yaml
@@ -417,7 +417,7 @@ NXms_score_results:
               exists: optional
               doc: |
                 Bunge-Euler angle triplets for each grain.
-              unit: NX_DEGREE
+              unit: NX_ANGLE
               dimensions:
                 rank: 2
                 dim: [[1, n_grains], [2, 3]]

diff --git a/manual/source/cgms-structure.rst b/manual/source/cgms-structure.rst
@@ -193,24 +193,21 @@ to hold metadata for these features:
     :ref:`NXclustering`:
         A description for clustering of objects (such as atoms or features).
 
-    :ref:`NXatom_set`:
-        A set of atoms.
-
     :ref:`NXorientation_set`:
         A set of rotations to describe the relative orientation of members of a set of features/objects.
 
     :ref:`NXslip_system_set`:
         Metadata to a set of slip system/slip system family for
         a given crystal structure.
 
-..    :ref:`NXms_point_defect_set`:
-..        Metadata to a set of point defects.
+    :ref:`NXms_atom_set`:
+        Metadata to a set of atoms.
 
-..     :ref:`NXms_dislocation_set`:
-..        Metadata of a set of dislocation/disconnection (line) defects.
+    :ref:`NXms_dislocation_set`:
+        Metadata of a set of dislocation/disconnection (line) defects.
 
-..    :ref:`NXms_interface_set`:
-..        Metadata to a set of interfaces between crystals.
+    :ref:`NXms_interface_set`:
+        Metadata to a set of interfaces between crystals.
 
     :ref:`NXms_crystal_set`:
         A set of crystals, for e.g. a polycrystal, phases, 

diff --git a/manual/source/em-structure.rst b/manual/source/em-structure.rst
@@ -70,17 +70,7 @@ We developed entirely new base classes. Some of them are also used for other tec
     :ref:`NXibeam_column`:
         A base class serving the possibility to group the components relevant for generating and shaping an ion beam of an instrument to offer focused ion beam (milling) capabilities.
 
-    :ref:`NXimage_set_em_adf`
-    :ref:`NXimage_set_em_bf`
-    :ref:`NXimage_set_em_bse`
-    :ref:`NXimage_set_em_chamber`
-    :ref:`NXimage_set_em_df`
-    :ref:`NXimage_set_em_diffrac`
-    :ref:`NXimage_set_em_ecci`
-    :ref:`NXimage_set_em_kikuchi`
-    :ref:`NXimage_set_em_ronchigram`
-    :ref:`NXimage_set_em_se`
-    :ref:`NXimage_set_em`:
+    :ref:`NXimage_set_em_adf`, :ref:`NXimage_set_em_bf`, :ref:`NXimage_set_em_bse`, :ref:`NXimage_set_em_chamber`, :ref:`NXimage_set_em_df`, :ref:`NXimage_set_em_diffrac`, :ref:`NXimage_set_em_ecci`, :ref:`NXimage_set_em_kikuchi`, :ref:`NXimage_set_em_ronchigram`, :ref:`NXimage_set_em_se`, :ref:`NXimage_set_em`:
         Base classes for storing acquisition details for individual images or stacks of images collected via using e.g. different imaging modes. The suffixes specify **adf** annular dark field, **bf** bright field, **bse** backscattered electron, **chamber** camera to monitor the stage and chamber, **df** darkfield, **diffrac** diffraction, **ecci** electron channeling contrast imaging, **kikuchi** electron backscatter diffraction (EBSD), **ronchigram** - convergent beam diffraction pattern, **se** secondary electron, and **generic** images.
 
     :ref:`NXinteraction_vol_em`:
@@ -108,10 +98,7 @@ We developed entirely new base classes. Some of them are also used for other tec
     :ref:`NXscanbox_em`:
         A base class to represent the component of an electron microscope which realizes a controlled deflection (and eventually shift, blanking, and/or descanning) of the electron beam to illuminate the specimen in a controlled manner. This can be used to document the scan pattern.
 
-    :ref:`NXspectrum_set_em_eels`
-    :ref:`NXspectrum_set_em_xray`
-    :ref:`NXspectrum_set_em_auger`
-    :ref:`NXspectrum_set_em_cathodolum`:
+    :ref:`NXspectrum_set_em_eels`, :ref:`NXspectrum_set_em_xray`, :ref:`NXspectrum_set_em_auger`, :ref:`NXspectrum_set_em_cathodolum`:
         Base classes comparable to NXimage_set_em but for different techniques resulting in spectra. The suffixes specify **eels** electron energy loss spectroscopy, **xray** X-ray spectroscopy (EDS/STEM, EDX, SEM/EDX, SEM/EDS), **auger** Auger spectroscopy, and **cathodolum** cathodoluminescence.
 
     :ref:`NXstage_lab`: