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Merged
mkuehbach merged 4 commits into from
Aug 7, 2025
Merged

Connect more intricate concepts from NXmicrostructure #406

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c5d2001
Connect more intricate concepts from NXmicrostructure to the EBSD exa…
atomprobe-tc Aug 4, 2025
f36cded
Reintroduce the incorrectly removed nameType partial
atomprobe-tc Aug 4, 2025
6acdc27
Final polishing for the pynxtools v0.11.1 release
atomprobe-tc Aug 7, 2025
4a54840
Grammar
atomprobe-tc Aug 7, 2025
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74 changes: 70 additions & 4 deletions applications/NXem.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -1680,6 +1680,45 @@ is required to provide such information in this way!-->
<group name="indexing" type="NXprocess" optional="true">
<field name="number_of_scan_points" type="NX_UINT"/>
<field name="indexing_rate" type="NX_NUMBER" recommended="true"/>
<group name="microstructureID" type="NXmicrostructure" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="configuration" type="NXprocess">
<field name="dimensionality" type="NX_POSINT"/>
<field name="algorithm" type="NX_CHAR"/>
<field name="disorientation_threshold" type="NX_NUMBER"/>
<group name="programID" type="NXprogram" nameType="partial" recommended="true">
<field name="program" type="NX_CHAR">
<attribute name="version" type="NX_CHAR"/>
</field>
<group name="mtex" type="NXmicrostructure_mtex_config" optional="true"/>
</group>
</group>
<group name="grid" type="NXcg_grid" optional="true"/>
<group name="points" type="NXcg_point" optional="true"/>
<group name="polylines" type="NXcg_polyline" optional="true"/>
<group name="triangles" type="NXcg_triangle" optional="true"/>
<group name="polygons" type="NXcg_polygon" optional="true"/>
<group name="polyhedra" type="NXcg_polyhedron" optional="true"/>
<group name="crystals" type="NXmicrostructure_feature" optional="true">
<field name="representation" type="NX_CHAR" recommended="true"/>
<field name="number_of_crystals" type="NX_UINT"/>
<field name="index_offset" type="NX_INT"/>
</group>
<group name="interfaces" type="NXmicrostructure_feature" optional="true">
<field name="representation" type="NX_CHAR" recommended="true"/>
<field name="number_of_interfaces" type="NX_UINT"/>
<field name="index_offset" type="NX_INT"/>
</group>
<group name="triple_junctions" type="NXmicrostructure_feature" optional="true">
<field name="representation" type="NX_CHAR" recommended="true"/>
<field name="number_of_junctions" type="NX_UINT"/>
<field name="index_offset" type="NX_INT"/>
</group>
<group name="quadruple_junctions" type="NXmicrostructure_feature" optional="true">
<field name="representation" type="NX_CHAR" recommended="true"/>
<field name="number_of_junctions" type="NX_UINT"/>
<field name="index_offset" type="NX_INT"/>
</group>
</group>
<group name="source" type="NXnote" optional="true">
<field name="type" type="NX_CHAR" recommended="true"/>
<field name="file_name" type="NX_CHAR"/>
Expand Down Expand Up @@ -1739,11 +1778,38 @@ not wish to duplicate all payload data-->
</field>
</group>
</group>
<group name="odfID" type="NXmicrostructure_odf" nameType="partial" optional="true"/>
<group name="pfID" type="NXmicrostructure_pf" nameType="partial" optional="true"/>
<group name="odfID" type="NXmicrostructure_odf" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="configuration" type="NXparameters" recommended="true">
<field name="crystal_symmetry_point_group" type="NX_CHAR"/>
<field name="specimen_symmetry_point_group" type="NX_CHAR"/>
