Resolve coordinate offset problem

qupath · Nov 1, 2024 · 35d5d21 · 35d5d21
1 parent 974c482
commit 35d5d21
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/qubalab/images/labeled_server.py b/qubalab/images/labeled_server.py
@@ -106,7 +106,7 @@ def _read_block(self, level: int, region: Region2D) -> np.ndarray:
                         draw_geometry(
                             image.size,
                             drawing_context,
-                            self._geometries[i],
+                            shapely.affinity.translate(self._geometries[i], -region.x, -region.y),
                             1
                         )
                 full_image[label, :, :] = np.asarray(image, dtype=self.metadata.dtype)
@@ -119,7 +119,7 @@ def _read_block(self, level: int, region: Region2D) -> np.ndarray:
                 draw_geometry(
                     image.size,
                     drawing_context,
-                    self._geometries[i],
+                    shapely.affinity.translate(self._geometries[i], -region.x, -region.y),
                     self._feature_index_to_label[i]
                 )
             return np.expand_dims(np.asarray(image, dtype=self.metadata.dtype), axis=0)
diff --git a/tests/images/test_labeled_server.py b/tests/images/test_labeled_server.py
@@ -465,17 +465,16 @@ def test_multi_channel_labeled_image_with_region_request():
     downsample = 1
     features = [ImageFeature(geojson.LineString([(7, 5), (9, 5)]))]
     expected_image = np.array(
-        [[[[False, False, False, False, False],
+        [[[False, False, False, False, False],
           [False, False, False, False, False],
-          [False, False, False, False, False]]],
-          [[[False, False, False, False, False],
+          [False, False, False, False, False]],
+          [[False, False, False, False, False],
           [False, False, False, False, False],
-          [False, False, True, True, True]]]]
+          [False, False, True, True, True]]]
     )
     labeled_server = LabeledImageServer(sample_metadata, features, multichannel=True, downsample=downsample)
     region = Region2D(5, 3, labeled_server.metadata.width-5, labeled_server.metadata.height-3)
     image = labeled_server.read_region(1, region)
-
     np.testing.assert_array_equal(image, expected_image)
 
 def test_multi_channel_labeled_image_with_starting_downsample():