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Implement WsiAnnotations in C++ (#252)
* Updated workflows * Adding C++ TIFF writer - Bump version to 0.7 - Rebuild setup toolchain to pyproject.toml - Remove CLI utilities and tests - Rename dlup.types to dlup._types - Reduce cyclic imports - Remove color transform from internal_handler='pil' (working towards v1.0) - Bugfixes * Add ZSTD compression, reformat some files * First commit with geometries * First writing of Polygon * Some additional changes to cast the Polygon. * Commiting to not lose work * Updated for initial version of WsiAnnotations * updates * Some updates during development * Fix scaling issues * Added functionality to remove polygons and points and to rebuild the RTree * Implement complete initial version of geometry module * We actually need to iterate over all layers, not just polys * Implement scaling and offset functions * Adding functionality to reindex polygons * Created output container for results * Sensible updates * Add masking utility to AnnotationRegion * Memory optimizations * Adding sorting capabilities * Add bounding box * Added color LUT * Refactor * Extend dunder methods and code simplification for annotations (#251) * Add z_index to geojson properties when importing and exporting * Fix annotation crop for Polygons in read_region and test_annotations * Created new AnnotatedGeometry, adhere to shapely dunder and functions * Add helper function to utils and Enum for Darwin/ASAP annotation types * Add darwin_annotation_type to color look up and move Darwin util function to utils * Bugfix for WsiAnnotations.filter function Refactor into multiple modules Support pickling and some other features Extend dunder methods and code simplification for annotations (#251) * Add z_index to geojson properties when importing and exporting * Fix annotation crop for Polygons in read_region and test_annotations * Created new AnnotatedGeometry, adhere to shapely dunder and functions * Add helper function to utils and Enum for Darwin/ASAP annotation types * Add darwin_annotation_type to color look up and move Darwin util function to utils * Bugfix for WsiAnnotations.filter function Removing files, improving test coverage and mypy * Fixing the scaling, mypy and adding tests * minor changes in annotations * Updating geometry module, and its tests. * Rename modules, improve CI/CD * Almost done with the geometry module Strange bug remains. * Disable a few tests, squash pylint errors * Fixing some bugs when trees get invalidated This was a problem when the insertation order was not the same. * Do an allclose rather than equal * Weirdly enough different values on github * Maybe a sudo install won't hurt * Remove assert * Restructure C++ code * Restructure C++ code * Refactored code. * Refactoring * Refactor code * Rename functions, remove functions * Adhere to google C++ style guide * Maybe include stdexcept so that github understandS? * Reducing a few compiler warnings * Make sure mypy runs. * Convenient helper function * Implement XML export * Add xsdata to requirements * XML Schema reading now works * Order can be 0... * Several changes to support HaloXML * Improve test coverage * Improve test coverage to 90% * Streamlining * Trying to get better CI/CD coverage * Fix bug in annotations_experimental.py * Add more tests, and fix bug in process * Updating tests, updating schema, add box * Add more boxes functionality. * Refactor factory methods to factory.h * Refactor * Code simplifications * Some final memory improvements * Adding boxes to the geometry module * Improve CI/CD * Adding deprecation warnings * Streamline meson * Attempt lazy initialization of the geometry collection in the region class * Update tests for lazy evaluation * Fixing memory error in region.h. Fix tox * Improve workflows * Improve workflows * Update tox.ini * Remove line that doesn't work on github (?!) * Cleanup code * Try to run tests non-parallel * Squash errors for now * Fixes for ubuntu * Improving annotations to mask conversion * Reformat * Add Lazy Array * Added some extra functionality to lazy array * Added lazy evaluation for PolygonCollection * Added lazy evaluation for PolygonCollection * Make precommit run * Updates to CI * Fix mypy * Add ROI to the GeometryCollection * Added ROIs to DLUP XML * Added ROIs to output xml and parsing * move declarations to headers --------- Co-authored-by: Bart de Rooij <[email protected]> Co-authored-by: Jonas Teuwen <[email protected]> Co-authored-by: JorenB <[email protected]>
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