GIXSGUI: Grazing-incidence X-ray Scattering data visualization, reduction and analysis

GIXSGUI is GUI interface written in Matlab. GIXS image data and experiment parameters are input and data operations are achieved via built-in methods. This design allows both GUI and scripted operation, thus enabling customized data handling and analysis, batch processing and data automation.

GIXSGUI supports a variety of image formats including TIF (TIFF), MAT (Matlab), CBF, FTIS, and EDF. Depending on the experiment configuration, it selectively implements a series of data corrections to raw image data such as detector flat field and efficiency corrections, air path absorption correction, polarization and Lorenz corrections, solid angle correction, and any other user-defined corrections. It can reshape the image from pixel-based interpretation to q and/or angle space-based ones. It can reduce the 2D image to 1D profiles for further data modeling and fitting.

3D nano-structure indexing is a sub-package independent of GISXGUI which searches for allowed grazing-incidence X-ray diffractions from a polycrystalline films of a given space group or unit-cell construction, and labels their positions. While capable of running in a script mode by itself, this sub-package is integrated within GIXSGUI so that indexing can be compared directly on the experiment data.

A number of other features handy for the experiments and data analysis are included, for example, sample-to-detector distance calibration with diffraction from silver behenate standard or specular reflections from thin films or flat wafers, ROI counting to extract intensities over a series 2D image scans, and etc.

 

Distribution & Impact

GIXSGUI was developed for users at the dedicated GIXS beamline at Sector 8-ID-E, Advanced Photon Source. It is readily applied to GIXS data collected at other synchrotron facilities as well as laboratory-based instruments. The toolbox is actively maintained with new data exploration features and analysis methods implemented upon users’ need. It runs in Matlab 2010a or later. The toolbox is delivered with PDF documentation for installation and operation instructions, as well as a set of commented examples for beginners.

 

Funding Source

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

 

Please cite

Z. Jiang, GIXSGUI: a Matlab toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried 3D periodic nano-structured films (2015), J. Appl. Cryst. 48, 917-926 (doi:10.1107/S1600576715004434)

 

Future Work

GIXSGUI is designed with a GUI interface that runs on top of a Matlab handle class data type gixsdata. GIXS image data and experiment parameters are input and stored as properties of gixsdata, and data operations are achieved via built-in methods of gixsdata. This design allows running the toolbox in a script mode that is fully independent of GUI, thus enabling customized data handling and analysis, batch processing and data automation for large data set that often result from in-situ and time-resolved experiments.