11.1. File metadata

11.1.1. Tracking the data about your data

New in version 0.9.21: ATHENA has supported import and export of metadata using the XAS Data Interchange (XDI) specification.

When metadata can be gleaned from the file you import, it will be stored in the ATHENA project file and used to make the header portion of any output files written by ATHENA.

There are three categories of information displayed in ATHENA's metadata display tool. At the top is versioning information about the XDI specification as well versioning information for any data acquisition or analysis software that has touched the data.

Below that is a tree of metadata grouped into families of sensible, widely understood, semantic groupings of data. Some of these items are defined in the XDI dictionary, while others are associated with the software that has touched the data.

Finally, there is a section of user comments. This is any information associated with the file that has meaning to the user but which does not fit neatly into semantic groupings.

../_images/metadata.png

Fig. 11.2 The metadata display tool.

If the input data file is in the XDI format, all metadata and all user comments will be stored by ATHENA and displayed in this tool.

Because XDI is a new standard that has not yet been widely adopted, ATHENA provides a plugin mechanism whereby an input data file can be parsed for metadata as it is imported. This parsing is a beamline-specific chore, thus plugins are written which are tailored to the data files written as particular beamlines. The selection of beamline plugins is limited at this time. DEMETER ships with one plugin for several XAS beamlines at NSLS (many of the XAS beamlines at NSLS use the same data acquisition software) and another for the beamlines at Sector 10 at the APS.

The image above shows an example of the NSLS beamline plugin. The data displayed in that image are from NSLS beamline X23A2. The metadata was either gleaned from the data file or from a small database of facility and beamline metadata that comes with DEMETER.

Two pieces of metadata will always be displayed in the metadata viwewer, Element.symbol and Element.edge. These are two pieces of metadata that are required elements of the XDI specification. The periodic table is replete with examples of atoms that have absorption edges with very similar edge energies. For example, the tabulated values of the Cr K edge and the Ba LI edge are both 5989 eV. Without identification of the species of the absorbing atom and of the absorption edge measured, some data cannot cannot be unambiguously identified.

Since ATHENA always attempts to determine those two pieces of information for any data, those two are always available for display in the viewer.

11.1.2. Interacting with the metadata

This tool is not particularly interactive. Metadata is typically inserted into a file by a data acquisition or analysis program and is not intended to be altered by the user. The one exception is the user comments area. In ATHENA, this is a normal text editing control into which you can type whatever you want. The contents of this control will be saved as user comments when the Save comments button is pressed.

11.1.3. Beamline plugins

Metadata can extracted from any data file so long as a beamline plugin has been written. The plugin is contained in a .pm file in the Plugins/Beamlines/ folder of the DEMETER installation. This is a piece of perl code which performs the following chores:

  1. Very quickly recognize whether a file comes from the beamline. Speed is essential as every file will be checked sequentially against every beamline plugin. If a beamline plugin is slow to determine this, then the use of ATHENA or other applications will be noticeably affected.
  2. Recognize semantic content from the file header. Where possible, map this content onto defined XDI headers. Other semantic content is placed into extension headers. In the example above, metadata from the XDAC data acquisition program is placed into the XDAC family, which other metadata is placed into families defined in the XDI specification.
  3. Add versioning information for the data acquisition program into the XDI extra_version attribute. In the example above, the data file was collected using version 1.4 of XDAC, so the string “XDAC/1.4” is placed among the applications.

DEMETER also has a small database of metadata related to specific beamlines. This is found in the share/xdi/ folder of the DEMETER installation. Each of the files in that folder is a short .ini file containined common information about facilities and beamlines. Much of the metadata shown above actually came from the .ini file for NSLS beamline X23A2.

To add new beamlines to this part of ATHENA, it is necessary to write the plugin and the corresponding .ini file.



DEMETER is copyright © 2009-2016 Bruce Ravel – This document is copyright © 2016 Bruce Ravel

This document is licensed under The Creative Commons Attribution-ShareAlike License.

If DEMETER and this document are useful to you, please consider supporting The Creative Commons.