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This document is an effort of an ad hoc working group which will report to the International X-ray Absorption Society (IXAS) and the XAFS Commission of International Union of Crystallography (IUCr-XC). The charge of this working group is to propose standards for the storage and dissemination of XAS and related data.
The participants in this document are
- Matt NEWVILLE (University of Chicago Center for Advanced Radiation Sources, APS)
- Bruce RAVEL (National Institute of Standards and Technology, NSLS)
- V. Armando SOLÉ (ESRF)
- Gerd WELLENREUTHER (DESY)
We welcome participation. The efforts of this working group can be followed or joined at our mailing list or our Github organization.
This document describes the XAS Data Interchange Format (hereafter referred to as XDI), version 1.0.0, a simple file format for a single X-ray Absorption Spectroscopy (XAS) measurement. (See section 3.4.1 for an explanation of the versioning scheme.) This format intends to accomplish the following goals:
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Establish a common language for transferring data between XAS beamlines, XAS experimenters, data analysis packages, web applications, and anything else that needs to process XAS data.
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Increase the relevance and longevity of experimental data by reducing the amount of data archeology future interpretations of that data will require.
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Enhance the user experience by promoting inter-operability among data acquisition systems, data analysis packages, and other applications.
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Provide a mechanism for extracting and preserving a single XAS or XAS-like data set from a related experiment (for example, a DAFS or inelastic scattering measurement) or from a complex data structure (for example, a database or a hierarchical data file used to store a multi-spectral data set).
This format is intended to encode single-scan data files with metadata. It is not intended to encode relationships between many XAS measurements or between an XAS measurement and other parts of a multi-spectral experiment.
In order to fulfill these goals, XDI files provide a flexible, consistent representation of information common to many XAS experiments. This format is simpler than a format based on XML, HDF, or a database; it yields self-documenting files; and it is easy for both humans and computers to read. Its structure is inspired by that of Internet electronic mail, a plain-text data format which has proven to be robust, extensible, and enduring. Iy can be read easily by many existing programs for XAS and other data analysis and by many scientifc plotting programs.
It is not the intent of this specification to dictate file formats used by data acquisition systems during XAS experiments, although this is certainly a suitable format for that purpose. Any attempt to do so would be unreasonable due to the number of different data acquisition systems currently deployed at synchrotrons around the world, the variety of experiments performed at these installations, and the continuing development of new experimental techniques.
This specification addresses the representation of a single scan of XAS data after an experiment has been completed.
A beamline which adopts this specification shall either use this format as its native file format or shall provide their users with tools that convert between their native file formats and XDI . In short, they will send their users home with their XAS data stored in this format. We intend to encourage this practice by developing tools for reading, editing, writing, and validating XDI files. Beamlines may choose to modify their data acquisition systems to write data using this format in situations where that would be appropriate. Libraries will be developed for many popular programming languages to read, validate, manipulate, and write XDI files.
With their experiment data stored in XDI files, users will want data analysis packages and other applications which are capable of reading this format. It is our hope that, as this specification gains wider adoption, users will ultimately be freed from the responsibility of understanding peculiar, poorly documented file formats.
XDI files contain two sections, a header with information about one scan of an XAS experiment followed by the data collected during that scan. The header section consists of versioning information, a series of fields that contain information about the scan, an area for users to store comments about the experiment, and a sequence of labels for the columns of data. The data section contains these columns, with each row corresponding to one point of the scan.
The header has been designed to contain arbitrary metadata describing the contents of the file. This metadata is organized in a way that is easily readable by both humans and computers. These fields, described below, contain information about XAS experiments which is useful for both users and applications. A complete list of defined headers along with their specifications is found in Sec. 4.1.
This section of the XDI specification describes the formal structure of XDI files.
The key words "must", "must not", "required", "shall", "shall not", "should", "should not", "recommended", "may", and "optional" in this document are to be interpreted as described in RFC 2119.3, Key words for use in RFCs to Indicate Requirement Levels
An XDI implementation is not compliant if it fails to satisfy one or more of the must or required level requirements presented in this specification.
Several tokens are used throughout the definition of the XDI file.
XDI Tokens:
The white space token is a space (ASCII 32) or a tab (ASCII 9)
The comment token is a hash (
#)The end-of-line token can be carriage return (ASCII 13,
CR, Mac-style), newline (ASCII 10,LF, Unix-style), or a sequence of one carriage return + one newline (Windows-style)The field-end token consists of three or more foreward slash characters (
/, ASCII 47)The header-end token consists of three or more dash characters (
-, ASCII 45)
The header and data sections of an XDI file are comprised of structured US-ASCII text. Header field values that are "free-form" or "text" may contain UTF-8 encoded Unicode text, although Unicode support in applications that use XDI files should not be assumed, particularly those written in languages with weak or non-existent Unicode suport (e.g. Fortran). The US-ASCII coded character set is defined formally by ANSI X3.4-186. The Universal Character Set (Unicode) is defined by ISO/IEC 10646. The UTF-8 translation format is defined by IETF RFC 3629.
