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XAS Data Interchange: A file format for a single XAS spectrum

Bruce Ravel
August 22, 2015

XAS Data Interchange: A file format for a single XAS spectrum

This is my presentation on XDI for the XAFS16 Satellite meeting on Data acquisition, treatment, storage – quality assurance in XAFS spectroscopy at DESY on August 21 2015.

Bruce Ravel

August 22, 2015
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  1. need for XDI XDI specification XDI implementation
    XAS Data Interchange
    A file format for a single XAS spectrum
    Bruce Ravel1, Matt Newville2
    1
    NIST and NSLS-II, 2
    University of Chicago
    Data acquisition, treatment, storage – quality assurance in XAFS spectroscopy
    DESY
    21-22 August 2015
    PDF of this talk: https://goo.gl/Nv1l3G
    1 / 10
    XAS Data Interchange

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  2. need for XDI XDI specification XDI implementation
    Data challenges in the XAS world
    Even small data volumes and the simplest XAS experiments have
    persistent problems
    1 Data archaeology – have you ever tried to extract data from the Ferrel
    Lytle archive at IIT?
    2 Moving data from the beamline to the data analysis package
    3 Sharing data between different analysis packages
    4 Submitting supplemental data with a publication
    5 Building data-centered applications for the web, the desktop, and the
    palmtop (e.g. an editable archive of standards)
    6 Extracting XAS data from a multispectral data set
    2 / 10
    XAS Data Interchange

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  3. need for XDI XDI specification XDI implementation
    Beamline data formats
    Every beamline has it’s own way of recording
    data, many of which are perfectly cromulent
    Most use ASCII files, some use more complex
    data formats
    Each beamline team has good reasons (one
    hopes!) for doing things their own way
    NSLS XDAC
    XDAC V1.4 Datafile V1
    "au.b04" created on 3/15/09 at 1:28:27 PM on X-23A2
    Diffraction element= Si (311). Ring energy= 2.80 GeV
    E0= 11919.00
    NUM_REGIONS= 4
    SRB= -200 -20 30 60 20k
    SRSS= 10 0.25 0.05k 0.05k
    SPP= 1 1 1 0.25k
    Settling time= 0.30
    Offsets= 122.00 85.78 0.00
    Gains= 8.00 8.00 1.00
    Au foil, NSLS X23A2, 20% Ar in Io and It
    with harmonic rejection mirror
    -----------------------------------------------------------
    Energy I0 It IntTime
    11719.00294 18352.0000 15872.2222 1.0000
    11728.99732 18380.0000 15934.2222 1.0000
    11739.00126 18381.0000 15980.2222 1.0000
    ...
    Photon Factory / SPring-8 / Aichi / SAGA
    9809 KEK-PF BL12C
    G:hgcys-11.001 07.05.12 23:28 - 07.05.12 23:55
    Hg:H2Cys 1:2 pH=12.86, 100 mM, prep. at PF, 5mm Teflon, stirred 4 hr
    Ring : 2.5 GeV 348.8 mA - 342.8 mA
    Mono : SI(111) D= 3.13551 A Initial angle= 9.25969 deg
    BL12C Transmission( 2) Repetition= 6 Points= 818
    Param file : A:hgk16 energy axis(2) Block = 5
    Block Init-Eng final-Eng Step/eV Time/s Num
    1 12049.00 12150.00 6.00 1.00 17
    2 12150.00 12320.00 .35 1.00 486
    3 12320.00 12400.00 1.00 2.00 80
    4 12400.00 12600.00 2.50 3.00 80
    5 12600.00 13040.00 4.00 3.00 110
    Ortec(-1) NDCH = 3
    Angle(c) Angle(o) time/s 2 3
    Mode 0 0 1 2
    Offset 0 0 826.150 652.975
    9.44433 9.44420 1.00 252916 592687
    9.43958 9.43960 1.00 256349 604260
    9.43483 9.43480 1.00 256429 607846
    ...
    3 / 10
    XAS Data Interchange

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  4. need for XDI XDI specification XDI implementation
    Problems with beamline formats
    They require additional processing in order to display µ(E), including
    Conversion to energy
    Dead-time or other corrections
    Merging of 10s, 100s, or 1000s of scans and/or detectors
    Ambiguous metadata, for instance
    How is the beamline identified?
    What consitutes a user comment?
    What describes the condition of the source or the beamline?
    XAS data analysis software and plotting software may have difficulty
    importing and interpreting the data
    This data is probably not appropriate for submission to a journal as
    supplemental material
    Data interchange
    A standard for the interchange of µ(E) data
    would help address most of these concerns.
    4 / 10
    XAS Data Interchange

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  5. need for XDI XDI specification XDI implementation
    Goals of a data interchange format
    The smallest unit of currency is the µ(E) spectrum.
    1 Be easy for a human to read. Be easy for a computer to read.
    2 Establish a common language for transferring µ(E) spectra between XAS
    experimenters, data analysis packages, web applications, journals and
    anything else that needs to process XAS data. This will enhance the user
    experience.
    3 Increase the relevance and longevity of experimental data by reducing the
    amount of data archaeology future interpretations of that data will require.
    4 Provide a mechanism for extracting and preserving a single XAS or
    XAS-like data set from a multispectral experiment or from a complex data
    structure.
    5 Be a building block for hierarchical or relational data structures.
    5 / 10
    XAS Data Interchange

