README.md

GANDLF Preprocessing

Adding a new algorithm

• Define a new submodule under GANDLF.data.preprocessing.
• Ensure that the new algorithm is wrapped in a class, by following the example of GANDLF.data.preprocessing.non_zero_normalize.NonZeroNormalizeOnMaskedRegion.
  • This uses a torchio.Transform as a base class.
  • The class name is the algorithm's identifier for GaNDLF.
  • Add it as a new submodule.
  • Wrap the new algorithm in a _transform function, which makes it easier to define algorithmic properties (see GANDLF.data.preprocessing.threshold_and_clip as an example, where the same class is used for both threshold and clip functionalities) If new algorithm can be wrapped in a function:
  • Add function in the new submodule.
  • The _transform function is the algorithm's identifier for GaNDLF.
• Add the algorithm's identifier to GANDLF.data.preprocessing.__init__.global_preprocessing_dict as appropriate.
• Call the new algorithm from the config using the data_preprocessing key.