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fix: use P-axis length for ys calculation and clip S-axis bounds (#167) #180

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fix: use P-axis length for ys calculation and clip S-axis bounds (#167) #180

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b60bd3f
fix: use P-axis length for ys calculation and clip S-axis bounds
rtmalikian Jun 18, 2026
b3d97c3
Merge branch 'main' into fix/quickshear-ys-axis-calculation
neuronflow Aug 2, 2026
433edec
Merge branch 'main' into fix/quickshear-ys-axis-calculation
neuronflow Aug 2, 2026
498d60b
Merge branch 'main' into fix/quickshear-ys-axis-calculation
neuronflow Aug 19, 2026
5ad302b
Merge branch 'main' into fix/quickshear-ys-axis-calculation
neuronflow Nov 1, 2026
d74ba16
fix: read quickshear cutoff from ys[x] instead of mismatched zip pairing
rtmalikian Nov 1, 2026
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11 changes: 8 additions & 3 deletions brainles_preprocessing/defacing/quickshear/nipy_quickshear.py
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Original file line number Diff line number Diff line change
Expand Up @@ -155,11 +155,16 @@ def run_quickshear(bet_img: nb.nifti1.Nifti1Image, buffer: int = 10) -> NDArray:
slope = ydiffs[0] / xdiffs[0]

yint = low[1][0] - (low[0][0] * slope) - buffer
ys = np.arange(0, mask_RPS.shape[2]) * slope + yint
ys = np.arange(0, mask_RPS.shape[1]) * slope + yint
defaced_mask_RPS = np.ones(mask_RPS.shape, dtype="bool")

for x, y in zip(np.nonzero(ys > 0)[0], ys.astype(int)):
defaced_mask_RPS[:, x, :y] = 0
for x in np.nonzero(ys > 0)[0]:
# Read the cutoff from ys[x]: zipping the filtered indices with the
# unfiltered ys array pairs each position with the wrong cutoff
# whenever ys starts with a nonpositive prefix, and a negative cutoff
# would make the slice erase the wrong region.
y_clipped = min(int(ys[x]), mask_RPS.shape[2])
defaced_mask_RPS[:, x, :y_clipped] = 0

defaced_mask = nb.orientations.apply_orientation(defaced_mask_RPS, from_RPS)

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