v0.0.5

EPFL-Center-for-Imaging · Mar 14, 2024 · eff8f3b · eff8f3b
1 parent 3da89fe
commit eff8f3b
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = mousetumornet
-version = 0.0.4
+version = 0.0.5
 description = nnU-Net model for the segmentation of lung tumor nodules in mice CT scans.
 long_description = file: README.md
 long_description_content_type = text/markdown

diff --git a/src/mousetumornet/roi.py b/src/mousetumornet/roi.py
@@ -92,9 +92,9 @@ def compute_roi(img: np.ndarray):
     return df, lungs_bbox_data, body, roi
 
 
-def compute_roi_bones(img: np.ndarray):
+def compute_roi_bones(img: np.ndarray, q=0.99):
     """Computes a ROI encompassing the bones in the image - based on quantiles."""
-    bones = (img > np.quantile(img, 0.99)).astype(np.uint8)
+    bones = (img > np.quantile(img, q)).astype(np.uint8)
     if bones.sum() == 0:
         print("It looks like no bones were segmented.")
         x0 = 0