Surfer Plot

Data Analysis

Data Formats

Three data files are generated for each data acquisition with the Mythen detector with the extensions: .raw, .parab, and .xye.

  • Raw Files – Files with the extension .raw are comprised of the raw channel data without flat field correction. The data is in xy format, where x = detector channel number and y = counts.
  • Parab Files – These files contain meta-data, additional information relating to the experiment.  These data include: a time stamp, the data acquisition time, the integrated ion chamber counts, and the 2-theta axis position. Below is an example of the contents of a parab file.
  • XYE Files – These files have been corrected for intensity variations in the detector channels. The data is in xye format, where x = 2theta angle, y = corrected counts and e = error. 

Data Reduction

Data from the beamline needs to be put in a form that allows for further analysis. PDViper is used to combine data obtained from more than one detector position, and DIOPTAS is used to integrate 2D data.

PDViPeR

PDViPeR is a BSD-licensed data visualisation, processing and reporting software package for 1D powder diffraction data. PDViPeR is a python-based package that reads in and views Australian Synchrotron Powder Diffraction beamline data from the Mythen II microstrip detector, and is capable of efficient multi-detector position data merging. The package is capable of easily producing images for publication and reports, with a range of output options including raw, stack, 2D surface and 3D plots. Dataset normalisation, scaling, background subtraction and inputting of both XYE and XY file formats are additional features. 

The Australian Synchrotron thanks the National eResearch Collaboration Tools and Resources (NeCTAR) for generously providing funding for this project.

    PDViPeR Download

    To obtain the current software version, please enter your first name and email address in the field, and click 'Subscribe' to obtain download links. Collection of your email address enables us to get an idea of the number of users and is covered by our privacy policy, stated here. We may use this address to inform you of new versions of PDViPeR.  

    The PD team are interested in your feedback from your experiences with PDViPeR and would like suggestions for features to be added in the future. Please send bug reports and suggestions to pdviper@ansto.gov.au

    • DIOPTAS – DIOPTAS is a Python based program for the reduction and analysis of 2D powder diffraction data. It has been optimised for fast data reduction of the high amounts of data that are generated at synchrotron sources. The software is able to be used for calibration of a wide variety of geometries, and the 2D image and integrated pattern can be simultaneously explored. To learn more, visit the DIOPTAS website. 

    Search - Match

    Phase identification is needed for multiphase samples. Both the HighScore or DIFFRAC.EVA program can be used to carry out the search-match, together with either the COD or PDF ICDD database. Structural information can also be obtained from the ICSD database. 

    • HighScore– Phase identification can be carried out in the HighScore program from Malvern Panalytical. A large number of different data formats are accepted and multiple reference databases can be coupled to the program for search-matching. Other functions of the software include profile fitting and semi-quantitative phase analysis. 
    • DIFFRAC.EVA– Search matching of powder diffraction data can be performed in DIFFRAC.EVA by Bruker AXS. Other capabilities of the software include peak fitting, 2D data integration, cluster analysis and semi-quantitative phase analysis.
    • COD– The Crystallography Open Database is an open access database of crystal structures, which can be used with HighScore. Any researcher can contribute to the database through the websites automatic validation and deposition capability. To access the database, visit the COD here.
    • PDF-ICDD – The Powder Diffraction File database from the International Centre for Diffraction Data is the largest diffraction database, and includes Minerals and Organics versions. Patterns can be searched by a variety of ways, for example by name/chemical composition, crystallography and diffraction information, or physical properties. The ICDD database can be integrated with HighScore.
    • ICSD – The Inorganic Crystal Structure Database is produced by FIZ Karlsruhe and contains crystallographic information of inorganic structures. The information can be used as a starting point for structural refinement.  

    Analysis

    Quantitative structural information can be obtained from careful analysis of diffraction data. Data refinements can be carried out in GSAS II and peak fitting in CMPR. PDF patterns may be generated and modelled in PDFgetX3.  

    • GSAS II – GSAS II is an open source Python based program developed by Robert Von Dreele and Brian Toby. It is capable of accepting X-ray and neutron powder and single crystal data, as well as performing joint refinements. Further information can be found at the GSAS II website.
    • CMPR – The program is open source and is useful for viewing data, indexing and peak fitting. However, it is important to note that it is no longer developed or maintained by Brian Toby. Further information on CMPR can be found on the website. 
    • PDFgetX3 – PDFgetX3 is a command line program from the Simon Billinge group at Colombia University for generating pair distribution functions (PDF) from diffraction data. It is free for academic research only. This program uses an algorithm to correct for the additive and multiplicative contributions to the measured intensities in an experiment. Resultant PDFs can also be modelled using the PDFGUI. For more information, see the PDFgetX3 website. 

    Visualisation

    Crystal structures can be viewed in VESTA or CrystalMaker X, and in situ diffraction data plotted in Surfer.   

    • VESTA – VESTA is an open source program for viewing crystal structures in 3D. Structures can be rotated or orientated down a crystallographic axis, structural information such as site symmetries, fractional coordinates, bond lengths and angles can be displayed. Volumetric data including electron densities and wave functions can be visualised, and transparent isosurfaces compared with models. More information on VESTA can be found here.
    • CrystalMaker X – Crystal structures can be viewed using CrystalMaker X. Other capabilities include volumetric data visualisation, bond length and angle measurement, molecular modelling and the ability to create animations. A wide variety of data formats can be accepted.
    • Surfer – In situ diffraction data can be plotted using the Surfer program. Data is interpolated into a regularly spaced grid that can be presented in a variety of map styles. These include 3D surface maps and contour types. Plots are also able to be modelled and analysed, as well as orientated, scaled and coloured to highlight features of interested.