<field name="kernel_halfwidth" type="NX_NUMBER"/>
<field name="kernel_name" type="NX_CHAR"/>
<field name="resolution" type="NX_NUMBER"/>
</group>
<group name="characteristics" type="NXprocess" optional="true">
<field name="texture_index" type="NX_FLOAT"/>
</group>
<group name="phi_two_plot" type="NXdata">
<attribute name="signal" type="NX_CHAR"/>
<attribute name="axes" type="NX_CHAR"/>
<attribute name="AXISNAME_indices" type="NX_UINT" nameType="partial"/>
<field name="title" type="NX_CHAR" recommended="true"/>
<field name="intensity" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
</field>
<field name="varphi_one" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
</field>
<field name="capital_phi" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
</field>
<field name="varphi_two" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
</field>
</group>
</group>
<group name="pfID" type="NXmicrostructure_pf" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
</group>
<!--microstructure of the entire ROI-->
<group name="microstructureID" type="NXmicrostructure" nameType="partial" optional="true"/>
<group name="roi" type="NXdata" recommended="true">
<attribute name="signal" type="NX_CHAR"/>
<attribute name="axes" type="NX_CHAR"/>
Expand Down
160 changes: 148 additions & 12 deletions applications/nyaml/NXem.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -1638,6 +1638,56 @@ NXem(NXobject):
number_of_scan_points(NX_UINT):
indexing_rate(NX_NUMBER):
exists: recommended
microstructureID(NXmicrostructure):
nameType: partial
exists: ['min', '0', 'max', 'unbounded']
configuration(NXprocess):
dimensionality(NX_POSINT):
algorithm(NX_CHAR):
disorientation_threshold(NX_NUMBER):
programID(NXprogram):
nameType: partial
exists: recommended
program(NX_CHAR):
\@version(NX_CHAR):
mtex(NXmicrostructure_mtex_config):
exists: optional
grid(NXcg_grid):
exists: optional
points(NXcg_point):
exists: optional
polylines(NXcg_polyline):
exists: optional
triangles(NXcg_triangle):
exists: optional
polygons(NXcg_polygon):
exists: optional
polyhedra(NXcg_polyhedron):
exists: optional
crystals(NXmicrostructure_feature):
exists: optional
representation(NX_CHAR):
exists: recommended
number_of_crystals(NX_UINT):
index_offset(NX_INT):
interfaces(NXmicrostructure_feature):
exists: optional
representation(NX_CHAR):
exists: recommended
number_of_interfaces(NX_UINT):
index_offset(NX_INT):
triple_junctions(NXmicrostructure_feature):
exists: optional
representation(NX_CHAR):
exists: recommended
number_of_junctions(NX_UINT):
index_offset(NX_INT):
quadruple_junctions(NXmicrostructure_feature):
exists: optional
representation(NX_CHAR):
exists: recommended
number_of_junctions(NX_UINT):
index_offset(NX_INT):
source(NXnote):
exists: optional
type(NX_CHAR):
Expand Down Expand Up @@ -1704,15 +1754,35 @@ NXem(NXobject):
\@long_name(NX_CHAR):
odfID(NXmicrostructure_odf):
nameType: partial
exists: optional
exists: ['min', '0', 'max', 'unbounded']
configuration(NXparameters):
exists: recommended
crystal_symmetry_point_group(NX_CHAR):
specimen_symmetry_point_group(NX_CHAR):
kernel_halfwidth(NX_NUMBER):
kernel_name(NX_CHAR):
resolution(NX_NUMBER):
characteristics(NXprocess):
exists: optional
texture_index(NX_FLOAT):
phi_two_plot(NXdata):
\@signal(NX_CHAR):
\@axes(NX_CHAR):
\@AXISNAME_indices(NX_UINT):
nameType: partial
title(NX_CHAR):
exists: recommended
intensity(NX_NUMBER):
\@long_name(NX_CHAR):
varphi_one(NX_NUMBER):
\@long_name(NX_CHAR):
capital_phi(NX_NUMBER):
\@long_name(NX_CHAR):
varphi_two(NX_NUMBER):
\@long_name(NX_CHAR):
pfID(NXmicrostructure_pf):
nameType: partial
exists: optional

