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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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5 changes: 5 additions & 0 deletions applications/NXapm.nxdl.xml
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Expand Up @@ -361,6 +361,11 @@
</doc>
</field>
<group name="citeID" type="NXcite" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<field name="author" type="NX_CHAR" optional="true">
<doc>
The author(s) of that reference.
</doc>
</field>
<field name="doi" type="NX_CHAR"/>
</group>
<group name="noteID" type="NXnote" minOccurs="0" maxOccurs="unbounded" nameType="partial">
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85 changes: 79 additions & 6 deletions applications/NXem.nxdl.xml
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Expand Up @@ -231,7 +231,14 @@
start_time and end_time together.
</doc>
</field>
<group name="citeID" type="NXcite" minOccurs="0" maxOccurs="unbounded" nameType="partial"/>
<group name="citeID" type="NXcite" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<field name="author" type="NX_CHAR" optional="true">
<doc>
The author(s) of that reference.
</doc>
</field>
<field name="doi" type="NX_CHAR"/>
</group>
<group name="noteID" type="NXnote" minOccurs="0" maxOccurs="unbounded" nameType="partial">
<doc>
Collection of serialized resources associated with the experiment.
Expand Down Expand Up @@ -1680,13 +1687,52 @@ 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"/>
<field name="checksum" type="NX_CHAR" recommended="true"/>
<field name="algorithm" type="NX_CHAR" recommended="true"/>
</group>
<!--per scan point quantities (identifier_phase, matching_phase, positions, etc.)
<!--per scan point quantities (phase_id, matching_phase, positions, etc.)
just using the implicit optional, for the database example in NOMAD we do
not wish to duplicate all payload data-->
<group name="phaseID" type="NXphase" nameType="partial" minOccurs="0" maxOccurs="unbounded">
Expand Down Expand Up @@ -1739,11 +1785,38 @@ 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"/>
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11 changes: 10 additions & 1 deletion applications/nyaml/NXapm.yaml
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Expand Up @@ -308,6 +308,10 @@ NXapm(NXobject):
citeID(NXcite):
exists: ['min', '0', 'max', 'unbounded']
nameType: partial
author(NX_CHAR):
exists: optional
doc: |
The author(s) of that reference.
doi(NX_CHAR):
noteID(NXnote):
exists: ['min', '0', 'max', 'unbounded']
Expand Down Expand Up @@ -1531,7 +1535,7 @@ NXapm(NXobject):
dim: (n,)

# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
# 7bec46bfcbbb372ad9c37859e21fe81ecdd1e4ca1c8502c0fdcbf71e757f898c
# 2642b118e31af3d0c5cf93a12ba96d32f0458074c69b36c51821bfa5307ef97c
# <?xml version="1.0" encoding="UTF-8"?>
# <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
# <!--
Expand Down Expand Up @@ -1895,6 +1899,11 @@ NXapm(NXobject):
# </doc>
# </field>
# <group name="citeID" type="NXcite" minOccurs="0" maxOccurs="unbounded" nameType="partial">
# <field name="author" type="NX_CHAR" optional="true">
# <doc>
# The author(s) of that reference.
# </doc>
# </field>
# <field name="doi" type="NX_CHAR"/>
# </group>
# <group name="noteID" type="NXnote" minOccurs="0" maxOccurs="unbounded" nameType="partial">
Expand Down
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