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Minor fixes to segmentation #195

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merged 2 commits into from
Aug 15, 2022
Merged

Minor fixes to segmentation #195

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5f56a4e
Minor fixes to segmentation
CPBridge Aug 14, 2022
1533458
Fix docstring typo in type
CPBridge Aug 15, 2022
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2 changes: 1 addition & 1 deletion docs/usage.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
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13 changes: 2 additions & 11 deletions src/highdicom/seg/sop.py
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Expand Up @@ -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,
Expand Down Expand Up @@ -568,17 +570,6 @@ def __init__(
self.NumberOfFrames = 0
self.PerFrameFunctionalGroupsSequence: List[Dataset] = []

if pixel_array.ndim == 2:
pixel_array = pixel_array[np.newaxis, ...]
Comment on lines -571 to -572
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This is duplicated from above

if pixel_array.ndim not in [3, 4]:
raise ValueError('Pixel array must be a 2D, 3D, or 4D array.')
Comment on lines -573 to -574
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Moving this earlier simplifies things a bit


if pixel_array.shape[1:3] != (self.Rows, self.Columns):
raise ValueError(
'Pixel array representing segments has the wrong number of '
'rows and columns.'
)
Comment on lines -576 to -580
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This is true by construction of the self.Rows and self.Columns, so the check is pointless


# Check segment numbers
described_segment_numbers = np.array([
int(item.SegmentNumber)
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