[REF] use custom patching implementation and use Apache 2.0 license #153
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This implementation is licensed GPL3 and is incompatible with Apache 2.0 license. We would like to use Apache 2.0 so this commit removes the GPL3 licensed code.
We have removed code from CLAM and are no longer bound by GPL. As of this commit, wsinfer is licensed under Apache 2.0.
Before this commit, we were missing the bottom and right edge of patches because the stop of the coord range was set slightly too low. This commit fixes that, so now all patches are represented. This commit also sorts the coordinate indexes after shapely tree query, because it seems that the order query returns is arbitrary. Sorting that ensures that when we index the coordinates that are contained in the polygon, those coordinates are in ascending order (with y changing most rapidly).
Our patching algorithm ignores patches that go outside of the slide boundary.
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Our original patching algorithm used code from CLAM, which is licensed under GPL. This PR removes CLAM code and replaces it with a custom implementation.
The saved HDF5 file with patch coordinates is similar to that of CLAM to be inter-operable with patches that one might create using CLAM.
fixes #148
This is an image of model outputs in a TCGA BRCA image.