NXxas refactoring #1352
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| # Hidden files | ||
| .* | ||
| !.github | ||
| !.readthedocs.yaml | ||
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| # Python byte / compiled / optimized | ||
| *.py[cod] | ||
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| version: 2 | ||
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| build: | ||
| os: ubuntu-22.04 | ||
| tools: | ||
| python: "3.12" | ||
| commands: | ||
| - pip install -r requirements.txt | ||
| - make prepare | ||
| - make html | ||
| - mkdir -p $READTHEDOCS_OUTPUT/html | ||
| - cp -r build/manual/build/html/* $READTHEDOCS_OUTPUT/html/ |
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| <?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) 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 | ||||||
| # 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_new" 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="nEnergy"> | ||||||
| <doc>Number of energy data points</doc> | ||||||
| </symbol> | ||||||
| <symbol name="nTransitions"> | ||||||
| <doc>Number of electronic transitions</doc> | ||||||
| </symbol> | ||||||
| </symbols> | ||||||
| <doc> | ||||||
| This is an application definition for X-ray absorption spectroscopy. | ||||||
| </doc> | ||||||
| <group type="NXentry"> | ||||||
| <field name="definition"> | ||||||
| <doc> Official NeXus NXDL schema to which this file conforms. TODO: replace NXxas </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> | ||||||
|
Contributor
There was a problem hiding this comment. What if I want to do a scan that includes multiple absorption edges (e.g. Carbon K-edge and K L-edge)? Can I specify multiple elements? |
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| </group> | ||||||
| <group type="NXedge" name="edge"> | ||||||
| <doc>Absorption edge</doc> | ||||||
| </group> | ||||||
| <field name="calculated" type="NX_BOOLEAN" units="NX_UNITLESS" optional="true"> | ||||||
| <doc>Specify if the data commes from a calculation</doc> | ||||||
| </field> | ||||||
| <field name="energy" type="NX_FLOAT" units="NX_ENERGY"> | ||||||
| <doc>TODO</doc> | ||||||
| <dimensions rank="1"> | ||||||
| <dim index="1" value="nEnergy" /> | ||||||
| </dimensions> | ||||||
| </field> | ||||||
| <field name="intensity" type="NX_FLOAT" units="NX_ANY"> | ||||||
| <doc>TODO</doc> | ||||||
| <dimensions rank="1"> | ||||||
| <dim index="1" value="nEnergy" /> | ||||||
| </dimensions> | ||||||
| </field> | ||||||
| <field name="intensity_errors" type="NX_FLOAT" units="NX_ANY"> | ||||||
| <doc>TODO</doc> | ||||||
| <dimensions rank="1"> | ||||||
| <dim index="1" value="nEnergy" /> | ||||||
| </dimensions> | ||||||
| </field> | ||||||
| <group type="NXsample"> | ||||||
| <field name="name"> | ||||||
| <doc>Descriptive name of the sample</doc> | ||||||
| </field> | ||||||
| </group> | ||||||
| <group type="NXprocess" optional="true"> | ||||||
| <doc> | ||||||
| Description on how :ref:`energy </NXxas_new/ENTRY/energy-field>` | ||||||
| and :ref:`intensity </NXxas_new/ENTRY/intensity-field>` 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"/> | ||||||
|
Contributor
There was a problem hiding this comment. If you want to allow the "electron energy loss" mode, then you should also allow an "electron" probe type. |
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| </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"> | ||||||
|
Contributor
There was a problem hiding this comment. The i0 should have a corresponding NXmonitor group. There are also many ways of measuring an i0 that is useful to document in the file. For example, is the i0 measured in parallel with the sample absorption (or its proxy), or is it measured in sequence (e.g. before or after the sample), or is it sequential, but interleaved? There is also question of how "clean" the i0 data is, as in how directly/accurately does the i0 measurement follow the ideal incident flux signal? This issue is particularly significant for C K-edge measurements - one can read my article on the topic to further understand this issue. |
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| <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> | ||||||
| <link name="energy" target="/NXentry/energy"/> | ||||||
| <link name="intensity" target="/NXentry/intensity"/> | ||||||
| </group> | ||||||
| <group type="NXCollection" optional="true"> | ||||||
|
Contributor
There was a problem hiding this comment.
