Converting Topspin app5 Files

The NanoMegas Topspin (https://nanomegasusa.com/topspin/) app5 file format is an hdf5 file containing images and metadata from scanning precession electron diffraction (SPED) experiments. The source data is often 4-D, but the structure of the file is flat. This page provides an overview of a utiliity to convert the app5 files into a chuncked, compressed, multidimensional hdf5 file.

The format of the created file matches that of the Medipix3 files documented in Accessing and Converting Merlin Binary Files. The same sum images across detector and scan axes are generated during conversion and stored in the same places, making it easy to inspect and navigate the dataset. The same analysis techniques and algorithms may be applied to the converted app5 datasets, and viewing tools may be used. One of the main differences between the Medipix3 the converted app5 hdf5 files is that additional data are included for the latter; specifically, a survey image and additional scan details.

Conversion is generally simpler than for raw Medipix3 data and is performed with the topspin_app5_to_hdf5(): function.

>>> from fpd.fpd_io import topspin_app5_to_hdf5
>>> output_fn = topspin_app5_to_hdf5('input.app5')

Where input.app5 is the Topspin app5 file. One parameter not currently extracted is the precession angle. This can be specified during conversion by the prec_angle parameter. Additional parameters allow control over the chunking and compression settings, as documented in the docstring (topspin_app5_to_hdf5():).