Test and lint fixes

ImagingDataCommons · Oct 19, 2024 · 93d5d36 · 93d5d36
1 parent ded30b1
commit 93d5d36
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Showing 2 changed files with 52 additions and 18 deletions.
diff --git a/src/highdicom/sr/templates.py b/src/highdicom/sr/templates.py
@@ -2393,7 +2393,11 @@ def __init__(
         method: Optional[Union[CodedConcept, Code]] = None,
         properties: Optional[MeasurementProperties] = None,
         referenced_images: Optional[Sequence[SourceImageForMeasurement]] = None,
-        referenced_coordinates: Optional[Sequence[Union[CoordinatesForMeasurement, CoordinatesForMeasurement3D]]] = None,
+        referenced_coordinates: Optional[
+            Sequence[
+                Union[CoordinatesForMeasurement, CoordinatesForMeasurement3D]
+            ]
+        ] = None,
         referenced_real_world_value_map: Optional[RealWorldValueMap] = None
     ):
         """
@@ -2515,7 +2519,10 @@ def __init__(
                 content.append(image)
         if referenced_coordinates is not None:
             for scoord in referenced_coordinates:
-                if not isinstance(scoord, (CoordinatesForMeasurement, Scoord3DContentItem)):
+                if not isinstance(
+                    scoord,
+                    (CoordinatesForMeasurement, Scoord3DContentItem)
+                ):
                     raise TypeError(
                         'Arguments "referenced_coordinates" must have type '
                         'CoordinatesForMeasurement or Scoord3DContentItem.'
@@ -2641,21 +2648,33 @@ def referenced_images(self) -> List[SourceImageForMeasurement]:
         return [SourceImageForMeasurement.from_dataset(m) for m in matches]
 
     @property
-    def referenced_coordinates(self) -> List[Union[CoordinatesForMeasurement, CoordinatesForMeasurement3D]]:
+    def referenced_coordinates(self) -> List[
+        Union[CoordinatesForMeasurement, CoordinatesForMeasurement3D]
+    ]:
         """List[Union[highdicom.sr.CoordinatesForMeasurement, highdicom.sr.CoordinatesForMeasurement3D]]:
-        referenced coordinates"""
+        referenced coordinates"""  # noqa: E501
         if not hasattr(self[0], 'ContentSequence'):
             return []
         scoord_matches = find_content_items(
             self[0],
             value_type=ValueTypeValues.SCOORD
         )
-        coord = [CoordinatesForMeasurement.from_dataset(m) for m in scoord_matches]
+        coord: List[
+            Union[CoordinatesForMeasurement, CoordinatesForMeasurement3D]
+        ] = [
+            CoordinatesForMeasurement.from_dataset(m)
+            for m in scoord_matches
+        ]
         scoord3d_matches = find_content_items(
             self[0],
             value_type=ValueTypeValues.SCOORD3D
         )
-        coord.extend([CoordinatesForMeasurement3D.from_dataset(m) for m in scoord3d_matches])
+        coord.extend(
+            [
+                CoordinatesForMeasurement3D.from_dataset(m)
+                for m in scoord3d_matches
+            ]
+        )
         return coord
 
     @property
@@ -3327,8 +3346,8 @@ def __init__(
             for measurement in measurements:
                 if measurement.referenced_coordinates:
                     raise ValueError(
-                        'Referenced coordinates in measurements are not allowed in '
-                        f'{self.__class__.__name__}.'
+                        'Referenced coordinates in measurements are not '
+                        f'allowed in {self.__class__.__name__}.'
                     )
 
 
@@ -3348,7 +3367,7 @@ class PlanarROIMeasurementsAndQualitativeEvaluations(
     def __init__(
         self,
         tracking_identifier: TrackingIdentifier,
-        referenced_region: Union[ImageRegion, ImageRegion3D, None],
+        referenced_region: Union[ImageRegion, ImageRegion3D, None] = None,
         referenced_segment: Optional[ReferencedSegmentationFrame] = None,
         referenced_real_world_value_map: Optional[RealWorldValueMap] = None,
         time_point_context: Optional[TimePointContext] = None,

diff --git a/tests/test_sr.py b/tests/test_sr.py
@@ -2165,7 +2165,10 @@ def test_construction(self):
 
         assert len(item.ContentSequence) == 1
         assert item.ContentSequence[0] == self.source_image
-        assert item.ContentSequence[0].relationship_type == RelationshipTypeValues.SELECTED_FROM
+        assert (
+            item.ContentSequence[0].relationship_type ==
+            RelationshipTypeValues.SELECTED_FROM
+        )
 
 
 class TestReferencedSegment(unittest.TestCase):
@@ -2855,8 +2858,14 @@ def test_referenced_coordinates(self):
         assert len(measurement.referenced_coordinates) == 2
         assert scoord in measurement.referenced_coordinates
         assert scoord_3d in measurement.referenced_coordinates
-        assert isinstance(measurement.referenced_coordinates[0], CoordinatesForMeasurement)
-        assert isinstance(measurement.referenced_coordinates[1], CoordinatesForMeasurement3D)
+        assert isinstance(
+            measurement.referenced_coordinates[0],
+            CoordinatesForMeasurement
+        )
+        assert isinstance(
+            measurement.referenced_coordinates[1],
+            CoordinatesForMeasurement3D
+        )
 
 
 class TestQualitativeEvaluation(unittest.TestCase):
@@ -3124,13 +3133,19 @@ def test_constructed_with_measurements_coordinates(self):
             name=codes.SCT.Diameter,
             value=5,
             unit=codes.UCUM.Millimeter,
-            referenced_coordinates=[CoordinatesForMeasurement(
-                graphic_type=GraphicTypeValues.POLYLINE,
-                graphic_data=np.array([[1, 1], [2, 2]]),
-                source_image=self._image_for_region
-            )]
+            referenced_coordinates=[
+                CoordinatesForMeasurement(
+                    graphic_type=GraphicTypeValues.POLYLINE,
+                    graphic_data=np.array([[1, 1], [2, 2]]),
+                    source_image=self._image_for_region
+                )
+            ]
+        )
+        msg = (
+            'Referenced coordinates in measurements are not '
+            'allowed in PlanarROIMeasurementsAndQualitativeEvaluations.'
         )
-        with pytest.raises(ValueError) as exc:
+        with pytest.raises(ValueError, match=msg):
             PlanarROIMeasurementsAndQualitativeEvaluations(
                 tracking_identifier=self._tracking_identifier,
                 referenced_region=self._region,