Experimental Glue medical plugin
conda install -c conda-forge gdcm pydicom
To install the latest developer version of the plugin from the git repository, you can do:
pip install https://github.com/glue-viz/glue-medical/archive/master.zip
This will auto-register the plugin with Glue.
At the moment, this plugin provides a reader for DICOM files. You can give glue either a DICOM file or a directory containing DICOM files. For example, you can start glue using:
and you can also load files from inside glue. It is not yet possible to load a directory from the 'Open Data Set' menu in glue.
At the moment, if all the shapes of the DICOM files match inside the directory, we combine the arrays into an array with a higher dimensionality (for example we combine 2d arrays into a single 3d array). In future, we will make it possible for users to control this behavior.
To run the tests, do:
at the root of the repository. This requires the pytest module to be installed.