Suggested change
|
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| <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> | ||||||
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| <?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) 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 | ||
| # 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="NXedge" type="group" extends="NXobject" category="base" | ||
| 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> | ||
| An absorption edge is a sharp discontinuity in the X-ray absorption spectrum | ||
| of an element that occurs when the incident photon energy equals the binding | ||
| energy of a core electron, enabling photoionization of that shell. | ||
| </doc> | ||
| <field name="name" type="NX_CHAR" minOccurs="1" maxOccurs="1"> | ||
| <doc> | ||
| Name of the absorption edge specified using | ||
| `IUPAC notation`_ (e.g., ``K``, ``L2``, ``M5``), which identifies the | ||
| shell and sub-shell from which the electron is ejected. | ||
|
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| Correspondence between IUPAC and electronic level notations: | ||
|
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| .. list-table:: | ||
| :header-rows: 1 | ||
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| * - IUPAC | ||
| - Electronic level | ||
| * - K | ||
| - 1s | ||
| * - L1 | ||
| - 2s | ||
| * - L2 | ||
| - :math:`2p_{1/2}` | ||
| * - L3 | ||
| - :math:`2p_{3/2}` | ||
| * - M1 | ||
| - 3s | ||
| * - M2 | ||
| - :math:`3p_{1/2}` | ||
| * - M3 | ||
| - :math:`3p_{3/2}` | ||
| * - M4 | ||
| - :math:`3d_{3/2}` | ||
| * - M5 | ||
| - :math:`3d_{5/2}` | ||
| * - N1 | ||
| - 4s | ||
| * - N2 | ||
| - :math:`4p_{1/2}` | ||
| * - N3 | ||
| - :math:`4p_{3/2}` | ||
| * - N4 | ||
| - :math:`4d_{3/2}` | ||
| * - N5 | ||
| - :math:`4d_{5/2}` | ||
| * - N6 | ||
| - :math:`4f_{5/2}` | ||
| * - N7 | ||
| - :math:`4f_{7/2}` | ||
| * - O1 | ||
| - 5s | ||
| * - O2 | ||
| - :math:`5p_{1/2}` | ||
| * - O3 | ||
| - :math:`5p_{3/2}` | ||
| * - O4 | ||
| - :math:`5d_{3/2}` | ||
| * - O5 | ||
| - :math:`5d_{5/2}` | ||
| * - O6 | ||
| - :math:`5f_{5/2}` | ||
| * - O7 | ||
| - :math:`5f_{7/2}` | ||
| * - P1 | ||
| - 6s | ||
| * - P2 | ||
| - :math:`6p_{1/2}` | ||
| * - P3 | ||
| - :math:`6p_{3/2}` | ||
| * - P4 | ||
| - :math:`6d_{3/2}` | ||
| * - P5 | ||
| - :math:`6d_{5/2}` | ||
|
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| .. _IUPAC notation: https://doi.org/10.1002/xrs.1300200308 | ||
| </doc> | ||
| <enumeration> | ||
| <item value="K"></item> | ||
| <item value="L1"></item> | ||
| <item value="L2"></item> | ||
| <item value="L3"></item> | ||
| <item value="M1"></item> | ||
| <item value="M2"></item> | ||
| <item value="M3"></item> | ||
| <item value="M4"></item> | ||
| <item value="M5"></item> | ||
| <item value="N1"></item> | ||
| <item value="N2"></item> | ||
| <item value="N3"></item> | ||
| <item value="N4"></item> | ||
| <item value="N5"></item> | ||
| <item value="N6"></item> | ||
| <item value="N7"></item> | ||
| <item value="O1"></item> | ||
| <item value="O2"></item> | ||
| <item value="O3"></item> | ||
| <item value="O4"></item> | ||
| <item value="O5"></item> | ||
| <item value="O6"></item> | ||
| <item value="O7"></item> | ||
| <item value="P1"></item> | ||
| <item value="P2"></item> | ||
| <item value="P3"></item> | ||
| <item value="P4"></item> | ||
| <item value="P5"></item> | ||
| </enumeration> | ||
| </field> | ||
| <field name="energy" type="NX_FLOAT" units="NX_ENERGY"> | ||
| <doc> | ||
| Energy of the absorption edge. | ||
| </doc> | ||
| </field> | ||
| </definition> |
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