glue-medical 0.2

Plugin for glue to support medical data

Requirements

Note that this plugin requires glue to be installed - see this page for instructions on installing glue.

In addition, this plugin requires the GDCM and pydicom packages to be installed. If you are using conda, you can easily install these with:

conda install -c conda-forge gdcm pydicom

Installing

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.

Using

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:

glue mydata.dcm

or

glue directory_with_dicom_files

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.

Testing

To run the tests, do:

py.test glue_medical

at the root of the repository. This requires the pytest module to be installed.