Advanced Photon Source

An Office of Science National User Facility

Data Exchange

The simplest Scientific Data Exchange definition for storing raw tomographic dataScientific Data Exchange describes a simple data model that is designed to interface, or "exchange" data from different instruments to many data analysis tools, allowing sharing of capabilities between scientific domains. Its implementation uses the Hierarchical Data Format (HDF5), a widely used and well supported storage mechanism for scientific data as an underlying technology for data format independence. The Scientific Data Exchange format implementation for X-ray tomography is defined at DXfile; this is the native data storage format used by the tomography instruments of the APS Imaging group and it has been implemented using the area-detector  hdf5 plug-in customized using the following configuration files

To provide an interface between tomographic raw datasets collected at all major synchrotron facilities and tomoPy, a Python toolbox to perform tomographic data processing and image reconstruction tasks, we developed DXchange;

 

Distribution & Impact

Data Exchange is an open-source software, and the repository is on Github and it runs on all major platforms and operating systems. Anyone can download, use it freely, and contribute to it through GitHub. DXchange provides an interface with tomoPy and raw tomographic data collected at different synchrotron facilities by providing different tomographic raw data format importers.  The complete list of supported facilities is available online.

Data Exchange also allows tomography users running experiment at any synchrotron facility to share data in a unified model.

DXfile, implements the Scientific Data Exchange format for tomography providing definition, reader and writer and it is currently in use at the Advanced Photon Source beamline 2-BM and 32-ID, at the Swiss Light Source Tomcat beamline and at the Elettra SYRMEP beamline.

 

Funding Source

This project has been produced using operational funding from the APS, contract DE-AC02-06CH11357.

 

Please cite

Francesco De Carlo, Doga Gürsoy, Federica Marone, Mark Rivers, Dilworth Y. Parkinson, Faisal Khan, Nicholas Schwarz, David J. Vine, Stefan Vogt, Sophie-Charlotte Gleber, Suresh Narayanan, Matt Newville, Tony Lanzirotti, Yue Sun, Young Pyo Hong and Chris Jacobsen (2014). J. Synchrotron Rad. 21, doi:10.1107/S160057751401604X

Related Publication

D. Gürsoy, F. De Carlo, X. Xiao and C. Jacobsen, TomoPy: a framework for the analysis of synchrotron tomographic data (2014). J. Synchrotron Rad. 21, doi:10.1107/S1600577514013939

 

Future Work
  • Extend the Data Exchange module to support other techniques starting from the one being processed by tomoPy