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Update groundtruth file for fsd
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Fix an issue where the fsd feature boundaries could vary because of a
failure to check or guard bounds.
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manthey committed Dec 9, 2024
1 parent 4f7f093 commit 35feb5b
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Showing 2 changed files with 70 additions and 64 deletions.
6 changes: 6 additions & 0 deletions histomicstk/features/compute_fsd_features.py
Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,12 @@ def compute_fsd_features(im_label, K=128, Fs=6, Delta=8, rprops=None):
lmask = (im_label[min_row:max_row, min_col:max_col] == rprops[i].label).astype(
bool,
)
# trace_object_boundaries requires that that edge rows and columns be
# false as it does no bounds checking
if not min_row or not min_col or max_row + 1 == sizex or max_col + 1 == sizey:
lmask = np.pad(lmask, (
(1 if not min_row else 0, 1 if max_row + 1 == sizex else 0),
(1 if not min_col else 0, 1 if max_col + 1 == sizey else 0)))
# find boundaries
Bounds = trace_object_boundaries(
lmask,
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128 changes: 64 additions & 64 deletions tests/test_files/Easy1_nuclei_fsd_features.csv
Original file line number Diff line number Diff line change
@@ -1,65 +1,65 @@
Shape.FSD1,Shape.FSD2,Shape.FSD3,Shape.FSD4,Shape.FSD5,Shape.FSD6
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