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add base class for X-ray element and edge #1293

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e4a14b1
add base class for X-ray edge and element for describing X-ray absorp…
newville Jun 20, 2023
50003bf
Merge branch 'nexusformat:main' into main
newville Jun 21, 2023
2406afc
Fix reference with missing backticks (#1290)
PeterC-DLS Jun 21, 2023
0cd1c75
Add favicon to HTML pages of manual (#1256)
PeterC-DLS Jun 21, 2023
5224071
XML errors: make file and line more clear
woutdenolf Jun 20, 2023
1701c6e
Fix deployment in CI (#1294)
PeterC-DLS Jun 21, 2023
4737281
NXbeam: clarify how beams can be in either sample or instrument group…
Gigarrum Jun 21, 2023
a174658
Link to NAPI manual directly (#1298)
PeterC-DLS Jun 21, 2023
99456b6
WIP: proposed update to NXxas definition
newville Jun 22, 2023
c8544c4
Merge branch 'nexusformat:main' into main
newville Jun 22, 2023
5580d65
fix typos
newville Jul 31, 2023
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303 changes: 199 additions & 104 deletions applications/NXxas.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl" ?>
<!--
# NeXus - Neutron and X-ray Common Data Format
#
#
# Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
#
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
Expand All @@ -22,112 +22,207 @@
# For further information, see http://www.nexusformat.org
-->
<definition name="NXxas" extends="NXobject" type="group"
category="application"
xmlns="http://definition.nexusformat.org/nxdl/3.1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd "
>
<symbols>
<doc>
The symbol(s) listed here will be used below to coordinate datasets with the same shape.
</doc>
<symbol name="nP">
<doc>Number of points</doc>
</symbol>
</symbols>
category="application"
xmlns="http://definition.nexusformat.org/nxdl/3.1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd "
>
<symbols>
<doc>
This is an application definition for raw data from an X-ray absorption spectroscopy experiment.

This is essentially a scan on energy versus incoming/
absorbed beam.
The symbol(s) listed here will be used below to coordinate datasets with the same shape.
</doc>
<group type="NXentry">
<attribute name="entry">
<doc>
NeXus convention is to use "entry1", "entry2", ...
for analysis software to locate each entry.
</doc>
</attribute>
<field name="title"/>
<field name="start_time" type="NX_DATE_TIME"/>
<field name="definition">
<doc> Official NeXus NXDL schema to which this file conforms </doc>
<enumeration>
<item value="NXxas"></item>
</enumeration>
<symbol name="nP">
<doc>Number of points</doc>
</symbol>
</symbols>
<doc>
This is an application definition for raw data from an X-ray absorption spectroscopy experiment.

This is essentially a scan on energy versus incoming/
absorbed beam.
</doc>
<group type="NXentry">
<attribute name="entry">
<doc>
NeXus convention is to use "entry1", "entry2", ...
for analysis software to locate each entry.
</doc>
</attribute>
<field name="title"/>
<field name="start_time" type="NX_DATE_TIME"/>
<field name="definition">
<doc> Official NeXus NXDL schema to which this file conforms </doc>
<enumeration>
<item value="NXxas"></item>
</enumeration>
</field>
<group type="NXinstrument">
<group type="NXsource">
<field name="type"/>
<field name="name"/>
<field name="probe">
<enumeration>
<item value="x-ray"/>
</enumeration>
</field>
<group type="NXinstrument">
<group type="NXsource">
<field name="type"/>
<field name="name"/>
<field name="probe">
<enumeration>
<item value="x-ray"/>
</enumeration>
</field>
</group>
<group type="NXmonochromator" name="monochromator">
<field name="energy" axis="1" type="NX_FLOAT">
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
</group>
<group type="NXdetector" name="incoming_beam">
<field name="data" type="NX_NUMBER">
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
</group>
<group type="NXdetector" name="absorbed_beam">
<field name="data" type="NX_NUMBER">
<doc>This data corresponds to the sample signal.</doc>
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
</group>
</group>
<group type="NXsample">
<field name="name">
<doc>Descriptive name of sample</doc>
</field>
</group>
<group type="NXmonitor">
<field name="mode">
<doc>
Count to a preset value based on either clock time (timer)
or received monitor counts (monitor).
</doc>
<enumeration>
<item value="monitor"/>
<item value="timer"/>
</enumeration>
</field>
<field name="preset" type="NX_FLOAT">
<doc>preset value for time or monitor</doc>
</field>
<field name="data" type="NX_NUMBER">
<doc>This field could be a link to ``/NXentry/NXinstrument/incoming_beam:NXdetector/data``</doc>
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
</group>
<group type="NXdata">
<link name="energy" target="/NXentry/NXinstrument/monochromator:NXmonochromator/energy"/>
<link name="absorbed_beam" target="/NXentry/NXinstrument/absorbed_beam:NXdetector/data"/>
<field name="mode">
<doc>Detection method used for observing the sample absorption (pick one from the enumerated list and spell exactly)</doc>
<enumeration>
<item value="Total Electron Yield" />
<item value="Partial Electron Yield" />
<item value="Auger Electron Yield" />
<item value="Fluorescence Yield" />
<item value="Transmission" />
</enumeration>
</group>
<group type="NXmonochromator" name="monochromator">
<doc>
A monochromator selects the X-ray beam energy. An XAS
dataset will use an array of floats to represent the energy,
typically in units of eV, but occassionally and acceptably in
units of keV or degrees (angle of monochromator crystal).

