Refactoring in manipulate_x scripts

Author: hkjeldsberg

morphman/manipulate_area.py

@@ -402,8 +402,7 @@ def get_asymmetric_displacement(A, angle_asymmetric, factor_, frenet_normals_arr
 
 def update_factor(A, AB_length, B, P_mid, factor, tmp_id1, tmp_id2):
     """
-    Update values in Factor based on midpoint between
-    A and B.
+    Update values in Factor based on midpoint between A and B.
 
     Args:
         P_mid (ndarray): Midpoint
@@ -521,21 +520,19 @@ def read_command_line_area(input_path=None, output_path=None):
         args = parser.parse_args(["-i" + input_path, "-o" + output_path])
 
     if args.method in ["stenosis", "bulge", "linear"] and args.region_of_interest == "first_line":
-        raise ValueError("Can not set region of interest to 'first_line' for 'stenosis'," + \
-                         " 'bulge', or 'linear'")
+        raise ValueError("Can not set region of interest to 'first_line' for 'stenosis', 'bulge', or 'linear'")
 
     if args.method == "variation" and args.ratio is not None and args.beta != 0.5:
         print("WARNING: The beta value you provided will be ignored, using ratio instead.")
 
     if args.region_points is not None:
         if len(args.region_points) % 3 != 0 or len(args.region_points) > 6:
-            raise ValueError("ERROR: Please provide region point(s) as a multiple of 3, and maximum" +
-                             " two points.")
+            raise ValueError("ERROR: Please provide region point(s) as a multiple of 3, and maximum two points.")
 
     if args.no_smooth_point is not None and len(args.no_smooth_point):
         if len(args.no_smooth_point) % 3 != 0:
-            raise ValueError("ERROR: Please provide the no smooth point(s) as a multiple" +
-                             " of 3.")
+            raise ValueError("ERROR: Please provide the no smooth point(s) as a multiple of 3.")
+
     if args.angle_asymmetric is not None:
         angle_radians = args.angle_asymmetric * np.pi / 180  # Convert from deg to rad
     else:

morphman/manipulate_bifurcation.py

@@ -13,9 +13,8 @@
 from morphman.common.vessel_reconstruction_tools import *
 
 
-def manipulate_bifurcation(input_filepath, output_filepath, smooth, smooth_factor, angle,
-                           keep_fixed_1, keep_fixed_2, bif, lower, no_smooth, no_smooth_point,
-                           poly_ball_size, cylinder_factor, resampling_step,
+def manipulate_bifurcation(input_filepath, output_filepath, smooth, smooth_factor, angle, keep_fixed_1, keep_fixed_2,
+                           bif, lower, no_smooth, no_smooth_point, poly_ball_size, cylinder_factor, resampling_step,
                            region_of_interest, region_points, tension, continuity):
     """
     Objective rotation of daughter branches, by rotating
@@ -27,6 +26,8 @@ def manipulate_bifurcation(input_filepath, output_filepath, smooth, smooth_facto
     Includes the option to rotate only one of the daughter branches.
 
     Args:
+        tension (float): Tension parameter of Kochanek splines
+        continuity (float): Continuity parameter of Kochanek splines
         input_filepath (str): Path to input surface.
         output_filepath (str): Path to output surface.
         smooth (bool): Determine if the voronoi diagram should be smoothed.
@@ -144,8 +145,7 @@ def manipulate_bifurcation(input_filepath, output_filepath, smooth, smooth_facto
 
     # Clip the voronoi diagram
     print("-- Clipping Voronoi diagram")
-    voronoi_clipped, voronoi_bifurcation = get_split_voronoi_diagram(voronoi, [patch_cl,
-                                                                     clipped_centerline])
+    voronoi_clipped, voronoi_bifurcation = get_split_voronoi_diagram(voronoi, [patch_cl, clipped_centerline])
     write_polydata(voronoi_clipped, voronoi_clipped_path)
     write_polydata(voronoi_bifurcation, voronoi_bifurcation_path)
 
