Issue #21 tidied code

glenoidplanefitting/algorithms/models.py

@@ -57,9 +57,9 @@ def make_vault_model(point1,point2):
     line.SetPoint2(point2)
     return line
 
-def make_sphere_model(point):
+def make_sphere_model(point, radius = 5.0):
     """
-    Make a sphere source which we can use to represent a landmark 
+    Make a sphere source which we can use to represent a landmark
     point
 
     :param point: the point
@@ -70,5 +70,5 @@ def make_sphere_model(point):
     sphere_source.SetCenter(point)
     sphere_source.SetThetaResolution(12)
     sphere_source.SetPhiResolution(12)
-    sphere_source.SetRadius(5.0)
+    sphere_source.SetRadius(radius)
     return sphere_source

glenoidplanefitting/ui/glenoidplanefitting_demo.py

@@ -14,7 +14,7 @@
 from glenoidplanefitting.algorithms.models import make_plane_model, \
         make_friedman_model, make_vault_model
 
-
+#pylint: disable=too-many-locals
 def run_demo(model_file_name, planes="", fried_points="", vault_points="",
              corr_fried="", output="", visualise = False, config_file = None):
     """
@@ -55,15 +55,14 @@ def run_demo(model_file_name, planes="", fried_points="", vault_points="",
         slice for picking
         the new landmark points for the 3D corrected Friedman method.
 
-    :param config_file: We can pass a configuration file, currently 
+    :param config_file: We can pass a configuration file, currently
         focusing on visualisation parameters
     """
     configuration = {}
     if config_file is not None:
         configurer = ConfigurationManager(config_file)
         configuration = configurer.get_copy()
-    background_colour = configuration.get('background colour',  [0.8, 0.8, 0.8])
-    model_colour = configuration.get('model colour',  
+    model_colour = configuration.get('model colour',
             [0.89, 0.86, 0.79]) #bone from https://www.colorhexa.com/e3dac9
     plane_resolution = configuration.get('plane resolution', 1)
     plane_size =  configuration.get('plane size' , 200.0)
@@ -96,7 +95,7 @@ def run_demo(model_file_name, planes="", fried_points="", vault_points="",
 
         if visualise:
             vis_planes(model, [result, result2, result3], points1, points2,
-                    plane_resolution, plane_size, vary_plane_colour, 
+                    plane_resolution, plane_size, vary_plane_colour,
                     point_size)
 
 
@@ -125,7 +124,7 @@ def run_demo(model_file_name, planes="", fried_points="", vault_points="",
         result = vault.create_vault_line(anterior_glenoid,posterior_glenoid)
         if visualise:
             vis_vault(model, anterior_glenoid, posterior_glenoid,
-                    glenoid_centre, result)
+                    glenoid_centre, result, line_width = line_width)
 
     if corr_fried !="":
 

glenoidplanefitting/widgets/visualisation.py

@@ -6,10 +6,12 @@
         make_friedman_model, make_vault_model, make_sphere_model
 from glenoidplanefitting.algorithms.colour_palette import bang_list
 
-def renderer_common(bone, background_colour = [0.9, 0.9, 0.9]):
+def renderer_common(bone, background_colour = None):
     """
     Initialises a vtk renderer and adds the bone model
     """
+    if background_colour is None:
+        background_colour = [0.9, 0.9, 0.9]
 
     renderer = vtk.vtkRenderer() #pylint:disable=no-member
     renderer.SetBackground(background_colour)
@@ -40,14 +42,16 @@ def render_window_common(renderer, window_name):
     render_window.Finalize()
     del render_window_interactor, render_window
 
-def add_vtk_source(renderer, source, linewidth = 1.0, opacity = 1.0, wireframe = False, 
-        colour = [1.0, 1.0, 1.0]):
+def add_vtk_source(renderer, source, linewidth = 1.0, opacity = 1.0,
+        wireframe = False, colour = None):
     """
     simplifies adding a vtk geometry source to a renderer
 
     :param renderer: a vtk renderer to add to
     :param source: a vtk geometry source
     """
+    if colour is None:
+        colour = [1.0, 1.0, 1.0]
     mapper = vtk.vtkPolyDataMapper() #pylint:disable=no-member
     mapper.SetInputConnection(source.GetOutputPort())
     actor = vtk.vtkActor() #pylint:disable=no-member
@@ -61,16 +65,16 @@ def add_vtk_source(renderer, source, linewidth = 1.0, opacity = 1.0, wireframe =
         actor.GetProperty().SetSpecularColor(colour)
     else:
         actor.GetProperty().SetRepresentationToSurface()
-    
+
     actor.GetProperty().SetColor(colour)
     actor.GetProperty().SetEdgeColor(colour)
 
     renderer.AddActor(actor)
 
