Major changes
- Added support for SEG DICOM files for segmentation.
- Added support for processing RTDOSE files.
- It is now possible to combine and split masks, and to select the largest mask or mask slice, as part of the image
processing workflow. Masks can be combines by setting `mask_merge = True`, which merges all available masks for an
image into a single mask. This can be useful when, e.g., multiple regions of interest should be assessed as a single
(possibly internally disconnected) mask. Masks are split using `mask_split = True`, which separates every disconnected
region into its own mask that is assessed separately. This is used for splitting multiple lesions inside a single mask
into multiple separate masks. The largest region of interest in each mask is selected by
`mask_select_largest_region = True`. This can be used when, e.g., only the largest lesion of multiple lesions should be
assessed. Sometimes, only the largest slice (i.e. the slice containing most of the voxels in a mask) should be
assessed. This is done using `mask_select_largest_slice = True`. This also forces `by_slice = True`.
These mask operations are implemented in the following order: combination -> splitting -> largest region ->
largest slice.
- Masks from an RT-structure file that shares a frame of reference with an image but does not have a one-to-one
mapping to its voxel space can now be processed. This facilitates processing of masks from RT structure sets that
are, e.g., defined on CT images but applied to co-registered PET imaging, or from one MR sequence to another.
Fixes
- Providing a mask consisting of boolean values in a numpy array no longer incorrectly throws an error.
- Configuration parameters from `xml` files are now processed in the same manner as parameters defined as function
arguments. The same default values are now used, independent of the parameter source. This fixes a known issue where
outlier-based resegmentation would occur by default using `xml` files, whereas the intended default is that no
resegmentation takes place.
- Masks can now be exported to the file system without throwing an error.
- DICOM files from frontal or sagittal view data are now correctly processed.