# microstructure of the entire ROI
microstructureID(NXmicrostructure):
nameType: partial
exists: optional
exists: ['min', '0', 'max', 'unbounded']
roi(NXdata):
exists: recommended
\@signal(NX_CHAR):
Expand Down Expand Up @@ -1774,7 +1844,7 @@ NXem(NXobject):
# in https://github.com/FAIRmat-NFDI/nexus_definitions/commit/0b928c4352bc5636f673b5fb25ce990f1af8a099

# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
# e2e9a591eeb4374c8a4a83fcaf92d3f8f56b5c6ccb8c6c10d6a0d3c8b7a1ce9b
# 10bb99fb256ecd540dbd108c048d465f1d3c5e68bc4cab13a3cf1421d09b40a0
# <?xml version="1.0" encoding="UTF-8"?>
# <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
# <!--
Expand Down Expand Up @@ -3457,6 +3527,45 @@ NXem(NXobject):
# <group name="indexing" type="NXprocess" optional="true">
# <field name="number_of_scan_points" type="NX_UINT"/>
# <field name="indexing_rate" type="NX_NUMBER" recommended="true"/>
# <group name="microstructureID" type="NXmicrostructure" nameType="partial" minOccurs="0" maxOccurs="unbounded">
# <group name="configuration" type="NXprocess">
# <field name="dimensionality" type="NX_POSINT"/>
# <field name="algorithm" type="NX_CHAR"/>
# <field name="disorientation_threshold" type="NX_NUMBER"/>
# <group name="programID" type="NXprogram" nameType="partial" recommended="true">
# <field name="program" type="NX_CHAR">
# <attribute name="version" type="NX_CHAR"/>
# </field>
# <group name="mtex" type="NXmicrostructure_mtex_config" optional="true"/>
# </group>
# </group>
# <group name="grid" type="NXcg_grid" optional="true"/>
# <group name="points" type="NXcg_point" optional="true"/>
# <group name="polylines" type="NXcg_polyline" optional="true"/>
# <group name="triangles" type="NXcg_triangle" optional="true"/>
# <group name="polygons" type="NXcg_polygon" optional="true"/>
# <group name="polyhedra" type="NXcg_polyhedron" optional="true"/>
# <group name="crystals" type="NXmicrostructure_feature" optional="true">
# <field name="representation" type="NX_CHAR" recommended="true"/>
# <field name="number_of_crystals" type="NX_UINT"/>
# <field name="index_offset" type="NX_INT"/>
# </group>
# <group name="interfaces" type="NXmicrostructure_feature" optional="true">
# <field name="representation" type="NX_CHAR" recommended="true"/>
# <field name="number_of_interfaces" type="NX_UINT"/>
# <field name="index_offset" type="NX_INT"/>
# </group>
# <group name="triple_junctions" type="NXmicrostructure_feature" optional="true">
# <field name="representation" type="NX_CHAR" recommended="true"/>
# <field name="number_of_junctions" type="NX_UINT"/>
# <field name="index_offset" type="NX_INT"/>
# </group>
# <group name="quadruple_junctions" type="NXmicrostructure_feature" optional="true">
# <field name="representation" type="NX_CHAR" recommended="true"/>
# <field name="number_of_junctions" type="NX_UINT"/>
# <field name="index_offset" type="NX_INT"/>
# </group>
# </group>
# <group name="source" type="NXnote" optional="true">
# <field name="type" type="NX_CHAR" recommended="true"/>
# <field name="file_name" type="NX_CHAR"/>
Expand Down Expand Up @@ -3516,11 +3625,38 @@ NXem(NXobject):
# </field>
# </group>
# </group>
# <group name="odfID" type="NXmicrostructure_odf" nameType="partial" optional="true"/>
# <group name="pfID" type="NXmicrostructure_pf" nameType="partial" optional="true"/>
# <group name="odfID" type="NXmicrostructure_odf" nameType="partial" minOccurs="0" maxOccurs="unbounded">
# <group name="configuration" type="NXparameters" recommended="true">
# <field name="crystal_symmetry_point_group" type="NX_CHAR"/>
# <field name="specimen_symmetry_point_group" type="NX_CHAR"/>
# <field name="kernel_halfwidth" type="NX_NUMBER"/>
# <field name="kernel_name" type="NX_CHAR"/>
# <field name="resolution" type="NX_NUMBER"/>
# </group>
# <group name="characteristics" type="NXprocess" optional="true">
# <field name="texture_index" type="NX_FLOAT"/>
# </group>
# <group name="phi_two_plot" type="NXdata">
# <attribute name="signal" type="NX_CHAR"/>
# <attribute name="axes" type="NX_CHAR"/>
# <attribute name="AXISNAME_indices" type="NX_UINT" nameType="partial"/>
# <field name="title" type="NX_CHAR" recommended="true"/>
# <field name="intensity" type="NX_NUMBER">
# <attribute name="long_name" type="NX_CHAR"/>
# </field>
# <field name="varphi_one" type="NX_NUMBER">
# <attribute name="long_name" type="NX_CHAR"/>
# </field>
# <field name="capital_phi" type="NX_NUMBER">
# <attribute name="long_name" type="NX_CHAR"/>
# </field>
# <field name="varphi_two" type="NX_NUMBER">
# <attribute name="long_name" type="NX_CHAR"/>
# </field>
# </group>
# </group>
# <group name="pfID" type="NXmicrostructure_pf" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
# </group>
# <!--microstructure of the entire ROI-->
# <group name="microstructureID" type="NXmicrostructure" nameType="partial" optional="true"/>
# <group name="roi" type="NXdata" recommended="true">
# <attribute name="signal" type="NX_CHAR"/>
# <attribute name="axes" type="NX_CHAR"/>
Expand Down
6 changes: 3 additions & 3 deletions contributed_definitions/NXmicrostructure.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -312,9 +312,9 @@ examples for specific frequently discussed microstructural features-->
<doc>
Reference to an instance of:

* :ref:`NXcg_polyline` for a one-dimensional representation as only a projection is available (like in linear intercept analysis)
* :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments)
* :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D)
* :ref:`NXcg_polyline` for a one- or two-dimensional representation as only a projection is available (like in linear intercept analysis)
* :ref:`NXcg_polygon`, :ref:`NXcg_triangle`, or :ref:`NXcg_polyhedron` for a two- or three-dimensional representation as only a projection is available (like in most experiments)
* :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D)

which represent the geometrical entities of the discretization.
</doc>
Expand Down
2 changes: 1 addition & 1 deletion contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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" type="group" name="NXmicrostructure_mtex_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="base" type="group" name="NXmicrostructure_mtex_config" extends="NXparameters" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<symbols>
<symbol name="n_def_color_map">
<doc>
Expand Down
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