Fix typing errors reported by mypy

src/highdicom/ann/content.py

@@ -1,6 +1,6 @@
 """Content that is specific to Annotation IODs."""
 from copy import deepcopy
-from typing import List, Optional, Sequence, Tuple, Union
+from typing import cast, List, Optional, Sequence, Tuple, Union
 
 import numpy as np
 from pydicom.dataset import Dataset
@@ -24,7 +24,7 @@ class Measurements(Dataset):
     def __init__(
         self,
         name: Union[Code, CodedConcept],
-        values: np.array,
+        values: np.ndarray,
         unit: Union[Code, CodedConcept]
     ) -> None:
         """
@@ -152,7 +152,7 @@ def from_dataset(cls, dataset: Dataset) -> 'Measurements':
             )
         ]
 
-        return measurements
+        return cast(Measurements, measurements)
 
 
 class AnnotationGroup(Dataset):
@@ -588,9 +588,9 @@ def get_measurements(
                 if name is None or item.name == name
             ]
             if len(values) > 0:
-                values = np.vstack(values).T
+                value_array = np.vstack(values).T
             else:
-                values = np.empty((number_of_annotations, 0), np.float32)
+                value_array = np.empty((number_of_annotations, 0), np.float32)
             names = [
                 item.name for item in self.MeasurementsSequence
                 if name is None or item.name == name
@@ -600,10 +600,10 @@ def get_measurements(
                 if name is None or item.name == name
             ]
         else:
-            values = np.empty((number_of_annotations, 0), np.float32)
+            value_array = np.empty((number_of_annotations, 0), np.float32)
             names = []
             units = []
-        return (names, values, units)
+        return (names, value_array, units)
 
     def _get_coordinate_index(
         self,
@@ -726,4 +726,4 @@ def from_dataset(cls, dataset: Dataset) -> 'AnnotationGroup':
                 for ds in group.PrimaryAnatomicStructureSequence
             ]
 
-        return group
+        return cast(AnnotationGroup, group)

src/highdicom/ann/sop.py

@@ -2,7 +2,7 @@
 from collections import defaultdict
 from copy import deepcopy
 from operator import eq
-from typing import Any, Dict, List, Optional, Sequence, Tuple, Union
+from typing import Any, cast, Dict, List, Optional, Sequence, Tuple, Union
 
 import numpy as np
 from pydicom.dataset import Dataset
@@ -417,4 +417,4 @@ def from_dataset(
             for item in ann.AnnotationGroupSequence
         ]
 
-        return ann
+        return cast(MicroscopyBulkSimpleAnnotations, ann)

src/highdicom/ko/content.py

@@ -112,6 +112,7 @@ def __init__(
             meaning='Source',
         )
         for ds in referenced_objects:
+            reference_item: Union[ImageContentItem, CompositeContentItem]
             if 'Rows' in ds and 'Columns' in ds:
                 reference_item = ImageContentItem(
                     name=name,

src/highdicom/pm/sop.py

@@ -470,7 +470,7 @@ def __init__(
             raise ValueError('Pixel array must be a 2D, 3D, or 4D array.')
 
         # Acquisition Context
-        self.AcquisitionContextSequence = []
+        self.AcquisitionContextSequence: List[Dataset] = []
 
         # Image Pixel
         self.Rows = pixel_array.shape[1]
@@ -784,7 +784,6 @@ def _encode_frame(self, pixel_array: np.ndarray) -> bytes:
                 'in case of encapsulated format encoding.'
             )
         if self.file_meta.TransferSyntaxUID.is_encapsulated:
-            # Check that only a single plane was passed
             return encode_frame(
                 pixel_array,
                 transfer_syntax_uid=self.file_meta.TransferSyntaxUID,

src/highdicom/sr/templates.py

@@ -4023,6 +4023,7 @@ def get_planar_roi_measurement_groups(
                     matches.append(found_ref_type == reference_type)
 
                 if graphic_type is not None:
+                    found_gt: Union[GraphicTypeValues, GraphicTypeValues3D]
                     if isinstance(graphic_type, GraphicTypeValues):
                         if ref_value_type == ValueTypeValues.SCOORD:
                             found_gt = GraphicTypeValues(ref_item.GraphicType)
@@ -4278,6 +4279,7 @@ def get_volumetric_roi_measurement_groups(
                     matches.append(found_ref_type == reference_type)
 
                 if graphic_type is not None:
+                    found_gt: Union[GraphicTypeValues, GraphicTypeValues3D]
                     if isinstance(graphic_type, GraphicTypeValues):
                         if ref_value_type == ValueTypeValues.SCOORD:
                             found_gt = GraphicTypeValues(

src/highdicom/sr/value_types.py

@@ -218,7 +218,7 @@ def _from_dataset_base(cls, dataset: Dataset) -> 'ContentItem':
         item.ConceptNameCodeSequence = [
             CodedConcept.from_dataset(item.ConceptNameCodeSequence[0])
         ]
-        return item
+        return cast(ContentItem, item)
 
     @property
     def name(self) -> CodedConcept: