Extending number of segments to five by adding Deauville to store pre-treatment lesion locations; also, segments are added to segmentations that don't have them.

slicerModules/imageBrowser.py

@@ -412,6 +412,7 @@ class imageBrowserLogic(ScriptedLoadableModuleLogic):
         if not os.path.isdir(self.tempDir):
             os.mkdir(self.tempDir)
         self.lookups={}
+        self.segmentList=["Liver","Blood","Marrow","Disease","Deauville"]
         print('imageBrowserLogic setup complete')
     
 
@@ -626,6 +627,19 @@ class imageBrowserLogic(ScriptedLoadableModuleLogic):
         iData={'idx':'Segmentation','path':path,
                     'keepCached':0,'dataset':'SegmentationsMaster'}
         self.loadImage(iData)
+        #look for missing segments
+        segNode=self.volumeNode['Segmentation']
+        seg=segNode.GetSegmentation()
+        segNames=[seg.GetNthSegmentID(i) for i in range(seg.GetNumberOfSegments())]
+        print('Segments')
+        for s in self.segmentList:
+            if s not in segNames:
+                seg.AddEmptySegment(s,s)
+                print(s)
+        print('Done')
+
+
+
 
     def saveSegmentation(self):
         #get the latest key by adding an entry to SegmentationList
@@ -700,10 +714,8 @@ class imageBrowserLogic(ScriptedLoadableModuleLogic):
         slicer.mrmlScene.AddNode(segNode)
         segNode.CreateDefaultDisplayNodes()
         segNode.SetReferenceImageGeometryParameterFromVolumeNode(self.volumeNode['PET'])
-        segNode.GetSegmentation().AddEmptySegment("Liver","Liver")
-        segNode.GetSegmentation().AddEmptySegment("Blood","Blood")
-        segNode.GetSegmentation().AddEmptySegment("Marrow","Marrow")
-        segNode.GetSegmentation().AddEmptySegment("Disease","Disease")
+        for s in self.segmentList:
+            segNode.GetSegmentation().AddEmptySegment(s,s)