Fairmat 2025 contributed emapmms

.cspell/custom-dictionary.txt

@@ -6,6 +6,8 @@ FIELDNAME
 GROUPNAME
 NAPI
 NIAC
+TASKCONFIG
+TASKPROCESSED
 UDUNITS
 UDunits
 UNKNOWNTYPE
@@ -29,6 +31,7 @@ mtex
 stylesheet
 textalpha
 varphi
+mathfrak
 
 # Words related to experimental techniques
 360-gons
@@ -621,6 +624,7 @@ Miessen
 Mießen
 Monajem
 Morawiec
+Nadal
 NCNR
 NFDI
 NION
@@ -642,6 +646,7 @@ Pawley
 Pedersen
 Peltier
 Pennycock
+Poac
 Popko
 Poschenrieder
 Preiß
@@ -704,7 +709,9 @@ invizo
 kanapy
 kuehbach
 laplace_ritchardson
+lepoac
 mkuehbach
+nadal
 nion
 orientation_rodrigues
 piola
@@ -801,4 +808,4 @@ asscociated
 dimensioness
 folowing
 reproducability
-Uncentrainties
+Uncentrainties

contributed_definitions/NXapm_compositionspace_config.nxdl.xml

@@ -42,13 +42,16 @@
         <group name="reconstruction" type="NXnote">
             <doc>
                 Specification of the tomographic reconstruction used for this analysis.
-                Typically, reconstructions in the field of atom probe tomography are communicated via
-                files which store at least reconstructed ion positions and mass-to-charge-state-ratio
-                values. Container files like HDF5 though can store multiple reconstructions.
-                Therefore, the position and mass_to_charge concepts point to specific instances
-                to use for this analysis.
+
+                Reconstructions in the field of atom probe tomography are communicated via
+                a file which stores the reconstructed position and mass-to-charge-state-ratio
+                value for each ion.
+
+                Container file formats like HDF5, such as NeXus/HDF5 files using :ref:`NXapm`,
+                can store multiple reconstructions. In this case, the position and mass_to_charge
+                concepts point to specific instances in the file referred to by file_name for the
+                analysis with CompositionSpace.
             </doc>
-            <field name="type" type="NX_CHAR" optional="true"/>
             <field name="file_name" type="NX_CHAR"/>
             <field name="checksum" type="NX_CHAR" recommended="true"/>
             <field name="algorithm" type="NX_CHAR" recommended="true"/>
@@ -60,7 +63,7 @@
             </field>
             <field name="mass_to_charge" type="NX_CHAR" optional="true">
                 <doc>
-                    Name of the node which resolves the mass-to-charge-state ratio
+                    Name of the node which resolves the mass-to-charge-state-ratio
                     values for each reconstructed ion to use for this analysis.
                 </doc>
             </field>
@@ -69,17 +72,24 @@
             <doc>
                 Specification of the ranging definitions used for this analysis.
 
