.. include:: _defs.rst XAS schema for NeXuS based on XDI ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ As discussed in the :ref:`multispec_sect`, using HDF5+NeXuS as a format for sharing multiple XAS spectra is worth exploring. According to the criteria given there, this format should map well to XDI, as the conclusions for required metadata tags and array names was the result of considerable discussion by the working groups and XAS community. As it turns out, there is an existing XAS schema defined for NeXuS (see https://github.com/nexusformat/definitions/blob/main/applications/NXsas.nxdl.xml), though as far as I can tell it was not written by someone in the XAS community and is not used. A candidate revised schema is included in Pull Request at https://github.com/nexusformat/definitions/pull/1293. This proposed schema is deliberately based on and shares many concepts and names with XDI. An annotated description of the schema for each XAS group in the NeXus file is given in the table below. .. _nxxas_schema_table: Table of fields and meaning in the proposed NeXuS NXxas definition: Subgroups are all labeled, and all other values hold datasets. Several of the datasets under ``data`` will be links to other datasets, and are indicated with '->'. Datatypes described as Arrays are expected to be 1-D arrays unless otherwise noted (here, ``scan/data`` and ``data/rawdata``). This list need not be complete, and additional datasets can be added to any Group without loss of existing information. In addition, each dataset can have attributes, for example giving units ore additional metadata. +---------------------------------------------------+------------------------------------------+ | address | description | +===================================================+==========================================+ | definition | string, 'NXxas' identifying Group type | +---------------------------------------------------+------------------------------------------+ | start_time | time for start of scan (ISO 8601) | +---------------------------------------------------+------------------------------------------+ | title | string for title of data | +---------------------------------------------------+------------------------------------------+ | data | Group containing primary data | +---------------------------------------------------+------------------------------------------+ | data/column_labels | -> /scan/column_labels | +---------------------------------------------------+------------------------------------------+ | data/edge | -> /scan/xrayedge/edge | +---------------------------------------------------+------------------------------------------+ | data/element | -> /scan/xrayedge/element | +---------------------------------------------------+------------------------------------------+ | data/energy | -> /instrument/monochromator/energy | +---------------------------------------------------+------------------------------------------+ | data/i0 | -> /instrument/i0/data | +---------------------------------------------------+------------------------------------------+ | data/itrans | -> /instrument/itrans/data | +---------------------------------------------------+------------------------------------------+ | data/ifluor | -> /instrument/ifluor/data | +---------------------------------------------------+------------------------------------------+ | data/irefer | -> /instrument/irefer/data | +---------------------------------------------------+------------------------------------------+ | data/rawdata | -> /scan/data | +---------------------------------------------------+------------------------------------------+ | data/mode | string measurement mode ('Transmission') | +---------------------------------------------------+------------------------------------------+ | data/mutrans | :math:`mu(E)` for Transmission | +---------------------------------------------------+------------------------------------------+ | data/mufluor | :math:`mu(E)` for Fluorescence | +---------------------------------------------------+------------------------------------------+ | data/murefer | :math:`mu(E)` for Reference description | +---------------------------------------------------+------------------------------------------+ | data/column_labels | -> /scan/column_labels | +---------------------------------------------------+------------------------------------------+ | instrument | Group for instrument data | +---------------------------------------------------+------------------------------------------+ | instrument/monochromator | Group for monochromator | +---------------------------------------------------+------------------------------------------+ | instrument/monochromator/energy | Array of energy values | +---------------------------------------------------+------------------------------------------+ | instrument/monochromator/angle | Array of angle values | +---------------------------------------------------+------------------------------------------+ | instrument/monochromator/crystal | Group for mono crystal | +---------------------------------------------------+------------------------------------------+ | instrument/monochromator/crystal/chemical_formula | string for mono crystal (eg, 'Si') | +---------------------------------------------------+------------------------------------------+ | instrument/monochromator/crystal/d_spacing | d-spacing (in Ang) for reflection | +---------------------------------------------------+------------------------------------------+ | instrument/monochromator/crystal/reflection | string crystal reflection (eg, '1,1,1') | +---------------------------------------------------+------------------------------------------+ | instrument/i0 | Group for i0 detector | +---------------------------------------------------+------------------------------------------+ | instrument/i0/data | Array of i0 values | +---------------------------------------------------+------------------------------------------+ | instrument/itrans | Group for transmission detector | +---------------------------------------------------+------------------------------------------+ | instrument/itrans/data | Array of transmission values | +---------------------------------------------------+------------------------------------------+ | instrument/fluor | Group for fluorescence detector | +---------------------------------------------------+------------------------------------------+ | instrument/fluor/data | Array of fluorescence values | +---------------------------------------------------+------------------------------------------+ | instrument/refer | Group for reference detector | +---------------------------------------------------+------------------------------------------+ | instrument/refer/data | Array of reference values | +---------------------------------------------------+------------------------------------------+ | instrument/source | Group for Source (facility, beamline) | +---------------------------------------------------+------------------------------------------+ | instrument/source/beamline_name | string name of beamline | +---------------------------------------------------+------------------------------------------+ | instrument/source/facility_name | string name of facility | +---------------------------------------------------+------------------------------------------+ | instrument/source/probe | string for source probe ('X-ray') | +---------------------------------------------------+------------------------------------------+ | sample | Group for Sample information | +---------------------------------------------------+------------------------------------------+ | sample/name | string name of sample | +---------------------------------------------------+------------------------------------------+ | sample/prep | string description of sample prep | +---------------------------------------------------+------------------------------------------+ | scan | Group for Scan information | +---------------------------------------------------+------------------------------------------+ | scan/xrayedge | Group for Element and Edge of Scan | +---------------------------------------------------+------------------------------------------+ | scan/xrayedge/element | string of element symbol for scan | +---------------------------------------------------+------------------------------------------+ | scan/xrayedge/edge | string of edge probed | +---------------------------------------------------+------------------------------------------+ | scan/edge_energy | nominal edge energy | +---------------------------------------------------+------------------------------------------+ | scan/data | 2D (nCol x nP) raw scan data table | +---------------------------------------------------+------------------------------------------+ | scan/nCol | integer number of columns in scan/data | +---------------------------------------------------+------------------------------------------+ | scan/nP | integer number of rows in scan/data | +---------------------------------------------------+------------------------------------------+ | scan/column_labels | array of column labels for scan/data | +---------------------------------------------------+------------------------------------------+ | scan/scan_mode | string describing scan mode | +---------------------------------------------------+------------------------------------------+ Note that many of the arrays and datasets listed in the table above are optional. That is, it is not required to have a ``irefer`` or ``ifluor`` or even ``itrans`` array. But, it is expected that at least one of ``ifluor`` or ``itrans`` is given, and if a reference channel is to be included, it should be called ``irefer``. Arrays for ``mutrans``, ``mufluor``, and/or ``murefer`` are recommended if those intensity arrays are included, but are not required. Communicating the monochromator ``energy`` in eV (or keV) is recommended. Giving the monochromator in ``angle`` (in degrees) is acceptable, Worked example of XDI and NeXuS formatted XAS data ----------------------------------------------------------------------------- Examples of files using the proposed schema are given at https://millenia.cars.aps.anl.gov/nxxas/. This includes a number of the example XDI files from https://github.com/XraySpectroscopy/XAS-Data-Interchange/tree/master/data. The raw sources for these files, and the Python script for creating these files are at https://millenia.cars.aps.anl.gov/nxxas/ASCII_Sources/. The individual single spectrum files from the XDI sources are at https://millenia.cars.aps.anl.gov/nxxas/SingleSpectrumFiles/. An example of a multi-spectrum file with 26 spectra is given at https://millenia.cars.aps.anl.gov/nxxas/MultiSpectrumFiles/. For comparison, an plain Zip file of the original as-measured files is included as well as an Athena project file for these datasets and a Larch session file for these data files. Discussion --------------------------------------------------------------------- The example datasets are given are