misc

Wandrys-dev · Dec 20, 2022 · 3e21b26 · 3e21b26
1 parent 16721f5
commit 3e21b26
Showing 1 changed file with 19 additions and 20 deletions.
diff --git a/inst/py/cellpose_utils.py b/inst/py/cellpose_utils.py
@@ -363,26 +363,25 @@ def predict_slice(self, im_dat, dat_slices):
         for y in model_masks[i]:
           interm_labels[i] = np.maximum(interm_labels[i], y)
 
-    # go through all nuclei labels
-    # TODO generalise as this is the same as for mesmer
-    if len(model_masks['cyto']) > 0 and len(model_masks['nuc']) > 0:
-      self.logfile_utils.log(f'>> Merge nuclei and cyto')
-
-      # match cells to a nucleus - some cells might not have a nucleus
-      labels_merged = self.match_cells_and_nuclei(
-        # [interm_labels['nuc'], interm_labels['cyto']]
-        [interm_labels['cyto'], interm_labels['nuc']],
-        stitch_threshold = self.match_threshold,
-        remove_unmatched = self.remove_unmatched
-      )
-
-      self.logfile_utils.log(f'> Cells: {np.max(labels_merged[0])}')
-      self.logfile_utils.log(f'> Nuclei: {np.max(labels_merged[1])}')
-
-      # add masks to list
-      if np.max(labels_merged[0]) > 0 and np.max(labels_merged[1]) > 0:
-        interm_labels['cyto'] = labels_merged[0]
-        interm_labels['nuc'] = labels_merged[1]
+    # match labels
+    # if len(model_masks['cyto']) > 0 and len(model_masks['nuc']) > 0:
+    #   self.logfile_utils.log(f'>> Merge nuclei and cyto')
+    # 
+    #   # match cells to a nucleus - some cells might not have a nucleus
+    #   labels_merged = self.match_cells_and_nuclei(
+    #     # [interm_labels['nuc'], interm_labels['cyto']]
+    #     [interm_labels['cyto'], interm_labels['nuc']],
+    #     stitch_threshold = self.match_threshold,
+    #     remove_unmatched = self.remove_unmatched
+    #   )
+    # 
+    #   self.logfile_utils.log(f'> Cells: {np.max(labels_merged[0])}')
+    #   self.logfile_utils.log(f'> Nuclei: {np.max(labels_merged[1])}')
+    # 
+    #   # add masks to list
+    #   if np.max(labels_merged[0]) > 0 and np.max(labels_merged[1]) > 0:
+    #     interm_labels['cyto'] = labels_merged[0]
+    #     interm_labels['nuc'] = labels_merged[1]
 
     # final merge of cyto and base
     merged_labels = np.zeros(label_shape, dtype = np.uint32)