fix: Clean elements outside mask for multiple otsu method (#1319)

Czaki · web-flow · commit 3c5946c414d6 · 2025-10-15T08:56:27.000+02:00
Fix problem from image: ![IMG_20251015_011543.jpg](https://github.com/user-attachments/assets/f29d5b68-24b9-4273-a26e-18346485628e) ## Summary by Sourcery Bug Fixes: - Zero out segmentation voxels outside the mask when a mask is provided  ## Summary by CodeRabbit * **Bug Fixes** * Segmentation now properly respects masks: background/invalid regions are excluded from size calculations and threshold annotations, resulting in accurate component sizes and per-component thresholds when a mask is applied. * **Chores** * Project configuration updated to list an additional tool/library; this is a metadata change with no direct user-facing impact.
diff --git a/.github/project_dict.pws b/.github/project_dict.pws
@@ -24,3 +24,4 @@ sdk
 PR
 dependabot
 cooldown
+otsu
diff --git a/package/PartSegCore/segmentation/restartable_segmentation_algorithms.py b/package/PartSegCore/segmentation/restartable_segmentation_algorithms.py
@@ -642,6 +642,8 @@ def calculation_run(self, report_fun):
             self.new_parameters.valley,
         )
         res = SimpleITK.GetArrayFromImage(res)
+        if self.mask is not None:
+            res[self.mask == 0] = 0
         self._sizes_array = np.bincount(res.flat)[1:]
         self.threshold_info = []
         annotations = {}

Original file line number	Diff line number	Diff line change
`@@ -642,6 +642,8 @@ def calculation_run(self, report_fun):`
`642`	`642`	`self.new_parameters.valley,`
`643`	`643`	`)`
`644`	`644`	`res = SimpleITK.GetArrayFromImage(res)`
	`645`	`+ if self.mask is not None:`
	`646`	`+ res[self.mask == 0] = 0`
`645`	`647`	`self._sizes_array = np.bincount(res.flat)[1:]`
`646`	`648`	`self.threshold_info = []`
`647`	`649`	`annotations = {}`