Minor fixes to segmentation (#195)

* Minor fixes to segmentation * Fix docstring typo in type
ImagingDataCommons · Aug 15, 2022 · ed5901f · ed5901f
1 parent 366c58a
commit ed5901f
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Showing 3 changed files with 4 additions and 13 deletions.
diff --git a/docs/usage.rst b/docs/usage.rst
@@ -121,7 +121,7 @@ Derive a Segmentation image from a multi-frame Slide Microscopy (SM) image:
     )
 
     # Create the Segmentation instance
-    seg_dataset = Segmentation(
+    seg_dataset = hd.seg.Segmentation(
         source_images=[image_dataset],
         pixel_array=mask,
         segmentation_type=hd.seg.SegmentationTypeValues.BINARY,

diff --git a/src/highdicom/seg/content.py b/src/highdicom/seg/content.py
@@ -77,7 +77,7 @@ def __init__(
             "Anatomic Region", :dcm:`CID 4031 <part16/sect_CID_4031.html>`
             "Common Anatomic Regions", as as well as other CIDs for
             domain-specific anatomic regions)
-        primary_anatomic_structures: Union[Sequence[Union[highdicom.sr.Code, highdicom.sr.CodedConcept]], None], optional
+        primary_anatomic_structures: Union[Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]], None], optional
             Anatomic structure(s) the segment represents
             (see CIDs for domain-specific primary anatomic structures)
 

diff --git a/src/highdicom/seg/sop.py b/src/highdicom/seg/sop.py
@@ -312,6 +312,8 @@ def __init__(
 
         if pixel_array.ndim == 2:
             pixel_array = pixel_array[np.newaxis, ...]
+        if pixel_array.ndim not in [3, 4]:
+            raise ValueError('Pixel array must be a 2D, 3D, or 4D array.')
 
         super().__init__(
             study_instance_uid=src_img.StudyInstanceUID,
@@ -568,17 +570,6 @@ def __init__(
         self.NumberOfFrames = 0
         self.PerFrameFunctionalGroupsSequence: List[Dataset] = []
 
-        if pixel_array.ndim == 2:
-            pixel_array = pixel_array[np.newaxis, ...]
-        if pixel_array.ndim not in [3, 4]:
-            raise ValueError('Pixel array must be a 2D, 3D, or 4D array.')
-
-        if pixel_array.shape[1:3] != (self.Rows, self.Columns):
-            raise ValueError(
-                'Pixel array representing segments has the wrong number of '
-                'rows and columns.'
-            )
-
         # Check segment numbers
         described_segment_numbers = np.array([
             int(item.SegmentNumber)