Merge pull request #73 from KVSlab/fixes-bifurcation

Refactor centerline tolerance

Author: hkjeldsberg

morphman/common/centerline_operations.py

@@ -239,22 +239,21 @@ def get_curvilinear_coordinate(line):
     return curvilinear_coordinate
 
 
-def get_centerline_tolerance(centerline, n=50):
+def get_centerline_tolerance(centerline):
     """
     Finds tolerance based on
-    average length between first N points
+    average length between points
     along the input centerline.
 
     Args:
         centerline (vtkPolyData): Centerline data.
-        n (int): Number of points
 
     Returns:
         tolerance (float): Tolerance value.
     """
     line = extract_single_line(centerline, 0)
     length = get_curvilinear_coordinate(line)
-    tolerance = np.mean(length[1:n] - length[:n - 1]) / 2.0
+    tolerance = np.mean(length[1:] - length[:-1]) / 2.0
 
     return tolerance
 

morphman/common/surface_operations.py

@@ -56,6 +56,9 @@ def compute_centers(polydata, case_path=None, select_inlet=False):
         inlet (list): A list of points.
         outlet (list): A flattened list with all the outlets.
     """
+    # Perform a 'light' smoothing to obtain a more uniform boundary
+    polydata = vmtk_smooth_surface(polydata, method="laplace", iterations=100)
+
     # Get cells which are open
     cells = vtk_extract_feature_edges(polydata)