Metadata-Version: 2.1
Name: xrmreader
Version: 2.3
Summary: A reader and preprocessor for txrm/xrm data acquired by Zeiss microscopes.
Home-page: https://git5.cs.fau.de/mthies/xrm_reader
Author: Mareike Thies
Author-email: mareike.thies@fau.de
License: UNKNOWN
Description: ## 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 
        ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE.  If software is 
        modified to produce derivative works, such modified software should 
        be clearly marked, so as not to confuse it with the version available 
        from ANL.
        
        Additionally, redistribution and use in source and binary forms, with 
        or without modification, are permitted provided that the following 
        conditions are met:
        
        * Redistributions of source code must retain the above copyright 
        notice, this list of conditions and the following disclaimer. 
        
        * Redistributions in binary form must reproduce the above copyright 
        notice, this list of conditions and the following disclaimer in 
        the documentation and/or other materials provided with the 
        distribution. 
        
        * Neither the name of UChicago Argonne, LLC, Argonne National 
        Laboratory, ANL, the U.S. Government, nor the names of its 
        contributors may be used to endorse or promote products derived 
        from this software without specific prior written permission. 
        
        THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS 
        "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
        LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
        FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago 
        Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, 
        INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
        BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
        LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 
        LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN 
        ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
        POSSIBILITY OF SUCH DAMAGE.
        
        
        For the rest of the code, this applies.
        
        Copyright (c) 2021 Mareike Thies
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
        
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
