Fix decoding of graphic data in annotations group (#192)

Author: hackermd

src/highdicom/ann/content.py

@@ -502,7 +502,7 @@ def get_graphic_data(
         Parameters
         ----------
         coordinate_type: Union[str, highdicom.ann.AnnotationCoordinateTypeValues]
-            Coordinate type of annotation
+            Coordinate type of annotations
 
         Returns
         -------
@@ -512,7 +512,7 @@ def get_graphic_data(
 
         """  # noqa: E501
         coordinate_type = AnnotationCoordinateTypeValues(coordinate_type)
-        if self._graphic_data:
+        if len(self._graphic_data) > 0:
             if coordinate_type not in self._graphic_data:
                 raise ValueError(
                     'Graphic data is not available for Annotation Coordinate '
@@ -595,7 +595,7 @@ def get_graphic_data(
                 indices_or_sections=split_param
             )
 
-            self._graphic_data[coordinate_type] = graphic_data
+            self._graphic_data = {coordinate_type: graphic_data}
 
         return self._graphic_data[coordinate_type]
 
@@ -758,7 +758,7 @@ def from_dataset(cls, dataset: Dataset) -> 'AnnotationGroup':
         highdicom.ann.AnnotationGroup
             Item of the Annotation Group Sequence
 
-        """
+        """  # noqa: E501
         if not isinstance(dataset, Dataset):
             raise TypeError(
                 'Dataset must be of type pydicom.dataset.Dataset.'
@@ -770,7 +770,7 @@ def from_dataset(cls, dataset: Dataset) -> 'AnnotationGroup':
         )
         group = deepcopy(dataset)
         group.__class__ = cls
-        group._graphic_data = {}
+        group._graphic_data = {}  # will be handled by get_graphic_data()
 
         group.AnnotationPropertyCategoryCodeSequence = [
             CodedConcept.from_dataset(

src/highdicom/ann/sop.py

@@ -405,7 +405,8 @@ def from_dataset(
             )
         if dataset.SOPClassUID != '1.2.840.10008.5.1.4.1.1.91.1':
             raise ValueError(
-                'Dataset is not a Microscopy Bulk Simple Annotation.'
+                'Dataset is not a Microscopy Bulk Simple Annotations '
+                'instance.'
             )
         _check_little_endian(dataset)
         ann = deepcopy(dataset)

tests/test_ann.py

@@ -11,6 +11,7 @@
 
 from highdicom.ann.content import Measurements, AnnotationGroup
 from highdicom.ann.enum import (
+    AnnotationCoordinateTypeValues,
     AnnotationGroupGenerationTypeValues,
     GraphicTypeValues,
 )
@@ -231,6 +232,10 @@ def test_construction(self):
         assert values.shape == (2, 0)
 
     def test_alternative_construction_from_dataset(self):
+        coordinates_data = np.array(
+            [1.0, 1.0, 2.0, 2.0, 3.0, 3.0],
+            dtype=np.double
+        )
         dataset = Dataset()
         dataset.AnnotationGroupNumber = 1
         dataset.AnnotationGroupUID = str(UID())
@@ -249,19 +254,34 @@ def test_alternative_construction_from_dataset(self):
         dataset.AnnotationPropertyTypeCodeSequence = [annotated_type]
         dataset.NumberOfAnnotations = 3
         dataset.GraphicType = 'POINT'
-        dataset.DoublePointCoordinatesData = [1.0, 1.0, 2.0, 2.0, 3.0, 3.0]
+        dataset.DoublePointCoordinatesData = coordinates_data.tobytes()
         dataset.AnnotationAppliesToAllZPlanes = 'NO'
         dataset.AnnotationAppliesToAllOpticalPaths = 'YES'
 
         group = AnnotationGroup.from_dataset(dataset)
         assert isinstance(group, AnnotationGroup)
         assert isinstance(group.graphic_type, GraphicTypeValues)
-        assert isinstance(group.algorithm_type,
-                          AnnotationGroupGenerationTypeValues)
+        assert isinstance(
+            group.algorithm_type,
+            AnnotationGroupGenerationTypeValues
+        )
         assert group.algorithm_identification is None
         assert isinstance(group.annotated_property_category, CodedConcept)
         assert isinstance(group.annotated_property_type, CodedConcept)
 
+        graphic_data = group.get_graphic_data(
+            coordinate_type=AnnotationCoordinateTypeValues.SCOORD
+        )
+        assert isinstance(graphic_data, list)
+        assert len(graphic_data) == 3
+        assert graphic_data[0].dtype == np.double
+        assert graphic_data[0].shape[1] == 2
+        assert graphic_data[0].shape[0] == 1
+        assert np.array_equal(
+            graphic_data[0],
+            np.array([[1.0, 1.0]], dtype=np.double)
+        )
+
         names, values, units = group.get_measurements()
         assert names == []
         assert units == []