#193 - Changed the method to find the centroids

The centroids are now calculated with the myelin array rather than the axon array when trying to fill the axons.

ads_plugin.py

@@ -263,8 +263,8 @@ def onFillAxons_button(self, event):
         myelinArray = myelinMaskOverlay[:, :, 0]
 
         # Get the centroid indexes
-        watershedData, centroidIndexMap = self.getWatershedSegmentation(axonArray, myelinArray, returnCentroids=True)
-        del watershedData
+        centroidIndexMap = self.getMyelinCentroids(myelinArray)
+
 
         # # Crate an RGB array for the myelin image. The floodfill only uses RBG images.
         # arrayShape = [myelinArray.shape[0], myelinArray.shape[1]]
@@ -290,6 +290,16 @@ def onFillAxons_button(self, event):
         self.overlayList.append(axonMaskOverlay)
 
 
+    def getMyelinCentroids(self, im_myelin):
+        # Label each myelin object
+        im_myelin_label = measure.label(im_myelin)
+        # Find the centroids of the myelin objects
+        myelin_objects = measure.regionprops(im_myelin_label)
+        ind_centroid = ([int(props.centroid[0]) for props in myelin_objects],
+                        [int(props.centroid[1]) for props in myelin_objects])
+        return ind_centroid
+
+
 
     def getWatershedSegmentation(self, im_axon, im_myelin, returnCentroids=False):
         """
@@ -390,3 +400,4 @@ def getLogo(self):
     def supportedViews():
         from fsleyes.views.orthopanel import OrthoPanel
         return [OrthoPanel]
+