NXRefine 1.0.0b1

Data reduction for single crystal x-ray scattering

Introduction

NXRefine implements a complete workflow for both data acquisition and reduction of single crystal diffuse x-ray scattering collected as a series of area detector frames during continuous sample rotation. The data are stored in HDF5 files, which conform to the NeXus data format standard. These files contain a comprehensive set of metadata, including the incident wavelength, powder calibration scans used to define detector distances, beam centers, and yaw, pitch, and roll corrections. Automated peak searches of the three-dimensional data arrays define a set of Bragg peaks that are used to define an orientation matrix, defined according to Busing and Levy, which is then used to transform the data from angular coordinates to reciprocal space coordinates using the CCTW program. Multiple rotations at different detector translations and offset rotation axes are combined to ensure that there are no gaps in the reconstructed data, and allow the construction of masks to eliminate detector artifacts due to Compton scattering within the sensor layers. Finally, the data can be transformed into 3D-ΔPDF maps using the punch-and-fill method after symmetrization.

The workflow is implemented as plugins to the NeXpy package that are used to set up the basic experimental configuration and sample parameters, and determine the orientation matrix. The remaining components of the workflow can be run as command-line scripts, or submitted to a queue for distribution to multiple nodes or processes for simultaneous reduction of multiple datasets.

Instructions for running NXRefine are under development.

The NXRefine package is being developed as part of a DOE-funded project to utilize advanced computational methods for the analysis of single-crystal x-ray scattering from synchrotron sources, such as multidimensional spectral analysis and machine learning. Further details of this project are available on the AXMAS web pages.

Installing and Running

The source code can be downloaded from the NeXpy Git repository:

    $ git clone https://github.com/nexpy/nxrefine.git

To install in the standard Python location:

    $ pip install .

Prerequisites

Python Packages

The following packages are listed as dependencies.

• nexpy
• gemmi
• pyfai
• sqlalchemy
• psutil

CCTW

CCTW (Crystal Coordination Transformation Workflow) is a C++ package written by Guy Jennings. It is launched as a separate process by NXRefine, which uses the experimental metadata to define the settings file used to define the input and output grids. It has to be separately installed.

User Support

If you are interested in using this package, please contact Ray Osborn ([e-mail]). Please report any bugs as a Github issue, with relevant tracebacks.