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Software and data analysis

Data formats

Data is generated as HDF5 files and saved in '/data/visitor/proposal_number'.

  • Raw data are saved as multiple HDF5 files with ~100 measurements in each, with a master HDF5 that links to each.
  • Processed data saves as a single HDF5 file for each measurement, including both the integrated XRD map and XRF if taken. The h5py python package can be used for manipulation or creation of HDF5 files.

 

The following programs can be used to open and view HDF5 files:

  • Silx view: quick viewing of HDF5 structure and data
  • PyMCA: please see the Analysis Tools section below for details
  • Jupyter notebooks

Beamline interfaces

Bliss is the command-line software common to most beamlines. It is used to move motors and trigger measurements. Your local contact will train you in any use of Bliss necessary for your experiment. Queuing multiple measurements in Bliss requires creating a python script with the relevant commands.

Daiquiri is a Graphical User Interface that ID13 uses to image our samples with an optical microscope, outline regions of interest (ROIs) where we want to take measurements, and trigger or queue measurements. It is recommended for standard mapping experiments, as no coding knowledge is required for its use.

Online/Offline data analysis tools

The following tools are provided at the beamline and data analysis cluster:

  • PyMCA can display data as interactive map and isolate regions/peaks of interest in the map or diffraction pattern, but does not allow for XRD fitting. It can perform XRF fitting

  • XRDUA software can perform fitting of a peak intensity list (i.e not Rietveld, Pawley, or Le Bail fitting) derived from the CIFs multiple crystalline phases. Peaks of unknown phases can also be added

Tutorials for both can be found here, and for PyMCA on the ESRF Youtube channel.

  • Batch XRD fitting can be carried out in other softwares such as TOPAS and GSAS, but these are not designed for map visualisation

  • In-house software is in development at ESRF for Rietveld-esque (lattice-parameter-varying fitting with fixed peak intensity ratios) fitting of 2D maps. This is currently available as a Jupyter notebook, please ask your local contact for further details

Data policy and storage

The ESRF data policy is available here (https://www.esrf.fr/datapolicy).

Data is stored in active storage for three months after the experiment, and available from the beamline computers (on-site) and the computing cluster (off-site) under path 'data/visitor/proposal_number'.

After three months, the raw data is moved to permanent storage on tape, and will not be accessible unless restored (please ask your local contact if this is required).

Please download your data in due time. fore more information on data transfer: https://www.esrf.fr/Infrastructure/Computing/ComputingOffsite/FtpWindows.

The data is under embargo for three years after the experiment, after which it will be made publicly available.