kits21 is now a python package. It should be installed with pip install -e . so that the data is stored in the correct directory. Making this a package is necessary to allow code to be reused between the different folders. It will also enable users to re-use specific functions in their contributions to the challenge (from kits21 import ...). This also ensures all requirements are installed
code was added to sample valid segmentations from the annotations. Sampled segmentations are not yet uploaded because we still need to agree on an aggregation scheme (kidney <-> ureter discussion).
metric computation is implemented
deltas can now be computed for sampled segmentations (did not yet run, see above)
gauged score computation is implemented
Small Improvements:
paths are now defined in a central location: kits21.configuration.paths
added if __name__ == '__main__': in import.py (important safeguard!)
no longer crashes when KITS21_TEST_DIR or KITS21_SERVER_DATA is not in os.environ
probably some more things that I forgot
Metric implementation is still WIP, I am waiting for results of our nnU-Net baseline and a decision on the segmentation aggregation discussion.
Please have a look and verify that everything is still working on your end.
Hi Nick, there are lots of changes in here:
pip install -e .so that the data is stored in the correct directory. Making this a package is necessary to allow code to be reused between the different folders. It will also enable users to re-use specific functions in their contributions to the challenge (from kits21 import ...). This also ensures all requirements are installedSmall Improvements:
if __name__ == '__main__':in import.py (important safeguard!)KITS21_TEST_DIRorKITS21_SERVER_DATAis not in os.environMetric implementation is still WIP, I am waiting for results of our nnU-Net baseline and a decision on the segmentation aggregation discussion.
Please have a look and verify that everything is still working on your end.
Best,
Fabian