Merge pull request #40 from KVSlab/release-v0.3-and-refactor

Release v0.3 and minor refactoring

demo/demo_manipulate_area_inflation.py

@@ -11,7 +11,7 @@
 #       --method area --percentage -20 --region-of-interest first_line --poly-ball-size 250 250 250
 #  $ morphman-area --ifile C0002/surface/model.vtp --ofile C0002/surface/area_inflated.vtp \
 #       --method area --percentage 20 --region-of-interest first_line --poly-ball-size 250 250 250
-
+#
 # and a more detailed explenation could be found here:
 # https://morphman.readthedocs.io/en/latest/manipulate_area.html#inflation-deflation-of-an-arterial-segment
 

demo/get_test_data.py

@@ -12,27 +12,27 @@
 def download_case(case):
     abs_path = path.dirname(path.abspath(__file__))
     output_file = path.join(abs_path, "{}_models.tar.gz".format(case))
-    adress = "http://ecm2.mathcs.emory.edu/aneuriskdata/download/{}/{}_models.tar.gz".format(case, case)
+    url = "http://ecm2.mathcs.emory.edu/aneuriskdata/download/{}/{}_models.tar.gz".format(case, case)
 
     try:
         if platform == "darwin":
-            system("curl {} --output {}".format(adress, output_file))
+            system("curl {} --output {}".format(url, output_file))
             system("tar -zxvf {}".format(output_file))
             system("rm {}".format(output_file))
 
         elif platform == "linux" or platform == "linux2":
-            system("wget {}".format(adress))
+            system("wget {}".format(url))
             system("tar -zxvf {}".format(output_file))
             system("rm {}".format(output_file))
 
         elif platform == "win32":
-            system("bitsadmin /transfer download_model /download /priority high {} {}".format(adress, output_file))
+            system("bitsadmin /transfer download_model /download /priority high {} {}".format(url, output_file))
             system("tar -zxvf {}".format(output_file))
             system("del /f {}".format(output_file))
 
     except:
         raise RuntimeError("Problem downloading the testdata, please do it manually from "
-                           + adress + " and extract the compressed tarball in the"
+                           + url + " and extract the compressed tarball in the"
                            + " test folder")
 
 

docs/source/Miscellaneous.rst

@@ -82,14 +82,15 @@ For a more detailed description of the method, please see [3]_.
 
 Common
 ======
-In ``common.py`` we have collected generic functions used by multiple scripts.
-Many of the functions wrap existing vtk and vmtk functions in a more pythonic syntax.
+In the folder ``common`` we have collected utility scripts containing generic functions used by multiple scripts.
+Many of the functions wrap existing vtk and vmtk functions in a more pythonic syntax,
+collected in ``vtk_wrapper.py`` and ``vmtk_wrapper.py``, respectively.
 Instead of writing 6-7 lines of code to initiate a vtk-object, and set each parameter,
-and the input surface, one can call one function with multiple arguments instead,
-see for instance :meth:`common.threshold`.
+and the input surface, one may call one function with multiple arguments instead,
+see for instance :meth:`vtk_wrapper.vtk_compute_threshold`.
 
 In addition to wrapping vtk and vmtk functionality, there is also new methods for
-manipulating centerlines and Voronoi diagrams.
+manipulating centerlines, surface models and Voronoi diagrams, collected in their respective scripts.
 
 .. [1] Piccinelli, M., Bacigaluppi, S., Boccardi, E., Ene-Iordache, B., Remuzzi, A., Veneziani, A. and Antiga, L., 2011. Geometry of the internal carotid artery and recurrent patterns in location, orientation, and rupture status of lateral aneurysms: an image-based computational study. Neurosurgery, 68(5), pp.1270-1285.
 .. [2] Bogunović, H., Pozo, J.M., Cárdenes, R., Villa-Uriol, M.C., Blanc, R., Piotin, M. and Frangi, A.F., 2012. Automated landmarking and geometric characterization of the carotid siphon. Medical image analysis, 16(4), pp.889-903.

docs/source/conf.py

@@ -66,9 +66,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.2'
+version = u'0.3'
 # The full version, including alpha/beta/rc tags.
-release = u'0.2'
+release = u'0.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/installation.rst

@@ -21,7 +21,7 @@ The general dependencies of morphMan are
 Basic Installation
 ==================
 We recommend that you can install morphMan through Anaconda.
-First, install Anaconda or Miniconda (preferably the python 3.6 version).
+First, install Anaconda or Miniconda (preferably the Python 3.6 version).
 Then execute the following command in a terminal window::
 
