xrmreader 2.9.1
A reader and preprocessor for txrm/xrm data acquired by Zeiss microscopes.
Requires Python: >=3.6

## Reading and preprocessing x-ray projection data in Zeiss .txrm format

This package extends the [dxchange reader](https://github.com/data-exchange/dxchange "Dxchange github") to 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 run
```shell
conda install -c conda-forge dxchange
pip install xrmreader
```

This example code uses [pyconrad](https://git5.cs.fau.de/PyConrad/pyCONRAD "Pyconrad github") for visualization.

```python
import xrmreader
import pyconrad.autoinit
from edu.stanford.rsl.conrad.data.numeric import NumericGrid


projection_data = r'your_file.txrm'

metadata = xrmreader.read_metadata(projection_data)
print(metadata)

# load raw data
raw_projections = xrmreader.read_txrm(projection_data)
NumericGrid.from_numpy(raw_projections).show('Raw projections')

# preprocess data in individual steps
projections = 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')
```

## Copyright


As 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 
under U.S. Government contract DE-AC02-06CH11357 for Argonne National 
Laboratory (ANL), which is operated by UChicago Argonne, LLC for the 
U.S. Department of Energy. The U.S. Government has rights to use, 
reproduce, and distribute this software.  NEITHER THE GOVERNMENT NOR 
UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR 
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THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS 
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For the rest of the code, this applies.

Copyright (c) 2021 Mareike Thies

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