Segment a tube on click event

server/.gitignore

@@ -0,0 +1 @@
+__pycache__/*

server/helper.py

@@ -13,6 +13,19 @@ def print_matrix(itkmat, size=(3, 3)):
             sys.stdout.write('{} '.format(itkmat(i, j)))
         sys.stdout.write('\n')
 
+def itk_pos_to_array(itkpos):
+    return [itkpos.GetElement(i) for i in range(3)]
+
+def spatial_object_pt_to_radius(pt):
+    #forgive me
+    return float(str(pt).split("R: ")[1].split("\n")[0])
+
+
+def itk_image_dimension(itk_image):
+    return len(itk_image.GetLargestPossibleRegion().GetSize())
+def itk_pixel_type(itkimage):
+    return getattr(itk, "".join([char for char in repr(itkimage).split('itkImagePython.')[1].split(';')[0][8:] if char.isupper()]))
+
 # modified from: https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/itkwidgets/trait_types.py#L49
 def _itk_image_to_type(itkimage):
     component_str = repr(itkimage).split('itkImagePython.')[1].split(';')[0][8:]

server/protocol.py

@@ -19,17 +19,46 @@ def median_filter(self, image, radius):
         # TODO auto-serialize in objdir_wrap?
         return helper.itk_to_vtkjs_image(result)
 
+    @rpc('otsu_segment_filter')
+    @helper.objdir_wrap
+    def otsu_segment_filter(self, image):
+        print ("otsu_segment")
+
+        itk_image = helper.vtkjs_to_itk_image(image)
+
+        otsu_filter = itk.TubeTK.SegmentUsingOtsuThreshold[helper.itk_pixel_type(itk_image), 
+                                              helper.itk_image_dimension(itk_image), 
+                                              helper.itk_pixel_type(itk_image)].New()
+        otsu_filter.SetInput(itk_image)
+        otsu_filter.Update()
+
+        result = otsu_filter.GetOutput()
+
+        # TODO auto-serialize in objdir_wrap?
+        return helper.itk_to_vtkjs_image(result)
+
+
     @rpc('segment')
     @helper.objdir_wrap
     def segment(self, image, point):
+
         itk_image = helper.vtkjs_to_itk_image(image)
 
+        itk_image = itk.CastImageFilter[type(itk_image), itk.Image[itk.F, 3]].New()(itk_image)
+
         print('segment at:', point)
 
-        return [
-            {'point': [0, 10, 10], 'radius': 10},
-            {'point': [1, 11, 11], 'radius': 20},
-            {'point': [1, 12, 12], 'radius': 30},
-            {'point': [0, 13, 13], 'radius': 40},
-            {'point': [0, 14, 14], 'radius': 50},
-            ]
+        tuber = itk.TubeTK.SegmentTubes[type(itk_image)].New()
+
+        tuber.SetInputImage(itk_image)
+        atube = tuber.ExtractTube(point, 0, True)
+
+        tube_py = []
+        for j in range(atube.GetNumberOfPoints()):
+            pt = atube.GetPoint(j)
+            pos = helper.itk_pos_to_array(pt.GetPosition())
+            radius = helper.spatial_object_pt_to_radius(pt)
+            tube_py.append({'point': pos, 'radius': radius},)
+
+        return tube_py
+