The crystal should be specied, including chemical formula, miller
indices, and preferrably stating the d-spacing used to convert
between angle and energy.

</doc>
<field name="energy" axis="1" type="NX_FLOAT">
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
<field name="energy_units" type="NX_CHAR">
<doc>units used for monochromator energy. Choices are in the list.</doc>
<enumeration>
<item value="eV"/>
<item value="keV"/>
<item value="degrees"/>
<item value="angstrom"/>
</enumeration>
</field>

<group type="NXcrystal">
<doc>
Crystal used for monochromator:
chemical_formula, d_spacing, and reflection should be specified
</doc>
<field name="chemical_formula"></field>
<field name="d_spacing" type="NX_FLOAT" units="NX_LENGTH">
<doc>spacing between crystal planes of the reflection, in Angstroms</doc>
</field>
<field name="reflection" type="NX_INT" units="NX_UNITLESS">
<doc>Miller indices (hkl) values of nominal reflection</doc>
<dimensions><dim index="1" value="3"/></dimensions>
</field>
</group>
</group>
<group type="NXdetector" name="i0">
<doc>monitoring the intensity of the incident beam.</doc>
<field name="data" type="NX_NUMBER">
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
</group>

<group type="NXdetector" name="itrans">
<doc>monitoring the intensity of the transmitted beam.</doc>
<field name="data" type="NX_NUMBER">
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
</group>

<group type="NXdetector" name="ifluor">
<doc>monitoring the intensity of the fluorescence or emitted beam.</doc>
<field name="data" type="NX_NUMBER">
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
<field name="mode">
<doc>Type of fluorescence or emission signal detected (pick one from enumerated list)</doc>
<enumeration>
<item value="Total Fluorescence Yield" />
<item value="Partial Fluorescence Yield" />
<item value="Total Electron Yield" />
<item value="Partial Electron Yield" />
<item value="Other" />
</enumeration>
</field>
</group>

<group type="NXdetector" name="irefer">
<doc>monitoring the intensity of the reference channel beam</doc>
<field name="data" type="NX_NUMBER">
<dimensions rank="1">
<dim index="1" value="nP" />
</dimensions>
</field>
<field name="mode">
<doc>Type of reference channel used (pick one from enumerated list)</doc>
<enumeration>
<item value="Transmission, downstream of Itrans" />
<item value="Fluoresscence, upstream of sample" />
</enumeration>
</field>

</group>
</group>

<group type="NXsample">
<field name="name">
<doc>Descriptive name of sample</doc>
</field>
</group>

<group type="NXscan">

@woutdenolf woutdenolf Jun 27, 2023

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NXscan is an application definition, not a base class. If I'm not mistaken, you cannot use an application definition inside another application definition. Maybe NXxas could extend NXscan @benajamin ?

@woutdenolf woutdenolf Jun 27, 2023

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From what I see, there is no need for NXscan here. Just put those field directly under NXxas.

@newville newville Jun 27, 2023

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The intention here was to add infomation and data about the scan performed to collect the data, just as <group type="NXsample"> immediately above this would be used to describe the sample.

Yes, the scan here derives from and extends the base class. Like, that "NXscan" simply does not have enough data to describe a scan.

<doc>
description of the energy scan and detectors used
</doc>
<field name="start_time" type="NX_DATE_TIME"/>
<field name="end_time" type="NX_DATE_TIME"/>
<field name="nP" type="NX_INT">
<doc> number of data points, or rows in the data table </doc>
</field>
<field name="nCol" type="NX_INT">
<doc> number of detector channnels or columns in the data table </doc>
</field>
<group type="NXxrayedge" name="xrayedge">
<field name="element" type="NX_CHAR" minOccurs=1/>

@woutdenolf woutdenolf Jun 27, 2023

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Syntax error: minOccurs="1"

@newville newville Jun 27, 2023

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OK, will fix.

<field name="edge" type="NX_CHAR" minOccurs=1/>

@woutdenolf woutdenolf Jun 27, 2023

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Syntax error: minOccurs="1"

</group>
<field name="scan_mode">
<doc>Whether scan of energy was continuous or step scan</doc>
<enumeration>
<item value="Continuous" />
<item value="Step" />
</enumeration>
</field>
<field name="data" type="NX_NUMBER">
<doc> raw data table </doc>
<dimensions rank="2">
<dim index="1" value="nP" />
<dim index="2" value="nCol" />
</dimensions>
</field>
<field name="column_labels" type="NX_CHAR">
<doc> labels for columns in the raw data table </doc>
<dimensions rank="1">
<dim index="1" value="nCol" />
</dimensions>
</field>
</group>


<group type="NXdata">
<link name="energy" target="/NXentry/NXinstrument/monochromator:NXmonochromator/energy"/>
<link name="i0" target="/NXentry/NXinstrument/i0:NXdetector/data"/>
<link name="itrans" target="/NXentry/NXinstrument/itrans:NXdetector/data"/>
<link name="ifluor" target="/NXentry/NXinstrument/ifluor:NXdetector/data"/>
<link name="irefer" target="/NXentry/NXinstrument/irefer:NXdetector/data"/>
<link name="column_names" target="/NXentry/NXscan/column_names:/data"/>
<link name="rawdata" target="/NXentry/NXscan/data:NXdata/data"/>
<field name="mode">
<doc>Detection method used for measuring absorption (pick one from the enumerated list)</doc>
<enumeration>
<item value="Transmission" />
<item value="Fluorescence" />
</enumeration>
</field>
</group>
</group>
</definition>
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