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Small bug fixes #67

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Small bug fixes #67

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fdb39b3
dtye
robert-graf Sep 1, 2026
5535d0d
Merge branch 'main' into small_bug_fixes
robert-graf Sep 1, 2026
4536b28
prevent rais errors
robert-graf Sep 7, 2026
faa8da8
Merge branch 'main' into small_bug_fixes
Hendrik-code Sep 15, 2026
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7 changes: 3 additions & 4 deletions spineps/phase_post.py
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Original file line number Diff line number Diff line change
Expand Up @@ -751,11 +751,10 @@ def detect_and_solve_merged_vertebra(seg_nii: NII, vert_nii: NII) -> tuple[NII,
if first_stats[2] < MERGED_VERTEBRA_SIZE_RATIO * second_stats[2]:
# first is significantly smaller than second and they are close in height
# how many pixels are touching
vert_firsttwo_arr = vert_nii.extract_label(first_key).get_seg_array()
vert_firsttwo_arr2 = vert_nii.extract_label(second_key).get_seg_array()
vert_firsttwo_arr += vert_firsttwo_arr2 + 1
vert_firsttwo_arr = vert_nii.extract_label(first_key).get_seg_array().astype(np.uint8)
vert_firsttwo_arr[vert_nii.extract_label(second_key) > 0] = 2 # type: ignore
contacts = np_contacts(vert_firsttwo_arr, connectivity=3)
if contacts[(1, 2)] > isotropic_area_to_voxels(MERGED_VERTEBRA_MIN_CONTACT_MM2, vert_nii.zoom):
if (1, 2) in contacts and contacts[(1, 2)] > isotropic_area_to_voxels(MERGED_VERTEBRA_MIN_CONTACT_MM2, vert_nii.zoom):
logger.print("Found first two instance weird, will merge", Log_Type.STRANGE)
vert_nii.map_labels_({first_key: second_key}, verbose=False)

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