21 visualisation

CITATION.cff

@@ -0,0 +1,43 @@
+cff-version: 1.2.0
+message: "If you use any SciKit-Surgery packages in your research, please cite it as below."
+authors:
+- family-names: "Olafsdottir"
+  given-names: "Asta"
+- family-names: "Thompson"
+  given-names: "Stephen"
+  orcid: "https://orcid.org/0000-0001-7286-1326"
+title: "SciKit-SurgeryGlenoid"
+url: "https://github.com/SciKit-Surgery/scikit-surgery"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Thompson"
+    given-names: "Stephen"
+    orcid: "https://orcid.org/0000-0001-7286-1326"
+  - family-names: "Dowrick"
+    given-names: "Thomas"
+    orcid: "https://orcid.org/0000-0002-2712-4447"
+  - family-names: "Ahmad"
+    given-names: "Mian"
+    orcid: "https://orcid.org/0000-0002-4706-4146"
+  - family-names: "Xiao"
+    given-names: "Guofang"
+  - family-names: "Koo"
+    given-names: "Bongjin"
+    orcid: "https://orcid.org/0000-0002-3611-4988"
+  - family-names: "Bonmati"
+    given-names: "Ester"
+    orcid: "https://orcid.org/0000-0001-9217-5438"
+  - family-names: "Kahl"
+    given-names: "Kim"
+  - family-names: "Clarkson"
+    given-names: "Matthew"
+    orcid: "https://orcid.org/0000-0002-5565-1252"
+  doi: 10.1007/s11548-020-02180-5
+  journal: "International journal of computer assisted radiology and surgery"
+  start: 1075
+  end: 1084
+  title: "SciKit-Surgery: Compact Libraries for Surgical Navigation"
+  volume: 15
+  issue: 7
+  year: 2020

docs/dependency_graph.dot

@@ -3,6 +3,7 @@ digraph prof {
 	node [style=filled];
 	"SciKit-SurgeryGlenoid" -> "NumPy";
 	"SciKit-SurgeryGlenoid" -> "SciKit-SurgeryVTK" [color="0.515 0.762 0.762"];
+	"SciKit-SurgeryGlenoid" -> "SciKit-SurgeryCore" [color="0.515 0.762 0.762"];
 	"SciKit-SurgeryGlenoid" -> "VTK";
 
 	"SciKit-SurgeryVTK" -> "NumPy";

glenoidplanefitting/algorithms/colour_palette.py

@@ -0,0 +1,27 @@
+"""
+A colour palette based on Bang's colour pallette
+Wong, B. Points of view: Color blindness. Nat Methods 8, 441 (2011).
+https://doi.org/10.1038/nmeth.1618
+"""
+
+bang_palette={ 'black' : [0,0,0],
+               'orange' : [230./255., 159./255., 0],
+               'sky blue' : [86./255., 180./255., 233./255.],
+               'bluish green' : [0./255., 158./255., 115./255.],
+               'yellow' : [240./255., 228./255., 66./255.],
+               'blue' : [0./255., 114./255., 178./255.],
+               'vermillion' : [213./255., 94./255., 0./255.],
+               'reddish purple' : [204./255., 121./255., 167./255.]
+             }
+
+weiss_light_blue = [0.0, 0.384, 0.490]
+
+
+def bang_list():
+    """
+    Returns the bang palette as a list
+    """
+    bp_list = []
+    for _key, value in bang_palette.items():
+        bp_list.append(value)
+    return bp_list

glenoidplanefitting/algorithms/models.py

@@ -2,7 +2,7 @@
 Functions to create vtk models for visualisation of
 results
 """
-from vtk import vtkPlaneSource, vtkLineSource #pylint:disable=no-name-in-module
+from vtk import vtkPlaneSource, vtkLineSource, vtkSphereSource #pylint:disable=no-name-in-module
 
 def make_plane_model(plane_centre, normal_vector, resolution = 10,
         plane_size = 200.0):
@@ -56,3 +56,19 @@ def make_vault_model(point1,point2):
     line.SetPoint1(point1)
     line.SetPoint2(point2)
     return line
+
+def make_sphere_model(point, radius = 5.0):
+    """
+    Make a sphere source which we can use to represent a landmark
+    point
+
+    :param point: the point
+
+    :returns the vtkPointSource
+    """
+    sphere_source = vtkSphereSource()
+    sphere_source.SetCenter(point)
+    sphere_source.SetThetaResolution(12)
+    sphere_source.SetPhiResolution(12)
+    sphere_source.SetRadius(radius)
+    return sphere_source

glenoidplanefitting/ui/glenoidplanefitting_command_line.py

@@ -41,7 +41,7 @@ def main(args=None):
                         help="Landmark points file (vault)"
                         )
 
-    parser.add_argument("-c", "--corr_fried",
+    parser.add_argument("-cf", "--corr_fried",
                         required=False,
                         type=str,
                         default="",
@@ -62,6 +62,14 @@ def main(args=None):
                         help="Visualise the results"
                         )
 