-def vis_planes(bone, planes, points1 = [], points2 = [], 
-        resolution = 1, plane_size = 200.0, 
+def vis_planes(bone, planes, points1 = False, points2 = False,
+        resolution = 1, plane_size = 200.0,
         vary_plane_colour = False,
-        point_size = 1.0):
+        point_size = 5.0):
     """
     Visualisation for plane fitting methods
 
@@ -85,25 +89,27 @@ def vis_planes(bone, planes, points1 = [], points2 = [],
         if vary_plane_colour:
             colour = bang_list()[item]
 
-        plane_source = make_plane_model(plane[1], plane[2], resolution, plane_size)
+        plane_source = make_plane_model(plane[1], plane[2], resolution,
+                plane_size)
         add_vtk_source(renderer, plane_source, opacity = 0.15, colour = colour)
-        add_vtk_source(renderer, plane_source, linewidth = 2, opacity = 1.0, wireframe = True, 
-                colour = colour)
+        add_vtk_source(renderer, plane_source, linewidth = 2, opacity = 1.0,
+                wireframe = True, colour = colour)
 
-    for point in points1:
-        colour = bang_list()[0]
-        sphere_source = make_sphere_model(point)
-        add_vtk_source(renderer, sphere_source, colour = colour)
+    if points1:
+        for point in points1:
+            colour = bang_list()[0]
+            sphere_source = make_sphere_model(point, point_size)
+            add_vtk_source(renderer, sphere_source, colour = colour)
 
-    for point in points2:
-        colour = bang_list()[1]
-        sphere_source = make_sphere_model(point)
-        add_vtk_source(renderer, sphere_source, colour = colour)
+    if points2:
+        for point in points2:
+            colour = bang_list()[1]
+            sphere_source = make_sphere_model(point, point_size)
+            add_vtk_source(renderer, sphere_source, colour = colour)
 
     render_window_common(renderer, "Fitted Planes")
 
-def vis_fried(bone, cross1, cross2, glenoid1, result, resolution = 1, plane_size = 200.0, 
-        line_width = 5):
+def vis_fried(bone, cross1, cross2, glenoid1, result, line_width = 5):
     """
     Visualise the lines resulting from the friedman
     method.
@@ -116,7 +122,8 @@ def vis_fried(bone, cross1, cross2, glenoid1, result, resolution = 1, plane_size
 
     glenoid_line = make_friedman_model(cross1,cross2)
     colour = bang_list()[0]
-    add_vtk_source(renderer, glenoid_line, linewidth = line_width, colour = colour )
+    add_vtk_source(renderer, glenoid_line, linewidth = line_width,
+            colour = colour )
 
     sphere_source = make_sphere_model(cross1)
     add_vtk_source(renderer, sphere_source, colour = colour)
@@ -128,12 +135,13 @@ def vis_fried(bone, cross1, cross2, glenoid1, result, resolution = 1, plane_size
     add_vtk_source(renderer, sphere_source, colour = colour)
 
     friedman_line = make_friedman_model(glenoid1,result)
-    add_vtk_source(renderer, friedman_line, linewidth = line_width, colour = colour)
+    add_vtk_source(renderer, friedman_line, linewidth = line_width,
+            colour = colour)
 
     render_window_common(renderer, "Friedman Lines")
 
 
-def vis_vault(bone, cross1, cross2, glenoid1, result, resolution = 1, plane_size = 200.0):
+def vis_vault(bone, cross1, cross2, glenoid1, result, line_width = 5):
     """
     Visualise the lines resulting from the vault
     method.
@@ -145,9 +153,21 @@ def vis_vault(bone, cross1, cross2, glenoid1, result, resolution = 1, plane_size
     renderer = renderer_common(bone)
 
     glenoid_line = make_vault_model(cross1,cross2)
-    add_vtk_source(renderer, glenoid_line)
+    colour = bang_list()[0]
+    add_vtk_source(renderer, glenoid_line, linewidth = line_width,
+            colour = colour)
+
+    sphere_source = make_sphere_model(cross1)
+    add_vtk_source(renderer, sphere_source, colour = colour)
+    sphere_source = make_sphere_model(cross2)
+    add_vtk_source(renderer, sphere_source, colour = colour)
+
+    colour = bang_list()[1]
+    sphere_source = make_sphere_model(glenoid1)
+    add_vtk_source(renderer, sphere_source, colour = colour)
 
     vault_line = make_vault_model(glenoid1, result)
-    add_vtk_source(renderer, vault_line)
+    add_vtk_source(renderer, vault_line, linewidth = line_width,
+            colour = colour)
 
     render_window_common(renderer, "Vault Lines")