-                Indices start from 1. The value 0 is reserved for the null model of unranged positions whose
-                iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset.
+                Ranging definitions in the field of atom probe tomography are communicated via
+                a file which stores the mass-to-charge-state-ratio interval and the number of elements
+                of which each (molecular) ion is composed. These values are stored for each ion.
+
+                Container file formats like HDF5, such as NeXus/HDF5 files using :ref:`NXapm`,
+                can store multiple ranging definitions.
+
+                Indices of ions start from 1. The value 0 is reserved for the null model of unranged positions
+                whose iontype is referred to as the unknown_type. The value 0 is also reserved for voxels
+                that lie outside the dataset.
             </doc>
-            <field name="type" type="NX_CHAR" optional="true"/>
             <field name="file_name" type="NX_CHAR"/>
             <field name="checksum" type="NX_CHAR" recommended="true"/>
             <field name="algorithm" type="NX_CHAR" recommended="true"/>
             <field name="ranging_definitions" type="NX_CHAR">
                 <doc>
-                    Name of the (parent) node directly below which the ranging definitions for
-                    (molecular) ions are stored.
+                    Name of that (parent) node whose child stores the ranging definitions that
+                    are applied in this analysis with CompositionSpace.
                 </doc>
             </field>
         </group>
@@ -131,8 +141,8 @@
         </group>
         <group name="segmentation" type="NXprocess">
             <doc>
-                Step during which the voxel set is segmented into voxel sets with different
-                chemical composition.
+                Step during which the voxel set is segmented into voxel sets
+                with different chemical composition.
             </doc>
             <group name="pca" type="NXprocess" optional="true">
                 <doc>
@@ -185,14 +195,14 @@
         </group>
     </group>
     <!--meshing(NXprocess):
-  doc: |
-     TODO
-  distance_cut(NX_NUMBER):
-    doc: |
-      TODO
-    units: NX_ANY
-  normal_end_length(NX_NUMBER):
-    doc: |
-      TODO
-    units: NX_ANY-->
+doc: |
+TODO
+distance_cut(NX_NUMBER):
+doc: |
+TODO
+units: NX_ANY
+normal_end_length(NX_NUMBER):
+doc: |
+TODO
+units: NX_ANY-->
 </definition>

contributed_definitions/NXapm_compositionspace_results.nxdl.xml

@@ -85,13 +85,12 @@
             <doc>
                 Configuration file that was used in this analysis.
             </doc>
-            <field name="type" type="NX_CHAR" optional="true"/>
             <field name="file_name" type="NX_CHAR"/>
             <field name="algorithm" type="NX_CHAR" recommended="true"/>
             <field name="checksum" type="NX_CHAR" recommended="true"/>
         </group>
         <!--results-->
-        <group type="NXuser" optional="true"/>
+        <group name="userID" type="NXuser" optional="true" nameType="partial"/>
         <group name="specimen" type="NXsample" recommended="true">
             <doc>
                 Contextualize back to the specimen from which the
@@ -135,7 +134,7 @@
                     <item value="1"/>
                 </enumeration>
             </field>
-            <group name="cg_grid" type="NXcg_grid">
+            <group name="grid" type="NXcg_grid">
                 <field name="dimensionality" type="NX_POSINT">
                     <enumeration>
                         <item value="3"/>
@@ -147,7 +146,7 @@
                         <dim index="1" value="grid_dim"/>
                     </dimensions>
                 </field>
-                <field name="symmetry">
+                <field name="symmetry" type="NX_CHAR">
                     <enumeration>
                         <item value="cubic"/>
                     </enumeration>
@@ -200,7 +199,7 @@
                     <dim index="1" value="n_voxels"/>
                 </dimensions>
             </field>
-            <group type="NXatom" minOccurs="1" maxOccurs="unbounded">
+            <group name="ionID" type="NXatom" nameType="partial" minOccurs="1" maxOccurs="unbounded">
                 <field name="name" type="NX_CHAR">
                     <doc>
                         Chemical symbol of the element from the periodic table.
@@ -291,8 +290,8 @@
                     </field>
                     <field name="axis_pca_dimension" type="NX_UINT" units="NX_UNITLESS">
                         <doc>
-                            Elements identifier matching those from ENTRY/voxelization/ION
-                            as the principal component analysis.
+                            Elements identifier matching those from ENTRY/voxelization/ionID
+                            used during the principal component analysis.
                         </doc>
                         <dimensions>
                             <dim index="1" value="i"/>
@@ -366,8 +365,9 @@
         <group name="clustering" type="NXprocess" minOccurs="0" maxOccurs="1">
             <doc>
                 Step during which the chemically segmented voxel sets are analyzed for their spatial organization
-                into different spatial clusters of voxels in the same chemical set but representing individual object
-                not-necessarily watertight or topologically closed objects built from individual voxels.
+                into different spatial clusters of voxels in the same chemical set but representing individual objects.
+                The objects are constructed from blobs of neighboring voxels.
+                The objects are not necessarily watertight or topologically closed.
             </doc>
             <field name="sequence_index" type="NX_POSINT">
                 <enumeration>

contributed_definitions/NXapm_paraprobe_clusterer_config.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="application" type="group" name="NXapm_paraprobe_clusterer_config" extends="NXobject" 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="application" type="group" name="NXapm_paraprobe_clusterer_config" extends="NXapm_paraprobe_tool_config" 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.
@@ -46,21 +46,15 @@
     <doc>
         Application definition for a configuration file of the paraprobe-clusterer tool.
 
