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10x performance improvement of DownsampleSegForDSTransform2 in nnunet by moving 1 line of code #120

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10x performance improvement of DownsampleSegForDSTransform2 in nnunet by moving 1 line of code #120

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3 changes: 2 additions & 1 deletion batchgenerators/augmentations/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -591,11 +591,12 @@ def resize_segmentation(segmentation, new_shape, order=3):
:return:
'''
tpe = segmentation.dtype
unique_labels = np.unique(segmentation)

assert len(segmentation.shape) == len(new_shape), "new shape must have same dimensionality as segmentation"
if order == 0:
return resize(segmentation.astype(float), new_shape, order, mode="edge", clip=True, anti_aliasing=False).astype(tpe)
else:
unique_labels = np.unique(segmentation)
reshaped = np.zeros(new_shape, dtype=segmentation.dtype)

for i, c in enumerate(unique_labels):
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