Merge pull request #278 from FAIRmat-NFDI/sprint23_em_v3

Sprint23 EM v3 and microstructure replacing #267 and #270
FAIRmat-NFDI · Sep 11, 2024 · 05df4f0 · 05df4f0
2 parents 5a3e07d + 890c785
commit 05df4f0
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
       max-parallel: 5
     env:
       python_version: ${{ matrix.python-version }}

diff --git a/contributed_definitions/NXaberration.nxdl.xml b/contributed_definitions/NXaberration.nxdl.xml
@@ -25,12 +25,12 @@
     <doc>
          Quantified aberration coefficient in an aberration_model.
     </doc>
-    <field name="magnitude" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="magnitude" type="NX_NUMBER" units="NX_ANY">
         <doc>
              Value of the aberration coefficient.
         </doc>
     </field>
-    <field name="uncertainty" type="NX_NUMBER" units="NX_LENGTH">
+    <field name="uncertainty" type="NX_NUMBER" units="NX_ANY">
         <doc>
              Uncertainty of the value of the aberration coefficient
              according to uncertainty_model.

diff --git a/contributed_definitions/NXaberration_model.nxdl.xml b/contributed_definitions/NXaberration_model.nxdl.xml
diff --git a/contributed_definitions/NXaberration_model_ceos.nxdl.xml b/contributed_definitions/NXaberration_model_ceos.nxdl.xml
diff --git a/contributed_definitions/NXaberration_model_nion.nxdl.xml b/contributed_definitions/NXaberration_model_nion.nxdl.xml
diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml
@@ -201,7 +201,7 @@ the appdef definition here is nothing else then the documentation of this for a
             </enumeration>
         </field>
         <group type="NXuser" recommended="true">
-            <field name="name" type="NX_CHAR" recommended="true"/>
+            <field name="name" type="NX_CHAR" optional="true"/>
             <group name="identifier" type="NXidentifier" recommended="true">
                 <field name="service" type="NX_CHAR"/>
                 <field name="identifier" type="NX_CHAR"/>
@@ -226,7 +226,7 @@ the appdef definition here is nothing else then the documentation of this for a
                  used which are then arranged and documented with a description of the
                  workflow so that actionable graphs become instantiatable.
             </doc>
-            <field name="method" type="NX_CHAR">
+            <field name="type" type="NX_CHAR">
                 <doc>
                      A qualifier whether the sample is a real one
                      or a virtual one (in a computer simulation).
@@ -358,7 +358,7 @@ schema for heat treatment
             </group>
         </group>
         <group name="specimen" type="NXsample">
-            <field name="method" type="NX_CHAR">
+            <field name="type" type="NX_CHAR">
                 <doc>
                      A qualifier whether the specimen is a real one or a virtual one.
                 </doc>
@@ -664,31 +664,31 @@ NEW ISSUE: add section for propagation_delay(NXprocess) ?
 NEW ISSUE: make recon an own subentry NXapm_reconstruction
 NEW ISSUE: different algorithms used one could create a class for each reconstruction method
 NEW ISSUE: make this rather an own subentry NXapm_ranging-->
-            <group name="initial_specimen" type="NXimage_r_set" recommended="true">
+            <group name="initial_specimen" type="NXimage_set" recommended="true">
                 <doc>
                      SEM or TEM image of the initial specimen i.e.
                      ideally taken prior to the data acquisition.
                 </doc>
-                <group name="image_twod" type="NXdata">
+                <group name="image_2d" type="NXdata">
                     <attribute name="signal" type="NX_CHAR"/>
                     <attribute name="axes" type="NX_CHAR"/>
                     <attribute name="AXISNAME_indices" type="NX_CHAR"/>
-                    <field name="intensity" type="NX_NUMBER"/>
-                    <field name="axis_y" type="NX_NUMBER">
+                    <field name="real" type="NX_NUMBER"/>
+                    <field name="axis_j" type="NX_NUMBER">
                         <dimensions rank="1">
-                            <dim index="1" value="n_y"/>
+                            <dim index="1" value="n_j"/>
                         </dimensions>
                         <attribute name="long_name" type="NX_CHAR"/>
                     </field>
-                    <field name="axis_x" type="NX_NUMBER">
+                    <field name="axis_i" type="NX_NUMBER">
                         <dimensions rank="1">
-                            <dim index="1" value="n_x"/>
+                            <dim index="1" value="n_i"/>
                         </dimensions>
                         <attribute name="long_name" type="NX_CHAR"/>
                     </field>
                 </group>
             </group>
-            <!--one could use a stack_threed(NXdata) to record
+            <!--one could use a stack_3d(NXdata) to record
 a time series of the specimen shape evolution-->
             <group name="raw_data" type="NXprocess" recommended="true">
                 <field name="sequence_index" type="NX_POSINT" recommended="true"/>

diff --git a/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml b/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml
@@ -36,6 +36,11 @@
                  Maximum number of allowed atoms per (molecular) ion (fragment).
             </doc>
         </symbol>
+        <symbol name="n_variable">
+            <doc>
+                 Number of entries
+            </doc>
+        </symbol>
     </symbols>
     <doc>
          Base class to document an algorithm for recovering charge state and nuclide composition of a (molecular) ion.
@@ -76,7 +81,7 @@ input/config-->
              analysis may become very time consuming!
         </doc>
         <dimensions rank="1">
-            <dim index="1" value="i"/>
+            <dim index="1" value="n_variable"/>
         </dimensions>
     </field>
     <field name="mass_to_charge_range" type="NX_FLOAT" units="NX_ANY">

diff --git a/contributed_definitions/NXapm_hit_finding.nxdl.xml b/contributed_definitions/NXapm_hit_finding.nxdl.xml
@@ -94,7 +94,7 @@
         </dimensions>
         <attribute name="depends_on" type="NX_CHAR">
             <doc>
-                 The instance of :ref:`NXcoordinate_system` in which the positions are defined.
+                 Defines in which reference frame the positions are defined.
             </doc>
         </attribute>
     </field>

diff --git a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml
@@ -26,6 +26,11 @@
         <doc>
              The symbols used in the schema to specify e.g. dimensions of arrays.
         </doc>
+        <symbol name="n_variable">
+            <doc>
+                 Number of entries
+            </doc>
+        </symbol>
     </symbols>
     <doc>
          Application definition for a configuration file of the paraprobe-intersector tool.
@@ -181,7 +186,7 @@
                              automatically.
                         </doc>
                         <dimensions rank="1">
-                            <dim index="1" value="i"/>
+                            <dim index="1" value="n_variable"/>
                         </dimensions>
                     </field>
                 </group>
@@ -246,7 +251,7 @@
                              automatically.
                         </doc>
                         <dimensions rank="1">
-                            <dim index="1" value="i"/>
+                            <dim index="1" value="n_variable"/>
                         </dimensions>
                     </field>
                 </group>