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  6. need for XDI XDI specification XDI implementation
    Goals of a data interchange format
    The smallest unit of currency is the µ(E) spectrum.
    1 Be easy for a human to read. Be easy for a computer to read.
    2 Establish a common language for transferring µ(E) spectra between XAS
    experimenters, data analysis packages, web applications, journals and
    anything else that needs to process XAS data. This will enhance the user
    experience.
    3 Increase the relevance and longevity of experimental data by reducing the
    amount of data archaeology future interpretations of that data will require.
    4 Provide a mechanism for extracting and preserving a single XAS or
    XAS-like data set from a multispectral experiment or from a complex data
    structure.
    5 Be a building block for hierarchical or relational data structures.
    5 / 10
    XAS Data Interchange

    View full-size slide

  7. need for XDI XDI specification XDI implementation
    Goals of a data interchange format
    The smallest unit of currency is the µ(E) spectrum.
    1 Be easy for a human to read. Be easy for a computer to read.
    2 Establish a common language for transferring µ(E) spectra between XAS
    experimenters, data analysis packages, web applications, journals and
    anything else that needs to process XAS data. This will enhance the user
    experience.
    3 Increase the relevance and longevity of experimental data by reducing the
    amount of data archaeology future interpretations of that data will require.
    4 Provide a mechanism for extracting and preserving a single XAS or
    XAS-like data set from a multispectral experiment or from a complex data
    structure.
    5 Be a building block for hierarchical or relational data structures.
    5 / 10
    XAS Data Interchange

    View full-size slide

  8. need for XDI XDI specification XDI implementation
    Goals of a data interchange format
    The smallest unit of currency is the µ(E) spectrum.
    1 Be easy for a human to read. Be easy for a computer to read.
    2 Establish a common language for transferring µ(E) spectra between XAS
    experimenters, data analysis packages, web applications, journals and
    anything else that needs to process XAS data. This will enhance the user
    experience.
    3 Increase the relevance and longevity of experimental data by reducing the
    amount of data archaeology future interpretations of that data will require.
    4 Provide a mechanism for extracting and preserving a single XAS or
    XAS-like data set from a multispectral experiment or from a complex data
    structure.
    5 Be a building block for hierarchical or relational data structures.
    5 / 10
    XAS Data Interchange

    View full-size slide

  9. need for XDI XDI specification XDI implementation
    Goals of a data interchange format
    The smallest unit of currency is the µ(E) spectrum.
    1 Be easy for a human to read. Be easy for a computer to read.
    2 Establish a common language for transferring µ(E) spectra between XAS
    experimenters, data analysis packages, web applications, journals and
    anything else that needs to process XAS data. This will enhance the user
    experience.
    3 Increase the relevance and longevity of experimental data by reducing the
    amount of data archaeology future interpretations of that data will require.
    4 Provide a mechanism for extracting and preserving a single XAS or
    XAS-like data set from a multispectral experiment or from a complex data
    structure.
    5 Be a building block for hierarchical or relational data structures.
    5 / 10
    XAS Data Interchange

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  10. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    XDI is an ad hoc format loosely
    based on the format of e-mail and
    structured in a way that looks like
    a familiar column data file.
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

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  11. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    The data table is clearly organized
    into columns of numbers, with the
    abscissa (energy, in this case) as
    the left-most column. The non-data
    part of the file is clearly
    demarcated.
    This file can be imported as is into
    most common plotting and data
    processing tools (such as Excel,
    Origin, KaleidaGraph, and many
    others∗
    )
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

    such as that silly thing...

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  12. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    The version of the XDI format is
    identified in the first line as is the
    application that wrote this specific
    file.
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

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  13. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    Metadata is clearly identified and
    grouped into useful “namespaces”.
    The data columns are identified
    and, where appropriate, units are
    given.
    For the programmers in the
    audience, XDI headers map directly
    onto an associative array. (Other
    programming languages call this a
    dictionary, symbol table, hash, or
    map.)
    The metadata dictionary defines
    8 families, the six shown here plus
    Detector. and Sample.
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

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  14. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    Three pieces of metadata are
    required to be in the XDI file.
    The monochromator d-spacing is
    required if a correction needs to be
    made to the energy axis of the data.
    The symbol and edge of the element
    are required to unambiguously
    identify the data. For example, both
    Cr K and Ba LI have tabulated
    energies of 5989 eV, while Se K and
    Tl LIII are both at 12658 eV.
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

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  15. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    Five pieces of metadata are
    recommended to be in the XDI file.
    These establish the provenance of
    the data and tell the reader how to
    interpret the abscissa.
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

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  16. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    Extension metadata – metadata
    specific to a beamline, a data
    acquisition system, or a data
    processing program – is specified
    by “extension headers”.
    These use the same format as
    standard metadata headers, but
    with a domain specific “namespace”.
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

