Add function-based filters

[alexzwanenburg]

pyradiomics implements several filters that are used to transform intensities using simple functions, i.e. square, square root, logarithm and exponential transformations. To allow for validating and reproducing pyradiomics-based studies with MIRP, these filters need be implemented. Their mathematical descriptions are trivial.

However, it is not 100% clear where these filters should be placed in the image processing workflow. IBSI-conform processing suggests that filtering should be done after all other image processing, and prior to feature computation. It seems that at least the high-level interface to the processing workflow (the execute method of the RadiomicsFeatureExtractor class in radiomics/featureextractor.py) does in fact perform filtering last. This would mean that any image normalisation is conducted on the original image, not the filtered image, in the generality of cases in literature.

• [x] Implement as objects in mirp/imageFilters.
  • [x] square
  • [x] square root
  • [x] logarithm
  • [x] exponential
• [x] Add new transformed image object class in mirp/images/transformedImage.
  • [x] square
  • [x] square root
  • [x] logarithm
  • [x] exponential
• [x] Add filters to list in get_available_image_filters in ImageTransformationSettingsClass. Filter names should be pyradiomics_* to make it clear that these are re-implementations of the pyradiomics filters.
  • [x] square
  • [x] square root
  • [x] logarithm
  • [x] exponential
• [x] Add filter-specfic has_*_filter method to ImageTransformationSettingsClass.
  • [x] square
  • [x] square root
  • [x] logarithm
  • [x] exponential
• [x] Add filters to transform_images in the StandardWorkflow object to allow for their use in image processing.
  • [x] square
  • [x] square root
  • [x] logarithm
  • [x] exponential
• [x] Add test for filter.
  • [x] square
  • [x] square root
  • [x] logarithm
  • [x] exponential
• [x] Update documentation of ImageTransformationSettingsClass to mention these filters.

[alexzwanenburg]

@MaEmily @LukasDuenger

[alexzwanenburg]

Available on the 2.2.0 branch.