+    parser.add_argument("-c", "--config",
+                        required=False,
+                        type=str,
+                        default=None,
+                        help="A configuration file"
+                        )
+
+
     version_string = __version__
     friendly_version_string = version_string if version_string else 'unknown'
     parser.add_argument(
@@ -73,4 +81,4 @@ def main(args=None):
 
     run_demo(args.model, args.planes, args.fried_points,
              args.vault_points,args.corr_fried, args.output,
-             args.visualise)
+             args.visualise, args.config)

glenoidplanefitting/ui/glenoidplanefitting_demo.py

@@ -5,15 +5,18 @@
 from vtk import vtkXMLPolyDataWriter #pylint:disable=no-name-in-module
 import numpy as np
 from sksurgeryvtk.models.vtk_surface_model import VTKSurfaceModel
+from sksurgerycore.configuration.configuration_manager import (
+        ConfigurationManager
+        )
 from glenoidplanefitting.algorithms import plane_fitting, friedman, vault
 from glenoidplanefitting.widgets.visualisation import vis_planes, vis_fried, \
         vis_vault
 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):
+             corr_fried="", output="", visualise = False, config_file = None):
     """
     :param planes: File name pointing to file containing points for
         planes method.
@@ -51,9 +54,23 @@ def run_demo(model_file_name, planes="", fried_points="", vault_points="",
         used as the new axial
         slice for picking
         the new landmark points for the 3D corrected Friedman method.
-        """
 
-    model = VTKSurfaceModel(model_file_name, [1., 0., 0.])
+    :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()
+    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)
+    vary_plane_colour = configuration.get('vary plane colour', True)
+    point_size =  configuration.get('point size', 3.0)
+    line_width =  configuration.get('line width', 5)
+
+    model = VTKSurfaceModel(model_file_name, model_colour)
     version = None
     if planes != "":
 
@@ -77,7 +94,9 @@ def run_demo(model_file_name, planes="", fried_points="", vault_points="",
                                                      return_meta3)
 
         if visualise:
-            vis_planes(model, [result, result2, result3])
+            vis_planes(model, [result, result2, result3], points1, points2,
+                    plane_resolution, plane_size, vary_plane_colour,
+                    point_size)
 
 
     if fried_points != "":
@@ -92,7 +111,7 @@ def run_demo(model_file_name, planes="", fried_points="", vault_points="",
                 posterior_glenoid)
         if visualise:
             vis_fried(model, anterior_glenoid, posterior_glenoid,
-                    glenoid_centre, result)
+                    glenoid_centre, result, line_width = line_width)
 
 
     if vault_points !="":
@@ -105,7 +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

@@ -3,18 +3,19 @@
 """
 import vtk
 from glenoidplanefitting.algorithms.models import make_plane_model, \
-        make_friedman_model, make_vault_model
+        make_friedman_model, make_vault_model, make_sphere_model
+from glenoidplanefitting.algorithms.colour_palette import bang_list
 
-def renderer_common(bone):
+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)
 
-    bone.ambient = 1.0
-    bone.diffuse = 1.0
-    bone.specular = 1.0
     bone.actor.GetProperty().SetAmbient(1)
     bone.actor.GetProperty().SetDiffuse(1)
     bone.actor.GetProperty().SetSpecular(1)
@@ -41,20 +42,39 @@ def render_window_common(renderer, window_name):
     render_window.Finalize()
     del render_window_interactor, render_window
 
-def add_vtk_source(renderer, source):
+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
     actor.SetMapper(mapper)
+    actor.GetProperty().SetLineWidth(linewidth)
+    actor.GetProperty().SetOpacity(opacity)
+    if wireframe:
+        actor.GetProperty().SetRepresentationToWireframe()
+        actor.GetProperty().SetAmbientColor(colour)
+        actor.GetProperty().SetDiffuseColor(colour)
+        actor.GetProperty().SetSpecularColor(colour)
+    else:
+        actor.GetProperty().SetRepresentationToSurface()
+
+    actor.GetProperty().SetColor(colour)
+    actor.GetProperty().SetEdgeColor(colour)
+
     renderer.AddActor(actor)
 
-def vis_planes(bone, planes):
+def vis_planes(bone, planes, points1 = False, points2 = False,
+        resolution = 1, plane_size = 200.0,
+        vary_plane_colour = False,
+        point_size = 5.0):
     """
     Visualisation for plane fitting methods
 
@@ -64,13 +84,32 @@ def vis_planes(bone, planes):
 
     """
     renderer = renderer_common(bone)
-    for plane in planes:
-        plane_source = make_plane_model(plane[1], plane[2])
-        add_vtk_source(renderer, plane_source)
+    for item, plane in enumerate(planes):
+        colour = [1., 1., 1.]
+        if vary_plane_colour:
+            colour = bang_list()[item]
+
+        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)
+
+    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)
+
+    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):
+def vis_fried(bone, cross1, cross2, glenoid1, result, line_width = 5):
     """
     Visualise the lines resulting from the friedman
     method.
@@ -82,15 +121,27 @@ def vis_fried(bone, cross1, cross2, glenoid1, result):
     renderer = renderer_common(bone)
 
     glenoid_line = make_friedman_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)
 
     friedman_line = make_friedman_model(glenoid1,result)
-    add_vtk_source(renderer, friedman_line)
+    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):
+def vis_vault(bone, cross1, cross2, glenoid1, result, line_width = 5):
     """
     Visualise the lines resulting from the vault
     method.
@@ -102,9 +153,21 @@ def vis_vault(bone, cross1, cross2, glenoid1, result):
     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")

requirements.txt

@@ -5,3 +5,4 @@
 numpy
 vtk
 scikit-surgeryvtk
+scikit-surgerycore

setup.py

@@ -54,6 +54,7 @@
         'numpy',
         'vtk',
         'scikit-surgeryvtk'
+        'scikit-surgerycore'
     ],
 
     entry_points={

vis_config.json

@@ -0,0 +1,8 @@
+{
+	"model colour" : [0.89, 0.86, 0.79],
+	"plane resolution" : 1, 
+	"plane size" : 200.0,
+	"vary plane colour" : true,
+	"point size" : 3.0,
+	"line width" : 4
+}