@@ -284,7 +284,7 @@ def rotate_voronoi(clipped_voronoi, patch_cl, div_points, m, R):
     for i in range(1, patch_cl.GetNumberOfCells()):
         pnt = cell_line[i].GetPoints().GetPoint(0)
         new = cell_line[0].GetPoints().GetPoint(locator[0].FindClosestPoint(pnt))
-        if get_distance(pnt, new) < tolerance*10:
+        if get_distance(pnt, new) < tolerance * 10:
             not_rotate.append(i)
 
     def check_rotate(point):
@@ -369,7 +369,7 @@ def rotate_cl(patch_cl, div_points, rotation_matrices, R):
 
         start = cell.GetPoint(0)
         dist = line0.GetPoint(locator0.FindClosestPoint(start))
-        test = get_distance(start, dist) > tolerance*10
+        test = get_distance(start, dist) > tolerance * 10
 
         if test or len(div_points) == 2:
             locator = get_vtk_point_locator(cell)
@@ -615,7 +615,6 @@ def read_command_line_bifurcation(input_path=None, output_path=None):
     parser.add_argument("-c", "--continuity", type=float, default=0.8,
                         help="Set continuity of the KochanekSpline from -1 to 1")
 
-
     # Bifurcation reconstruction arguments
     parser.add_argument("--bif", type=str2bool, default=False,
                         help="interpolate bif as well")
@@ -638,7 +637,6 @@ def read_command_line_bifurcation(input_path=None, output_path=None):
     if not (-1 <= args.continuity <= 1):
         raise ValueError("Tension has to be between -1 and 1, not {}".format(args.continuity))
 
-
     return dict(input_filepath=args.ifile, smooth=args.smooth, output_filepath=args.ofile,
                 smooth_factor=args.smooth_factor, angle=ang_,
                 keep_fixed_1=args.keep_fixed_1, keep_fixed_2=args.keep_fixed_2,

morphman/manipulate_curvature.py

@@ -6,6 +6,7 @@
 ##      PURPOSE.  See the above copyright notices for more information.
 
 from argparse import ArgumentParser, RawDescriptionHelpFormatter
+
 from vtk.numpy_interface import dataset_adapter as dsa
 
 # Local import
@@ -66,9 +67,9 @@ def manipulate_curvature(input_filepath, smooth, smooth_factor, smooth_factor_li
                                           no_smooth_point, voronoi, pole_ids, resampling_step)
     # Get region of interest
     centerline_splined, centerline_remaining, \
-        centerline_diverging, region_points, diverging_ids = get_line_to_change(capped_surface, centerlines,
-                                                                                region_of_interest, "variation",
-                                                                                region_points, None)
+    centerline_diverging, region_points, diverging_ids = get_line_to_change(capped_surface, centerlines,
+                                                                            region_of_interest, "variation",
+                                                                            region_points, None)
 
     write_polydata(centerline_splined, centerline_spline_path)
     write_polydata(centerline_remaining, centerline_remaining_path)
@@ -129,8 +130,8 @@ def get_dx(p0, p1, smooth_line, cl_id, id_end, id_mid, id_start):
     """Get the displacement for the Voronoi point
 
     Args:
-        p0 (list): Point i on the old centerline.
-        p1 (list): Point i on the new centerline.
+        p0 (ndarray): Point i on the old centerline.
+        p1 (ndarray): Point i on the new centerline.
         smooth_line (bool): Turn on/off increasing curvuature.
         cl_id (int): ID of point i
         id_end (int): Point ID of start transition region.
@@ -200,7 +201,7 @@ def make_voronoi_smooth(voronoi, old_cl, new_cl, smooth_line, div_voronoi, div_p
 
     # Offset diverging centerlines
     div_offset = []
-    if div_voronoi != []:
+    if len(div_voronoi) > 0:
         for i in range(len(div_voronoi)):
             cl_id = locator.FindClosestPoint(div_points[i])
             p0 = np.asarray(old_cl.GetPoint(cl_id))

morphman/manipulate_surface.py

@@ -422,8 +422,8 @@ def read_command_line_surface(input_path=None, output_path=None):
 
     if args.frequency_deviation <= 0:
         raise ArgumentTypeError("The standard deviation has to be larger than zero." +
-                                " Please provide a valid value, not {}" \
-                                .format(args.frequency_deviation))
+                                " Please provide a valid value, not" +
+                                " {}".format(args.frequency_deviation))
 
     return dict(input_filepath=args.ifile, smooth=args.smooth, output_filepath=args.ofile,
                 smooth_factor=args.smooth_factor, resampling_step=args.resampling_step,