Developer documentation

Adding a feature processing toolbox

We suggest to use the wrapping we did around the PyRadiomics toolbox as an example.

  1. Check if config type is in fastr.types: else, make your own. See the WORC datatypes for examples.

  2. Make a fastr tool, which basically is a XML wrapper around your tool telling fastr what the inputs and outputs are. You can take our wrappers around pyradiomics as example: see the command line wrapper for when your toolbox is command line executable, or the Python wrapper for when your toolbox needs an interpreter such as Python. In the latter case, you will also need to include an actual script using the interpreter, which is by default placed in the bin folder together with the wrapper. The script will need to parse the arguments defined in the XML, see here for the one using PyRadiomics.

    For more information, visit the fastr documentation.

  3. In WORC, go to the WORC.WORC.WORC.add_feature_calculator function and change the following:

  1. Add a converter for your config file if you do not use the .ini format WORC by default uses.

  2. If you followed a, also add a config safe function to WORC.WORC.WORC.save_config.

  3. Make sure you add both sources and sinks for your tools.

  4. Link these sources and sinks to the fastr network in the WORC.WORCWORC.set function.

  5. Add part to feature converter

  1. To convert the feature files from your toolbox to WORC compatible format, add the neccesary functionality to the WORC.featureprocessing.FeatureConverter function.

  2. Tell WORC to use your feature calculator by changing the relevant config field: config['General']['FeatureCalculators].

Testing and example data

WIP

Adding methods to hyperoptimization

WIP