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Enforce all transforms to be sf.Affine objects before call to SamsegLongitudinal class in the long cli #35

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Merged
oulap merged 2 commits into from
Aug 5, 2026
Merged

Enforce all transforms to be sf.Affine objects before call to SamsegLongitudinal class in the long cli #35

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03b33df
Added additional step to load input volumes and extract geometry in t…
jnolan14 Aug 3, 2026
4be07f3
Removed wrapper calls to sf.Affine. All transforms are handled in the…
jnolan14 Aug 3, 2026
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4 changes: 2 additions & 2 deletions samseg/SamsegLongitudinal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -855,12 +855,12 @@ def generateSubjectSpecificTemplate(self, saveWarp=False):
# Read in the various time point images, and compute the average
numberOfTimepoints = len(contrastImageFileNames)
image0 = sf.load_volume(contrastImageFileNames[0])
imageBuffer = image0.transform(sf.Affine(self.tpToBaseTransforms[0]))
imageBuffer = image0.transform(self.tpToBaseTransforms[0])
# Make sure that we are averaging only non zero voxels
count = np.zeros(imageBuffer.shape)
count[imageBuffer > 0] += 1
for timepointNumber in range(1, numberOfTimepoints):
tmp = sf.load_volume(contrastImageFileNames[timepointNumber]).transform(sf.Affine(self.tpToBaseTransforms[timepointNumber])).data
tmp = sf.load_volume(contrastImageFileNames[timepointNumber]).transform(self.tpToBaseTransforms[timepointNumber]).data
imageBuffer += tmp
count[tmp > 0] += 1
# Make sure that we are not dividing by zero for, e.g., background voxels
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3 changes: 2 additions & 1 deletion samseg/cli/run_samseg_long.py
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Expand Up @@ -169,7 +169,8 @@ def check_lta_file(filepath):
else:
print("Assuming an identity transformation between base and each time point")
for tp in args.timepoint:
tpToBaseTransforms.append(sf.Affine(np.eye(4)))
tpVol = sf.load_volume(tp)
tpToBaseTransforms.append(sf.Affine(np.eye(4), source=tpVol.geom, target=tpVol.geom))


# ------ Run Samsegment ------
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