The header section of an XDI file appears at the beginning of the file and is comprised of structured text.
Header line rules:
Every line of the header must begin with a comment token and must end with an end-of-line token
Header lines may be of any length, but users of XDI should remember that XAS software may be implemented in a programming language without dynamic memory allocation (e.g. Fortran) and so should restrict lines to 2048 characters.
Header lines are subdivided into four subsections -- versioning information, header fields, user comments, and column labels -- with two separator lines, one of which is always required. These subsections must occur in the following sequence:
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The required first line of the file is the version line, described in Sec. 3.4.1.
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This is followed by header fields, which can be defined headers or extension headers. These two header types are explained in Sec. 3.4.2. Some headers are required, as explained in Sec. 4.4.
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The header lines are separated from the user comments by the field-end line. If the comment section is present, this separator line must also be present. If the comment sectionn is absent, the header lines may terminate with the end-of-header line. The field-end line is defined at the end of this section.
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The optional comment section is for user-supplied, free-format text. Each line begins with a comment token and ends with an end-of-line. See Sec. 3.4.3.
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The comment section ends with the required header-end line. The header-end line is defined at the end of this section.
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The last line before the data is a line of optional column labels which identify the columns of data. If present, there must be as many labels as there are columns. The label line begins with a comment character and ends with an end-of-line. See Sec. 3.4.4.
The field-end and header-end separator lines serve specific, syntactic purposes in the XDI grammar. For the human reader, the line of dashes is a visual cue denoting the end of the headers and beginning of the data. The field-end line serves to separate and distinguish field lines from freely-formatted user comments, which may resemble a header fields or other grammatical constructs. Similarly, the header-end line serves to distinguish column labels from user comments, which are otherwise grammatically identical elements of the data file.
Separator lines:
Field-end line: comment token + field-end token + end-of-line token
# /////////////Header-end line: comment token + header-end token + end-of-line token
# -------------
The first line of the XDI header contains the XDI version to which the
file conforms. XDI represents versions of the file format with a
<version>.<subversion>.<release> numbering scheme. The
<subversion> number is incremented when changes are made to the
format that do not affect compatibility with previous versions, as
when new defined header fields are defined. (A parser compliant with
an earlier minor version would treat the newly defined header as an
extension field. Propagated to an output file as an extension field,
this field would then be interpreted correctly by a more recent
parser.) The <version> number is incremented when major changes are
made to the format, as when the definition of the contents of a
defined header field is altered. The <release> is incremented when
the library or its documentation is altered without altering the
specification in any way. Use of the <release> number in XDI files
is optional.
A series of optional entries denoting further versioning information, separated by white space, may follow the XDI version. There may be any number of extra versioning strings. These version entries allow programs to annotate the file as it proceeds through the collection and analysis process. Such annotation is optional although version information must be included in this sequence by software that create XDI files containing extension fields (see section 4.2). When an application adds versioning information to this line, it should be appended to the end of the line. The order of the optional version entries is undefined but should be preserved by application reading the file in order to accurately represent the time sequence in which applications have manipulated the file.
Note that the XDI version, subversion, and release numbers must be treated as integers that may contain more than a single digit. “XDI/1.12” is a higher (more recent) version than “XDI/1.2”.
This specification does not impose a restriction on how applications identify and version themselves. However, a single application must identify and version itself using a single text sequence without white space. Some acceptable examples follow. The first example shows an application which uses the same format as the XDI version rule, which is the recommended format for application versioning; the second shows the names of the data acquisition and data processing programs are specified by name but without version numbers.
# XDI/1.0 Datacollectatron/7.75
# XDI/1.0 XDAC Athena
The name of the the additional applications must be used for any extension headers associated with that application (see section 4.2).
Immediately following the version line is the header fields subsection. These fields are arranged in a manner similar to the the header of an Internet electronic mail message, although XDI fields must not span multiple lines. Each field consists of a case-insensitive name, a separating colon, and an associated value. The structure of the name is presented in section 4. When multiple occurrences of the same field are present the value of the last occurrence must be used as the value for the field.
Except in the case of a defined header whose value has a defined structure, values are assumed to be free-form text, as explained in Sec. 3.3. The defined fields are explained in section 4.1.
When a user comments section is present, the header fields subsection must end with a field-end line. When a comments section is absent, the header fields subsection nust end with a field-end line. See section 3.4 for the definitions of the separator lines.