-        This tool is part of the paraprobe-toolbox. Inspect :ref:`NXapm_paraprobe_tool_config` for details.
+        The tool paraprobe-clusterer evaluates how points cluster in space.
     </doc>
     <group type="NXentry" minOccurs="1" maxOccurs="1">
         <field name="definition" type="NX_CHAR">
-            <attribute name="version" type="NX_CHAR"/>
             <enumeration>
                 <item value="NXapm_paraprobe_clusterer_config"/>
             </enumeration>
         </field>
-        <field name="number_of_tasks" type="NX_UINT" units="NX_UNITLESS">
-            <doc>
-                How many cluster_analysis tasks should the tool execute.
-            </doc>
-        </field>
-        <group name="cameca_to_nexus" type="NXapm_paraprobe_tool_config" minOccurs="0" maxOccurs="1">
+        <group name="cameca_to_nexus" type="NXapm_paraprobe_tool_parameters" minOccurs="0" maxOccurs="1">
             <doc>
                 This process maps results from a cluster analysis made with IVAS / AP Suite
                 into an interoperable representation. IVAS / AP Suite usually exports such results
@@ -70,7 +64,6 @@
                 point numbers.
             </doc>
             <group name="reconstruction" type="NXnote">
-                <field name="type" type="NX_CHAR"/>
                 <field name="file_name" type="NX_CHAR"/>
                 <field name="checksum" type="NX_CHAR"/>
                 <field name="algorithm" type="NX_CHAR"/>
@@ -86,7 +79,6 @@
                     quadruplet encode the position of the ion. The fourth value is the integer identifier
                     of the cluster encoded as a floating point number.
                 </doc>
-                <field name="type" type="NX_CHAR"/>
                 <field name="file_name" type="NX_CHAR"/>
                 <field name="checksum" type="NX_CHAR"/>
                 <field name="algorithm" type="NX_CHAR"/>
@@ -108,82 +100,20 @@ evaporation_id a bitmask which identifies which of the positions
 in dataset/dataset/dataset_name_reconstruction where covered
 by the IVAS/APSuite cluster analysis. This can be useful to recover
 the region of interest.-->
-        <group name="cluster_analysisID" type="NXapm_paraprobe_tool_config" nameType="partial" minOccurs="0" maxOccurs="unbounded">
+        <group name="cluster_analysisID" type="NXapm_paraprobe_tool_parameters" nameType="partial" minOccurs="0" maxOccurs="unbounded">
             <doc>
                 This process performs a cluster analysis on a
                 reconstructed dataset or a ROI within it.
             </doc>
-            <group name="reconstruction" type="NXnote">
-                <field name="type" type="NX_CHAR"/>
-                <field name="file_name" type="NX_CHAR"/>
-                <field name="checksum" type="NX_CHAR"/>
-                <field name="algorithm" type="NX_CHAR"/>
-                <field name="position" type="NX_CHAR"/>
-                <field name="mass_to_charge" type="NX_CHAR"/>
-            </group>
-            <group name="ranging" type="NXnote">
-                <field name="type" type="NX_CHAR"/>
-                <field name="file_name" type="NX_CHAR"/>
-                <field name="checksum" type="NX_CHAR"/>
-                <field name="algorithm" type="NX_CHAR"/>
-                <field name="ranging_definitions" type="NX_CHAR"/>
-            </group>
             <group name="surface_distance" type="NXnote" optional="true">
                 <doc>
                     Distance between each ion and triangulated surface mesh.
                 </doc>
-                <field name="type" type="NX_CHAR"/>
                 <field name="file_name" type="NX_CHAR"/>
                 <field name="checksum" type="NX_CHAR"/>
                 <field name="algorithm" type="NX_CHAR"/>
                 <field name="distance" type="NX_CHAR"/>
             </group>
-            <group name="spatial_filter" type="NXspatial_filter">
