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X-RAY RUNS: Apply for Beamtime

2017  May 17 - June 29

2017  October 11 - December 21
2017  Proposal deadline: 08/01/17
2017  BTR deadline: 09/10/17

CHESS supports a wide variety of x-ray techniques, many of which require use of multiple sophisticated, highly-specialized software packages to form a data analysis “pipeline” to reduce and process the data generated here. In many cases, these software packages are “research code”: works in progress written by scientists, not software developers, who are willing to share their effort with other scientists.

Sharing software, however, requires the additional effort to build, package, and distribute the program and its supporting libraries. It is a complicated and time consuming undertaking for those of us who support such projects.

For users, installing scientific software can also be problematic. Some data analysis pipelines may require multiple loosely-related programs and support libraries. For example, the Praxes software used for real-time analysis of scanning x-ray fluorescence microscopy experiments at CHESS requires nine packages to operate, each of which needed to be installed independently. Users often reported difficulty and frustration with this process.

In response, researchers at CHESS have been contributing to a new open-source package manager developed by Continuum Analytics called “Conda”, which provides simple access to a wide variety of scientific software packages written in C, Fortran, Python, R, etc. Developers of scientific software specify a project’s dependencies, and conda compiles and packages the software for Windows, Linux, or OSX, and uploads the result for distribution.

 

As a CHESS user, once you install the Anaconda Scientific Python Distribution via http://continuum.io/downloads, go to the start menu and run Anaconda’s “Launcher” program1. In the upper right corner, click on “Manage Channels”:

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1Anaconda’s “Launcher” is not included in the linux installer. To obtain it, open a terminal and run “conda install launcher”

Anaconda screen 1

which will open a dialog allowing you to specify additional “channels” for conda to search for new software. We recommend adding the “chess” and “fable” channels, to which CHESS contributes software packages. The Fable channel provides packages comprising the Fable software framework, which is frequently used at CHESS for studies of structural materials. The CHESS channel provides the “Praxes” software used for scanning x-ray fluorescence microscopy, and HEXRD, which is used for diffraction studies of individual grains in bulk materials:

Anaconda screen 2

 

Once conda knows to search these channels, additional software will appear in the list:

Anaconda screen 3

HEXRD can now be obtained simply by clicking its “install” button.

Anaconda screen 4

 

Once installed, click the “Launch” button to start the program:

Anaconda screen 5

and that’s it! You now have HEXRD and all ten of its supporting libraries (and all of their supporting libraries) installed on your computer:

Anaconda screen 6

 

CHESS has been working with collaborators at AFRL, LLNL, and Continuum Analytics to improve the efficiency of HEXRD such that data can now be processed and results obtained at the beamline (recently achieving more than a 100x speedup.) We have also greatly simplified how users operate HEXRD from the command line, and are in the process of making the graphical user interface both more capable and more intuitive. Here is a sneak peek:

Anaconda screen 7

 

CHESS researchers have been collaborating with colleagues from the European Synchrotron Radiation Facility and Technical University of Denmark on development and distribution of the Fable software framework. Fable does not yet appear in the Anaconda Launcher list, but the software is available via conda. To obtain the Fable software needed for 3D-XRD experiments at CHESS, open a terminal or DOS shell and run the command “conda install 3dxrd-scripts”, which again will install everything you need to analyze your data.

Instructions on use of fable for far-field indexing and near-field grain mapping can be found here: PDF

Example data for testing software: Si data (zip file)