Following the dividing line at the end of the header fields subsection is the area of the header that contains user comments. This area is reserved for comments supplied by the experimenter and must not be used by software as a place to store other information. Refer to section 4.3 for information about using extension fields for this purpose.
This section may contain zero lines of commentary or empty lines containing no text other than the required comment toiken. An empty line must be treated as a zero-length comment line. This section must end with a header-end separator line.
When extracting the comment subsection from an XDI file, software may remove no more than one leading space and any trailing white space from each comment line but must not further alter the line’s contents, all interior whitespace must be preserved.
Applications must preserve all user comments, including empty lines, when exporting the XDI data as an XDI file.
The final line of the XDI header contains the labels for each column of data in the data section of the file, separated by white space. There must be one label present for each column of data present in the data section.
The number of column labels must equal the number of columns of data in the data section.
Note that each column label must be a word, white space must separate the labels, and labels must not contain white space. For specific column labels which, in natural language, would consist of two or more words, the use of CamelCase, underscores, or some other way of substituting for white space is required.
The column labels in the column label line must match the values
of the headers in the Column. namespace. See
section 4.2.
Several common array labels are defined in the Dictionary of Metadata and must be used when those arrays are present in a file.
The data section of the file contains white space separated columns of floating-point numbers. Line in the data section must not begin with comment tokens. A line in the data section may begin with white space. Leading white space on a line in the data section must be ignored.
The first (left-most) column of data must contain the abscissa (energy or angle) array.
Blank lines in this section must be discarded. The number of columns must be the same for all lines that contain data. All columns, including columns containing a measurement of time, must be represented as inegers or as floating point numbers.
It is recommended that measurements of time be represented as a
numerical offset relative to the value of the Scan.start_time
header.
When present, header fields must comply with the associated parsing rules. Any fields which fail to do so must be ignored by an application.
XDI fields use a simple namespace concept as their structure. The
name of the field must be of two words. The first word in the
name much start with a letter and must not start with a
number, underscore, or dash. The second word must consist of
letters, numbers, underscore, or dash. Letters are ASCII 65 through
90 (A-Z) and ASCII 97-122 (a-z). Numbers are ASCII 48-57
(0-9). Underscore (_) is ASCII 95 and dash (-) is ASCII 45.
The two words in the name must be separated by the dot character
(., ASCII 46). The name must end with a colon (:, ASCII 58),
which is the character which delimits the field name from its value.
The colon may be followed by white space, then must be
followed by the value of the field. A missing value must be
interpreted as an empty string.
Here are some examples which demonstrate both the format of the XDI field and the namespace concept:
# Beamline.name: APS 20BM
# Beamline.source: bend magnet
# Column.1: energy eV
# Column.3: i0
The namespaces are used to group related fields. In the example
above, two namespaces are shown. The Beamline namespace conveys
characteristics of the beamline at which the data were measured, the
Column namespace conveys hints about interpreting the columns
in the data section.
There are two kinds of namespaces. Defined namespaces (Section 4.1) are defined in the dictionary of metadata. Extension namespaces (Section 4.3) may be added by application developers to insert metadata into the data file.
Header fields are case insentitive. As an example, the following lines must be interpreted identically:
# Beamline.name: APS 20BM
# beamline.name: APS 20BM
# BEAMLINE.NAME: APS 20BM
Capitalization (like the first of the three examples above) of the namespace is recommended.
See the Dictionary of Metadata for the current list of defined namespace and defined metadata.
Three defined fields are required in a valid XDI file:
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Element.symbol: The symbol of the absorber element -
Element.edge: The measured absorption edge -
Mono.d_spacing: The d-spacing of the monochromator crystal. This is only required when the energy axis is conveyed as monochromator angle or encoder step count. When the energy axis is conveyed in energy units or pixel count, providing the d-spacing is strongly recommended to enable correction of the energy axis for a miscalibration due to inaccuracies in the translation from angular position of the monochromator to energy,.
All other fields are optional, although some are recommended, as explained in the Dictionary of Metadata.
A header in a defined namespace should not appear more than once in a file. When multiple occurrences of the same field are present the value of the last occurrence must be used as the value for the field.
The Column namespace is the mechanism by which XDI files provide hints about how to extract useful information from the columns in the data section of the file.
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All fields in this namespace must be of the form
Column.N, where N represents an integer. The integer is used to identify a particular column in the data file. These integers begin at 1 and count from the left-most column in the data section. The value of a Column field is used to indicate the contents of that column. -
There are several defined column labels. These are words that must be used to describe a column when that column is present in the data file and identified among the header fields. The list of defined column labels is given in the Dictionary of Metadata.
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The abscissa of the data must be in the first (left-most) column and must be identified by the
Column.1header. -
Data may be stored using any reasonable units for the abscissa, but that choice of units must be identified in the value of the
Column.1header. Allowed abscissa choices include energy (in units of eV or keV), pixel (appropriate for dispersive detection of XAS), or angle (in units of degrees, radians, or motor steps). eV units are recommended. If units of motor steps are chosen, then adequate information must be provided via headers in theMono.namespace to translate the abscissa into energy units. -
The abscissa column must be the first column in that data file and must be identified by the
Column.1header. -
The header identifying the abscissa must provide two values: the column label for the abscissa and the corresponding units. It looks something like this:
# Column.1: energy eV. All other headers in the Column namespace must provide one value -- the column label -- and may provide units, if appropriate.
A list of column labels and their meanings along with unit definitions for the abscissa are defined in the Dictionary of metadata. Any such array included in an XDI file must use those label definitions. Along with column labels defining the abscissa and various detectors, labels for representing EXAFS data in various stages of data processing (μ(E), normalized μ(E), χ(k), the Fourier transform of χ(k), or the Fourier filter of χ(k)) are provided.
Extension fields are fields present in the header of an XDI file that are not defined in the XDI specification. Such fields must be structured by the same syntax as a defined field. The values of extension fields must be interpreted as free-form text. Any field not defined in section 4.1 must be considered an extension field.
Data acquisition systems and data analysis packages may embed
additional information in an XDI file by adding extension fields to
the header. Extension fields created by applications should begin
with a form of the application name used in the version line, followed
by a separator dot and an additional work (in appendix A
examples such as MX.SSRS are shown in the example data file, where
MX is the name of the data acquisition software at that beamline and
SRSS is a paremeter relevant to the software).
Extension field namespaces may not collide with the defined namespaces.
Applications that read XDI files may attempt to parse the values of extension fields to extract the additional information about the scan. They should propagate these fields into output files they create, and must propagate the associated version information if they do so.
Multiple occurrences of the same field are discouraged. When present, the value of the last occurrence (reading linearly from the beginning of the file) must be preserved.
The following is a summary of the required elements of an XDI file:
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The first line of the file must contain version information. See section 3.4.1.
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The column containing the abscissa of the data and the units of the abscissa must be identified by a header field in the
Column.namespace. For example, if the first column of the data file contains energy in eV units, the following header field must appear in the file:# Column.1: energy eV. -
The column containing the abscissa of the data must be the first (left-most) column in the data section.
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The
Mono.d-spacingheader field must be specified if the abscissa is conveyed as monochromator angle. -
The
Element.symbolandElement.edgeheaders are required in order to definatively identify the XAS measurement. -
If user comments (see Sec. 3.4.3) are present in the header, the field-end separator line must be present to separate headers from user comments.
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The header-end separate line must be present.
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A data section must be present and each line of data must contain the same number of data fields and each field must be interpretable as an integer or a floating point number.
All other content is optional. When present certain content must meet further requirements. See the Dictionary of metadata.
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Headers containing time stamps, such as
Time.startandTime.endmust use the time stamp format of ISO 8601. -
Headers in the
Column.namespace must use the label columns defined in the Dictionary of metadata as values identifying the column types given in that table. Energy units must be one of the units specified in that table. Columns containing other kinds of data arrays may be labeled in a free-form manner according to the rules for header values.
There are several open areas of discussion for the current specification and grammar. Errors can be reported and issues can be suggested at the XDI issue tracker.
Here is an example of a file conforming to this specification and
providing substantial metadata. This was edited by hand from a real
data file measured at beamline 10ID at the APS in 2005. The lines
beginning MX. are extension fields denoting parameters of the MX data
acquisition system in use at the beamline.
# XDI/1.0 MX/2.0
# Element.symbol: Fe
# Element.edge: K
# Column.1: energy eV
# Column.2: i0
# Column.3: itrans
# Column.4: ifluor
# Column.5: irefer
# Facility.name: APS
# Facility.energy: 7.00
# Facility.xray_source: APS Undulator A
# Scan.start_time: 2005-03-08T20:08:57
# Mono.name: Si 111
# Mono.d-spacing: 3.1356
# Beamline.name: 10ID
# Beamline.undulator-harmonic: 1
# Beamline.collimation: none
# Beamline.focusing: none
# Beamline.harmonic-rejection: flat Rh-coated mirror
# 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 i0 itrans ifluor irefer
6899.9609 48120 19430 2250 54540
6900.1421 48390 19540 2260 54860
6900.5449 48520 19610 2250 55110
6900.9678 48930 19780 2280 55650
6901.3806 48460 19590 2250 55110
(....etc....)