   $ conda create -n your_environment -c vmtk -c morphman morphman

docs/source/manipulate_area.rst

@@ -9,7 +9,7 @@ Tutorial: Manipulate area
 Manipulation of the cross-sectional area is performed by running ``morphman-area`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_area.py``. We have also created a
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 In this tutorial, we are using the model with

docs/source/manipulate_bend.rst

@@ -10,7 +10,7 @@ The goal of ``morphman-bend``, is to alter one specific bend in the
 vasculature, like shown in Figure 1. This can be performed by running ``morphman-bend`` in the terminal,
 followed by the respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_bend.py``. We have also created a 
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 .. figure:: Bend_moving.png

docs/source/manipulate_bifurcation.rst

@@ -24,7 +24,7 @@ is a file `./C0005/surface/model.vtp`, relative to where you execute the command
 Performing the manipulation can be achieved by running ``morphman-bifurcation`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_bifurcation.py``. We have also created a 
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 Shown in Figure 2 is the result of rotating the two daughter branches with both

docs/source/manipulate_branch.rst

@@ -7,13 +7,13 @@ Tutorial: Manipulate branch
 ===========================
 
 The goal of ``manipulate_branch.py`` is to manipulate a specific branch of a
-vascular model, either through pure tranlation and rotation, or by completely removing it, as depicted in Figure 1.
+vascular model, either through pure tranlsation and rotation, or by completely removing it, as depicted in Figure 1.
 In particular, we have defined a branch as any branch branching out of the longest tubular structure,
 defined by the physical length of the tube.
 The manipulation can be achieved by running ``morphman-branch`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_branch.py``. We have also created a
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 .. figure:: Branch.png

docs/source/manipulate_curvature.rst

@@ -11,7 +11,7 @@ total curvature/torsion in a vascular segment, see Figure 1 for an example.
 The manipulation can be achieved by running ``morphman-curvature`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_curvature.py``. We have also created a 
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 .. figure:: Curvature.png

docs/source/manipulate_surface.rst

@@ -24,7 +24,7 @@ is a file `./C0005/surface/model.vtp`, relative to where you execute the command
 Performing the manipulation can be achieved by running ``morphman-surface`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_surface.py``. We have also created a 
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 Shown in Figure 2 is the result of smoothing the surface.

morphman/common/centerline_operations.py

@@ -276,8 +276,7 @@ def get_clipped_diverging_centerline(centerline, clip_start_point, clip_end_id):
     return patch_cl
 
 
-def get_line_to_change(surface, centerline, region_of_interest, method, region_points,
-                       stenosis_length):
+def get_line_to_change(surface, centerline, region_of_interest, method, region_points, stenosis_length):
     """
     Extract and spline part of centerline
     within the geometry where

morphman/common/vtk_wrapper.py

@@ -504,7 +504,7 @@ def create_vtk_array(values, name, k=1):
     """Given a set of numpy values, and a name of the array create vtk array
 
     Args:
-        values (numpy.ndarray): List of the values.
+        values (list, ndarray): List of the values.
         name (str): Name of the array.
         k (int): Length of tuple.
 

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_branch.py

@@ -572,26 +572,26 @@ def get_exact_surface_normal(capped_surface, new_branch_pos_id):
     return new_normal
 
 
-def get_estimated_surface_normal(diverging_centerline_branch):
+def get_estimated_surface_normal(centerline):
     """
     Estimate the surface normal at initial diverging centerline branch.
 
     Args:
-        diverging_centerline_branch (vtkPolyData): Diverging centerline to be moved.
+        centerline (vtkPolyData): Diverging centerline to be moved.
 
     Returns:
         normal_vector (ndarray): Estimated normal vector at diverging centerline
     """
-    line = vmtk_compute_geometric_features(diverging_centerline_branch, True)
-    curvature = get_point_data_array("Curvature", line)
+    centerline = vmtk_compute_geometric_features(centerline, True)
+    curvature = get_point_data_array("Curvature", centerline)
     first_local_maxima_id = argrelextrema(curvature, np.greater)[0][0]
 
     # TODO: Generalize choice of end point factor
     factor = 0.6
     start_point = 0
     end_point = int(first_local_maxima_id * factor)
-    normal_vector = np.asarray(diverging_centerline_branch.GetPoint(end_point)) - np.asarray(
-        diverging_centerline_branch.GetPoint(start_point))
+    normal_vector = np.asarray(centerline.GetPoint(end_point)) - np.asarray(
+        centerline.GetPoint(start_point))
 
     normal_vector /= la.norm(normal_vector)
 
@@ -605,7 +605,7 @@ def manipulate_centerline_branch(centerline_branch, origin, R, dx, normal, angle
 
     Args:
         manipulation (str): Type of manipulation, either 'rotate' or 'translate'
-        centerline_branch (vtkPolyData): Centerline through surface
+        centerline_branch (vtkPolyData): Centerline branch to be manipulated
         dx (float): Distance to translate branch
         R (ndarray): Rotation matrix, rotation from old to new surface normal or around new surface normal
         origin (ndarray): Adjusted origin / position of new branch position
@@ -681,7 +681,6 @@ def get_rotation_axis_and_angle(new_normal, old_normal):
     return u, angle
 
 
-
 def manipulate_voronoi_branch(voronoi, dx, R, origin, centerline, normal, angle, manipulation):
     """
     Depending on manipulation method, either translates or
@@ -745,6 +744,7 @@ def manipulate_voronoi_branch(voronoi, dx, R, origin, centerline, normal, angle,
     new_voronoi.SetPoints(voronoi_points)
     new_voronoi.SetVerts(cell_array)
     new_voronoi.GetPointData().AddArray(radius_array)
+
     return new_voronoi