-                <field name="windowing_method" type="NX_CHAR"/>
-                <group name="hexahedron_set" type="NXcg_hexahedron" optional="true">
-                    <field name="dimensionality" type="NX_POSINT"/>
-                    <field name="cardinality" type="NX_POSINT"/>
-                    <field name="index_offset" type="NX_INT"/>
-                    <group name="hexahedra" type="NXcg_face_list_data_structure">
-                        <field name="vertices" type="NX_UINT"/>
-                    </group>
-                </group>
-                <group name="cylinder_set" type="NXcg_cylinder" optional="true">
-                    <field name="dimensionality" type="NX_POSINT"/>
-                    <field name="cardinality" type="NX_POSINT"/>
-                    <field name="index_offset" type="NX_INT"/>
-                    <field name="center" type="NX_NUMBER"/>
-                    <field name="height" type="NX_NUMBER"/>
-                    <field name="radii" type="NX_NUMBER"/>
-                </group>
-                <group name="ellipsoid_set" type="NXcg_ellipsoid" optional="true">
-                    <field name="dimensionality" type="NX_POSINT"/>
-                    <field name="cardinality" type="NX_POSINT"/>
-                    <field name="index_offset" type="NX_INT"/>
-                    <field name="center" type="NX_NUMBER"/>
-                    <field name="half_axes_radii" type="NX_NUMBER"/>
-                    <field name="orientation" type="NX_NUMBER"/>
-                </group>
-                <group name="polyhedron_set" type="NXcg_polyhedron" optional="true"/>
-                <!--TODO-->
-                <group name="bitmask" type="NXcs_filter_boolean_mask" optional="true">
-                    <field name="number_of_objects" type="NX_UINT"/>
-                    <field name="bitdepth" type="NX_UINT"/>
-                    <field name="mask" type="NX_UINT"/>
-                </group>
-            </group>
-            <group name="evaporation_id_filter" type="NXsubsampling_filter" optional="true">
-                <field name="min_incr_max" type="NX_INT"/>
-            </group>
-            <group name="iontype_filter" type="NXmatch_filter" optional="true">
-                <field name="method" type="NX_CHAR"/>
-                <field name="match" type="NX_NUMBER"/>
-            </group>
-            <group name="hit_multiplicity_filter" type="NXmatch_filter" optional="true">
-                <field name="method" type="NX_CHAR"/>
-                <field name="match" type="NX_NUMBER"/>
-            </group>
-            <!--config-->
             <field name="ion_type_filter" type="NX_CHAR">
                 <doc>
                     How should iontypes be considered during the cluster analysis.
@@ -359,21 +289,7 @@ dim: (j,)-->
                 </field>
             </group>
         </group>
-        <!--ADD FURTHER ALGORITHMS, see L. Stephenson for further details
-e.g. https://doi.org/10.1017/S1431927607070900-->
-        <group name="common" type="NXapm_paraprobe_tool_common">
-            <field name="status" type="NX_CHAR"/>
-            <group type="NXprogram" minOccurs="1" maxOccurs="unbounded">
-                <field name="program" type="NX_CHAR">
-                    <attribute name="version" type="NX_CHAR"/>
-                </field>
-            </group>
-            <group name="profiling" type="NXcs_profiling" recommended="true">
-                <field name="start_time" type="NX_DATE_TIME"/>
-                <field name="end_time" type="NX_DATE_TIME"/>
-                <field name="total_elapsed_time" type="NX_FLOAT"/>
-                <field name="current_working_directory" type="NX_CHAR"/>
-            </group>
-        </group>
     </group>
+    <!--ADD FURTHER ALGORITHMS, see L. Stephenson for further details
+e.g. https://doi.org/10.1017/S1431927607070900-->
 </definition>