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[WIP] XAS specialization using subclasses #7

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[WIP] XAS specialization using subclasses #7

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900b60c
Remove NXxas_mode
mretegan Feb 17, 2026
ef88cf6
Add transmission subclass
mretegan Feb 17, 2026
24678b6
Add the intensity field for transmission
mretegan Feb 17, 2026
33a4a7b
Formatting
mretegan Feb 17, 2026
6dd4089
Update transmission and add TFY
mretegan Feb 22, 2026
2c17cbd
Clean the base class
mretegan Feb 23, 2026
41a69d8
Update NXxas_trans
mretegan Feb 23, 2026
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100 changes: 16 additions & 84 deletions applications/NXxas_new.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
# Copyright (C) 2024-2026 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
Expand Down Expand Up @@ -36,18 +36,15 @@
</symbol>
</symbols>
<doc>
This is an application definition for X-ray absorption spectroscopy.
This is a generic application definition for X-ray absorption spectroscopy. Specialized definitions are available for different acquisition modes.
</doc>
<group type="NXentry">
<field name="definition">
<doc> Official NeXus NXDL schema to which this file conforms. TODO: replace NXxas </doc>
<doc> Official NeXus NXDL schema to which this file conforms.</doc>
<enumeration>
<item value="NXxas_new"></item>
</enumeration>
</field>
<group type="NXxas_mode" name="mode">
<doc></doc>
</group>
<group type="NXelement" name="element">
<doc>Excited element</doc>
</group>
Expand All @@ -58,19 +55,27 @@
<doc>Specify if the data commes from a calculation</doc>
</field>
<field name="energy" type="NX_FLOAT" units="NX_ENERGY">
<doc>TODO</doc>
<doc>
The energy axis of the spectrum.
</doc>
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
<field name="intensity" type="NX_FLOAT" units="NX_ANY">
<doc>TODO</doc>
<doc>
The intensity of the spectrum. The precise definition of what is
meant by intensity depends on the acquisition mode, and will be
specified by each subclass application definition.
</doc>
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
<field name="intensity_errors" type="NX_FLOAT" units="NX_ANY">
<doc>TODO</doc>
<field name="intensity_errors" type="NX_FLOAT" units="NX_ANY" optional="true">
<doc>
The errors associated with the intensity of the spectrum.
</doc>
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
Expand All @@ -80,83 +85,10 @@
<doc>Descriptive name of the sample</doc>
</field>
</group>
<group type="NXprocess" optional="true">
<doc>
Description on how :ref:`energy &lt;/NXxas_new/ENTRY/energy-field&gt;`
and :ref:`intensity &lt;/NXxas_new/ENTRY/intensity-field&gt;` were obtained
from the raw data.
</doc>
</group>
<group type="NXinstrument" optional="true">
<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" optional="true">
<field name="energy" type="NX_FLOAT" units="NX_ENERGY" optional="true">
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
<group type="NXcrystal" name ="crystal" optional="true">
<field name="d_spacing" type="NX_FLOAT" units="NX_LENGTH">
<doc>spacing between crystal planes of the reflection</doc>
</field>
<field name="type">
<doc>Type or material of monochromating substance (Si, Ge, Multilayer).</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" minOccurs="0" maxOccurs="unbounded">
<field name="data" type="NX_NUMBER">
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
</group>
<group type="NXdetector" name="i0" optional="true">
<field name="data" type="NX_NUMBER">
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
</group>
</group>
<group type="NXdata" optional="true">
<doc>XAS intensity versus energy plot</doc>
<doc>Plot of the X-ray absorption intensity versus energy</doc>
<link name="energy" target="/NXentry/energy"/>
<link name="intensity" target="/NXentry/intensity"/>
</group>
<group type="NXCollection" optional="true">
<group type="NXdata" optional="true">
<doc>Table like data structure common in the XAS domain.</doc>
<field name="data" type="NX_NUMBER">
<dimensions rank="2">
<dim index="1" value="nChan" />
<dim index="2" value="nEnergy" />
</dimensions>
</field>
<field name="columns" type="NX_CHAR">
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
<group type="NXuser" name="data_collector" optional="true">
<field name="name"></field>
<field name="orcid"></field>
</group>
</group>
</group>
</group>
</definition>
69 changes: 69 additions & 0 deletions applications/NXxas_tfy.nxdl.xml
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@@ -0,0 +1,69 @@
<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl" ?>
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2026 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
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# For further information, see http://www.nexusformat.org
-->
<definition name="NXxas_tfy" extends="NXxas_new" 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 ">
<doc>
In total fluorescence yield (TFY), the absorption coefficient :math:`\mu(E)` is
proportional to the ratio of the intensity of the emitted fluorescence
:math:`I_f` and the incident beam :math:`I_0`:

.. math:: \mu(E) \propto I_f/I_0

where :math:`I_f` is the intensity of the fluorescence emission, and :math:`I_0` is
the intensity of the incident beam.
</doc>
<group type="NXentry">
<field name="definition">
<doc> Official NeXus NXDL schema to which this file conforms. </doc>
<enumeration>
<item value="NXxas_tfy"/>
</enumeration>
</field>
<field name="intensity" type="NX_FLOAT" units="NX_ANY">
<doc>
The absorption coefficient :math:`\mu(E)` defined above.
</doc>
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
<field name="i0" type="NX_FLOAT" units="NX_ANY" optional="true">
<doc>
The intensity of the incident beam.
</doc>
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
<field name="if" type="NX_FLOAT" units="NX_ANY" optional="true">
<doc>
The intensity of the total fluorescence emission.
</doc>
<dimensions rank="1">
<dim index="1" value="nEnergy" />
</dimensions>
</field>
</group>
</definition>
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