Fix rename labels (#164)

* Fix transform to rename labels
* Fix openslide backend vendor call

MANIFEST.in

@@ -1,9 +1,10 @@
 include CONTRIBUTING.rst
 include LICENSE
 include README.md
+include dlup/py.typed
 
 recursive-include tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
-recursive-include docs *.rst *.md conf.py Makefile make.bat *.jpg *.png *.gif *.typed
+recursive-include docs *.rst *.md conf.py Makefile make.bat *.jpg *.png *.gif

dlup/data/transforms.py

@@ -13,7 +13,7 @@
 
 import dlup.annotations
 from dlup._exceptions import AnnotationError
-from dlup.annotations import AnnotationType
+from dlup.annotations import AnnotationClass, AnnotationType
 
 _AnnotationsTypes = dlup.annotations.Point | dlup.annotations.Polygon
 
@@ -171,13 +171,17 @@ def __call__(self, sample):
                 output_annotations.append(annotation)
                 continue
 
-            if isinstance(annotation, dlup.annotations.Polygon):
-                output_annotations.append(dlup.annotations.Polygon(annotation, label=self._remap_labels[label]))
-
-            elif isinstance(annotation, dlup.annotations.Point):
-                output_annotations.append(dlup.annotations.Point(annotation, label=self._remap_labels[label]))
+            if annotation.a_cls.a_cls == AnnotationType.BOX:
+                a_cls = AnnotationClass(label=self._remap_labels[label], a_cls=AnnotationType.BOX)
+                output_annotations.append(dlup.annotations.Polygon(annotation, a_cls=a_cls))
+            elif annotation.a_cls.a_cls == AnnotationType.POLYGON:
+                a_cls = AnnotationClass(label=self._remap_labels[label], a_cls=AnnotationType.POLYGON)
+                output_annotations.append(dlup.annotations.Polygon(annotation, a_cls=a_cls))
+            elif annotation.a_cls.a_cls == AnnotationType.POINT:
+                a_cls = AnnotationClass(label=self._remap_labels[label], a_cls=AnnotationType.POINT)
+                output_annotations.append(dlup.annotations.Point(annotation, a_cls=a_cls))
             else:
-                raise AnnotationError(f"Unsupported annotation type {type(annotation)}")
+                raise AnnotationError(f"Unsupported annotation type {annotation.a_cls.a_cls}")
 
         sample["annotations"] = output_annotations
         return sample

dlup/experimental_backends/openslide_backend.py

@@ -74,7 +74,7 @@ def magnification(self) -> int | None:
     @property
     def vendor(self) -> str:
         """Returns the scanner vendor."""
-        return self.properties.properties[openslide.PROPERTY_NAME_VENDOR]
+        return self.properties.get(openslide.PROPERTY_NAME_VENDOR, None)
 
     @property
     def slide_bounds(self) -> tuple[tuple[int, int], tuple[int, int]]:

setup.cfg

@@ -20,3 +20,6 @@ replace = {new_version}
 
 [aliases]
 test = pytest
+
+[options.package_data]
+dlup = py.typed

tests/test_annotations.py

@@ -13,7 +13,6 @@
 from dlup.annotations import AnnotationClass, AnnotationType, Polygon, WsiAnnotations
 from dlup.utils.imports import DARWIN_SDK_AVAILABLE
 
-
 ASAP_XML_EXAMPLE = b"""<?xml version="1.0"?>
 <ASAP_Annotations>
     <Annotations>

tests/test_transforms.py

@@ -0,0 +1,29 @@
+# coding=utf-8
+# Copyright (c) dlup contributors
+import pytest
+
+from dlup.data.transforms import AnnotationClass, AnnotationType, RenameLabels
+
+
+class Polygon:
+    def __init__(self, coordinates, a_cls):
+        self.coordinates = coordinates
+        self.label = a_cls.label
+        self.a_cls = a_cls
+
+
+class Point:
+    def __init__(self, coordinates, a_cls):
+        self.coordinates = coordinates
+        self.label = a_cls.label
+        self.a_cls = a_cls
+
+
+@pytest.fixture
+def remap_labels():
+    return {"old_label1": "new_label1", "old_label2": "new_label2"}
+
+
+@pytest.fixture
+def renamer(remap_labels):
+    return RenameLabels(remap_labels)