pygix 2022.11.14

Software library for grazing-incidence/fibre X-Ray data analysis

pygix

Pygix is a generic python library for performing reduction of grazing-incidence and fiber X-ray scattering data.

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The pygix library has been developed to reduce 2D X-ray scattering data for experiments recorded in grazing-incidence (GISAXS, GIWAXS, GIXRD, GIXD, collectively referred to as GIXS) and fiber diffraction modes. Both 2D image projections and 1D line profile extraction are handled. The package is designed to be as generic as possible, i.e., it makes no assumptions about the data (passed by the user as numpy arrays) and all detector and geometric corrections can be handled at the point of data reduction.

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Please refer to the wiki for more detailed discussion!

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Example usage:

    import pygix
    import pygix.plotting as pp

    pg = pygix.Transform()
    pg.load('detector_calibration.poni')
    pg.indcident_angle = 0.2

    # transform image into reciprocal space:
    i, qxy, qz = pg.transform_reciprocal(data)

    pp.implot(i, qxy, qz, xlim=(-5, 28), ylim=(-.5, 32), mode='rsm')

Which will generate the following image:

Pygix uses the fiber transformation originally described by Stribeck [1] (based on earlier work by Polayni [2]), which has recently been formulated for the case of grazing-incidence scattering [3]. The reciprocal space transformation for the fiber and grazing-incidence X-ray scattering are thus equivalent, meaning this python library is generic for both classes of experiments.

Pygix is heavily based on the pyFAI library for conventional 2D transmission azimuthal integration [4].

References

1. Stribeck and Nöchel, J. Appl. Crystallogr., (2009), 42, 295–301
2. Polanyi, Z. Physik, (1921), 7, 149-180
3. Lilliu and Dane, arXiv:1511.06224 [cond-mat.soft]
4. Ashiotis, Deschildre, Nawaz, Wright, Karkoulis, Picca and Kieffer, J. Appl. Crystallogr., 2015, 48, 510–519 (https://github.com/silx-kit/pyFAI/)

Installation

In the near future, pygix will be available via PIP. In the meantime, download the source code in .zip format from the github repository and unpack it.

    unzip pygix-master.zip

Go to the pygix-master directory, build and install the package:

    cd pygix-master
    python setup.py build install

Credits

• pygix was written by Thomas Dane with contributions and assistance from Jerome Kieffer.
• The derivation of the reciprocal space transformation was done in collaboration with Samuele Lilliu.
• pygix relies heavily on the pyFAI library.