Package: xrmreader
Reading and preprocessing x-ray projection data in Zeiss .txrm formatThis package extends thedxchange readerto read the Zeiss proprietary data format .txrm to python lists or arrays. In particular, the import of metadata from the file headers is extended to access information needed for reconstructing x-ray projection data, e.g. acquired on Zeiss x-ray microscopes. Further, the package contains some simple functions to preprocess x-ray projections in preparation for reconstruction. These include flat field correction, revision of detector shifts, downsampling, conversion into line integral domain and truncation correction.For installation, please runcondainstall-cconda-forgedxchange
pipinstallxrmreaderThis example code usespyconradfor visualization.importxrmreaderimportpyconrad.autoinitfromedu.stanford.rsl.conrad.data.numericimportNumericGridprojection_data=r'your_file.txrm'metadata=xrmreader.read_metadata(projection_data)print(metadata)# load raw dataraw_projections=xrmreader.read_txrm(projection_data)NumericGrid.from_numpy(raw_projections).show('Raw projections')# preprocess data in individual stepsprojections=xrmreader.read_txrm(projection_data)projections=xrmreader.divide_by_reference(projections,metadata['reference'])projections=xrmreader.revert_shifts(projections,metadata['x-shifts'],metadata['y-shifts'])projections=xrmreader.downsample(projections,spatial_factor=2)projections=xrmreader.negative_logarithm(projections)projections=xrmreader.truncation_correction(projections)NumericGrid.from_numpy(projections).show('Preprocessed projections version 1')# load and preprocess data in one step (this does the same thing as the individual steps above, but needs less memory)preprocessed_projections=xrmreader.read_and_preprocess_txrm(projection_data)NumericGrid.from_numpy(preprocessed_projections).show('Preprocessed projections version 2')CopyrightAs the reading functionality is modified from the dxchange project by De Carlo et al.
(https://github.com/data-exchange/dxchange), we reproduce their copyright notice.Copyright (c) 2016, UChicago Argonne, LLC. All rights reserved.Copyright 2016. UChicago Argonne, LLC. This software was produced
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