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  17. need for XDI XDI specification XDI implementation
    XDI: XAS Data Interchange
    User supplied comments (typically,
    but not exclusively, at the time of
    data acquisition) are clearly
    demarcated by a line of slashes and
    line of dashes.
    White space must be preserved,
    that is, a user comment like this
    must be preserved faithfully:
    -- --
    / \ / \
    / \/ \
    \ Best /
    \ Sample /
    \ Ever /
    \ !! /
    \ /
    \/
    # XDI/1.0 MX/2.0
    # Beamline.name: 10ID
    # Beamline.harmonic_rejection: flat Rh-coated mirror
    # Facility.name: APS
    # Facility.xray_source: undulator A
    # Facility.energy: 7.00 GeV
    # Mono.name: Si 111
    # Mono.d_spacing: 3.1356 Angstrom
    # Element.symbol: Fe
    # Element.edge: K
    # Scan.edge_energy: 7112.00 eV
    # Scan.start_time: 2005-03-08T20:08:57
    # Column.1: energy eV
    # Column.2: mutrans
    # Column.3: i0
    # MX.Num-regions: 1
    # MX.SRB: 6900
    # MX.SRSS: 0.5
    # MX.SPP: 0.1
    # MX.Settling-time: 0
    # MX.Offsets: 11408.00 11328.00 13200.00 10774.00
    # MX.Gains: 8.00 7.00 7.00 9.00
    #///
    # Fe K-edge, Lepidocrocite powder on kapton tape, RT
    # 4 layers of tape
    # exafs, 20 invang
    #---
    # energy mutrans i0
    6899.9609 -1.3070486 149013.70
    6900.1421 -1.3006104 144864.70
    6900.5449 -1.3033816 132978.70
    6900.9678 -1.3059724 125444.70
    6901.3806 -1.3107085 121324.70
    (....etc....)
    6 / 10
    XAS Data Interchange

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  18. need for XDI XDI specification XDI implementation
    Validation
    Example code in C
    1 #include "xdifile.h"
    XDIFile *xdifile;
    int ret;
    4
    xdifile = malloc(sizeof(XDIFile));
    ret = XDI_readfile (xdifile , "mydata.xdi");
    7 /* test return code ‘ret ’ for errors */
    /* test for required metadata */
    10 j = XDI_required_metadata (xdifile);
    if (j != 0 ) {
    printf("\n# ( requirement code %ld):\n%s\n",
    13 j, xdifile -> error_message );
    }
    /* test for recommended metadata */
    16 j = XDI_recommended_metadata (xdifile);
    if (j != 0 ) {
    printf("\n# ( recommendation code %ld):\n%s\n",
    19 j, xdifile -> error_message );
    }
    /* examine each individual metadata item */
    22 for (i=0; i < xdifile ->nmetadata; i++) {
    j = XDI_validate_item (xdifile ,
    xdifile -> meta_families [i],
    25 xdifile -> meta_keywords [i],
    xdifile -> meta_values [i]);
    /* test return value ‘j’ */
    28 }
    /* ************************ */
    /* do stuff with the data */
    31 /* ************************ */
    XDI_cleanup(xdifile , ret);
    free(xdifile);
    1 Read the XDI file. Without
    obvious errors (inconsistent
    number of data columns,
    non-numbers in data table,
    etc.), file content stored in a
    struct. (Lines 1-6)
    2 Test if required metadata items
    are present. (Lines 10-14)
    3 Test if recommended metadata
    items are present.
    (Lines 16-20)
    4 Validate individual items
    against the dictionary.
    (Lines 22-28)
    Steps 2-4 are optional
    7 / 10
    XAS Data Interchange

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  19. need for XDI XDI specification XDI implementation
    GitHub repository
    https://github.com/XraySpectroscopy/XAS-Data-Interchange
    8 / 10
    XAS Data Interchange

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  20. need for XDI XDI specification XDI implementation
    What’s implemented?
    1 A specification
    2 A dictionary of metadata families and items with guidelines for
    appropriate values
    3 An API written in C
    4 An API written in Fortran
    5 Bindings to the C API in Python and Perl
    6 A test suite of valid and invalid XDI data
    7 Dynamic analysis with Valgrind – no memory leaks in the C library!
    XDI is ready for use
    We hope it will be picked up by authors of data acquisition and data
    analysis software.
    9 / 10
    XAS Data Interchange

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  21. need for XDI XDI specification XDI implementation
    What’s not implemented
    1 Dictionary definitions for metadata related to non-monochromatic sources,
    such as dispersive optics or plasma sources.
    2 Dictionary items related to grating monochromators could be stronger.
    3 Bindings for many popular languages: Matlab, R, IDL,
    LabView, Ruby, Lua, Mathematica, . . . . . . . . . . . . . . .
    and whatever language you like best.
    Contribute new bindings!
    Fork the repository, add more language bindings, make a pull request.
    We’ll take all comers!
    10 / 10
    XAS Data Interchange

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