Kikuchi diffraction via pyxem

In recent years shortcomings of classical text-based file formats for serializing Kikuchi diffraction data have been realized and lead to a replacement of these formats with proprietary and open-source alternatives that use binary containers like Hierarchical Data Format (HDF)5. At the point when we started the implementation of the Kikuchi diffraction examples for the FAIRmat project, several of these formats were not yet supported by MTex. In parallel, we acknowledge the complementary analyses capabilities for Python users that the work of the pyxem and hyperspy developers providers for the electron microscopy community. Therefore, we decided that as a technical implementation example we will implement the first version such that it uses, apart from MTex, the I/O and orientation math capabilities of these Python libraries.

As a result, this pyxem-based parsing of HDF5-serialized Kikuchi diffraction content equips the pynxtools-em parser and normalizer currently with functionalities to read the following content and map on respective NeXus concepts that are defined in the NXem application definition and the NXem_ebsd base class:

Orientation, phase	NeXus/HDF5
Oxford Instruments H5OINA HDF5
Bruker Esprit HDF5
H5EBSD-based community format
ThermoFisher Velox
EDAX APEX
DREAM.3D v6	()
EMsoft HDF5	()