Extend dunder methods and code simplification for annotations

[BPdeRooij]

This PR implements some new features, refactors the annotations code and aims to simplify it. Most importantly are the addition of AnnotatedGeometry and new dunder methods in WsiAnnotations. It is an initial idea and implementation for features, which could be useful. It would be great to further discuss these ideas and get feedback.

Changes

• Added class AnnotatedGeometry to inheret from for Point and Polgyon classes. This simplifies code for the Point and Polygon classes. This also allows us to extend to new annotated geometries for MultiPolygon or MultiPoint with our own annotation classes.
• Added __iadd__ and __isub__ methods for AnnotatedGeometry that raises a TypeError.
• Modified __new__ function to be in line with shapely. This allows polygons (with holes) to be created directly as a dlup Polygon.
• Combined annotation_type lookup into a single enum for ASAP, V7 and GeoJSON.
• Added annotation_type to DarwinV7Metadata lookup for colors. This is useful when a class for keypoints and polygons have the same label, but different colors. In that case annotation_type is needed to retrieve the correct color.
• Simplified _is_rectangle and added _is_alligned_rectangle for determining unrotated bounding boxes.
• Use of Shapely affinity transformation instead of transform
• Added a utils file with utility functions for annotations. Perhaps, DarwinV7Metadata and _get_v7_metadata can also be moved here.
• Export z-index into geometry properties class. (Still being discussed here: z-index is not imported or exported with GeoJSONs #240)
• Slightly improved type hinting.
• Incorporated _ComplexDarwinPolygonWrapper directly into _parse_darwin_complex_polygon.
• Fixed test_point_pickling in test_annotations.py by pickling dlup point instead of ShapelyPoint

Changes made to WsiAnnotations:

• Changed _available_labels to use set instead of list for efficiency
• Added sorting layers in place to WsiAnnotations
• Directly use shapely.affinity.affine_transform in the read_region function.
• Extended WsiAnnotations dunder methods:
  • Added __len__ as length of _layers
  • Extend __contains__ to check if a Point or Polygon is in layers
  • Implemented __add__, __iadd__ and __radd__ for addition, in-place addition and right side addition.
  • Added templates for methods __sub__, __isub__ and __rsub__
• Added tests for dunder methods.

Further changes and comments:

• Define behavior for __radd__ of lists of Polygons and Points
• Add same functionalities for subtracting from WsiAnnotations.
• Write more tests for (new) dunder methods
• Move DarwinV7Metadata and _get_v7_metadata to utils file. This is not possible now because AnnotationType is added to the metadata.
• Move other helper function and classes (such as _geometry_to_geojson, GeoJsonDict, CoordinatesDict, _is_rectangle, _is_allagined_rectangle) to util file to simplify code.
• The WsiAnotations.copy function uses deepcopy. The test and behavior for this method are not completely in line with the shallow and deep copy operations defined in the standard python library. Another __copy__ and __deepcopy__ method could be added.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.63%. Comparing base (548fc87) to head (faa019e).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #251      +/-   ##
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+ Coverage   98.53%   98.63%   +0.09%     
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  Files          14       14              
  Lines        1091     1169      +78     
==========================================
+ Hits         1075     1153      +78     
  Misses         16       16              

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[jonasteuwen]

LGTM, nice work!