Bumping dependencies in requirements.txt to latest versions, and modi…

…fying MorphologyModule.py to compensate for lack of backward compatibility in scikit-image remove_small_holes
choosehappy · Mar 22, 2021 · 7151c41 · 7151c41
1 parent 7c130fe
commit 7151c41
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/MorphologyModule.py b/MorphologyModule.py
@@ -54,9 +54,9 @@ def removeFatlikeTissue(s, params):
     kernel_size = int(params.get("kernel_size", 3))
     max_keep_size = int(params.get("max_keep_size", 1000))
 
-    img_reduced = morphology.remove_small_holes(s["img_mask_use"], min_size=fat_cell_size)
+    img_reduced = morphology.remove_small_holes(s["img_mask_use"], area_threshold=fat_cell_size)
     img_small = img_reduced & np.invert(s["img_mask_use"])
-    img_small = ~morphology.remove_small_holes(~img_small, min_size=9)
+    img_small = ~morphology.remove_small_holes(~img_small, area_threshold=9)
 
     mask_dilate = morphology.dilation(img_small, selem=np.ones((kernel_size, kernel_size)))
     mask_dilate_removed = remove_large_objects(mask_dilate, max_keep_size)
@@ -82,7 +82,7 @@ def removeFatlikeTissue(s, params):
 def fillSmallHoles(s, params):
     logging.info(f"{s['filename']} - \tfillSmallHoles")
     min_size = int(params.get("min_size", 64))
-    img_reduced = morphology.remove_small_holes(s["img_mask_use"], min_size=min_size)
+    img_reduced = morphology.remove_small_holes(s["img_mask_use"], area_threshold=min_size)
     img_small = img_reduced & np.invert(s["img_mask_use"])
 
     io.imsave(s["outdir"] + os.sep + s["filename"] + "_small_fill.png", img_as_ubyte(img_small))

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
-openslide-python==1.1.1
-scikit-image==0.15.0
-scikit-learn==0.21.3
-numpy==1.17.4
-scipy==1.3.2
-matplotlib==3.1.2
+openslide-python==1.1.2
+scikit-image==0.18.1
+scikit-learn==0.24.1
+numpy==1.20.1
+scipy==1.6.1
+matplotlib==3.3.4