Bug/fix annotation sorting #203
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jonasteuwen
requested review from
EricMarcus-ai,
sinberlin2,
AjeyPaiK,
VanessaBotha and
BPdeRooij
sinberlin2
reviewed
Nov 29, 2023
sinberlin2
reviewed
Nov 29, 2023
sinberlin2
reviewed
Nov 29, 2023
sinberlin2
reviewed
Dec 1, 2023
| annotation = shapely.geometry.MultiPoint(annotation_list) | ||
| json_dict = _geometry_to_geojson(annotation, label=label) | ||
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| json_dict["id"] = str(idx) |
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there could be a placeholder for id in _geometry_to_geojson. Also is the key "id" in data ever used?
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We can do a placeholder, but we cannot set it as it denotes the order of the annotations and this is only available in this function. It’s also required by GeoJSON
sinberlin2
approved these changes
Dec 1, 2023
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Changes in this PR:
- Split_by_label option removed in as_geojson() of WsiAnnotations.
- Consecutive annotations are grouped as long as they are of the same label to reduce the size of the output
- The proper order of annotations is retained in in as_geojson() of WsiAnnotations.
Tests:
A number of annotations for a slide are defined using ASAP format. The test checks whether the annotations are the same after being converted to geojson. The tests covers areas with annotations and an area of the slide where there are no annotations (and area is therefore None).
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This PR fixes the way the annotations are sorted in the GeoJSON output. Previously, the output of
WsiAnnotations.as_geojson()exported them in the order they were inserted without taking into account the sorting order selected while this is actually required to get the proper order of annotations. Also the tests are updated to reflect this.