dicom-decompress

A command-line utility for decompressing DICOM files with compressed pixel data. Optionally, ff photometric interpretation is one of YBR_FULL, YBR_FULL_422, PALETTE COLOR pixel data will be transcoded to RBG.

Installation

pip install dicom-decompress

This will install the terminal command dicom-decompress in your environment.

Some transfer syntaxes need the c++ library GDCM installed. Install this by

conda install gdcm -c conda-forge

See here on how to install conda.

To decompress a single file run

dicom-decompress in.dcm out.dcm

where in.dcm is the file to decompress and out.dcm is the decompressed target file. To attempt transcoding for non monochrome or rgb images add the --transcode flag:

dicom-decompress --transcode in.dcm out.dcm

To decompress multiple files in-place run e.g.

find . -name "*.dcm" -exec echo {} \; -exec dicom-decompress --transcode {} {} \;

Dependencies

• numpy
• pydicom

Development

Update your .pypirc file in your home directory to include

index-servers = 
	pypi
	<your other servers...>
    
[pypi]
repository: https://upload.pypi.org/legacy/
username: <your pypi username>

...

• To build: python setup.py sdist bdist_wheel (requires python3 + wheel package)
• To install: pip install --force-reinstall dist/dicom_decompress-x.y.z-py3-none-any.whl, (x.y.z is version, see setup.py)
• To publish
  • Install twine: pip install twine
  • Build package (cf. above)
  • Make sure it passes the twine check: twine check dist/*
  • Publish: twine upload dist/*