From 8fac11480cdd6b18fb9006787b4521ce3e2a99b1 Mon Sep 17 00:00:00 2001
From: Mariska Wesseling <M.G.H.Wesseling@tudelft.nl>
Date: Fri, 17 Jun 2022 17:16:01 +0200
Subject: [PATCH] updates to notebooks
---
LigamentStudy/VisualiseSSM.py | 47 +--
LigamentStudy/VisualizeMeanSSM.ipynb | 183 +++++++++--
LigamentStudy/testVisualizeSSM.py | 441 +++++++++++++++++++++++++++
3 files changed, 631 insertions(+), 40 deletions(-)
create mode 100644 LigamentStudy/testVisualizeSSM.py
diff --git a/LigamentStudy/VisualiseSSM.py b/LigamentStudy/VisualiseSSM.py
index 2414586..6d64647 100644
--- a/LigamentStudy/VisualiseSSM.py
+++ b/LigamentStudy/VisualiseSSM.py
@@ -296,6 +296,7 @@ if __name__ == '__main__':
mapper2.SetInputData(point_cloud_lig)
actor2 = vtk.vtkActor()
actor2.SetMapper(mapper2)
+ actor2.GetProperty().RenderPointsAsSpheresOn()
actor2.GetProperty().SetColor(1, 0, 0)
actor2.GetProperty().SetPointSize(7.5)
@@ -314,6 +315,7 @@ if __name__ == '__main__':
surf_actor.GetProperty().SetOpacity(1.0)
legend = vtk.vtkScalarBarActor()
+ legend.SetOrientationToHorizontal()
labelFormat = vtk.vtkTextProperty()
labelFormat.SetFontSize(16)
titleFormat = vtk.vtkTextProperty()
@@ -338,10 +340,13 @@ if __name__ == '__main__':
# text_prop_cb.SetFontSize(500)
text_prop_cb.ShadowOff()
legend.SetLabelTextProperty(text_prop_cb)
- legend.SetMaximumWidthInPixels(75)
- legend.SetMaximumHeightInPixels(300)
+ # legend.SetMaximumWidthInPixels(75)
+ # legend.SetMaximumHeightInPixels(300)
+ legend.SetMaximumWidthInPixels(300)
+ legend.SetMaximumHeightInPixels(75)
legend.SetTitleTextProperty(text_prop_cb)
- legend.SetPosition(0.85,0.5)
+ # legend.SetPosition(0.85,0.5)
+ legend.SetPosition(0.5, 0.85)
# Renderer
renderer = vtk.vtkRenderer()
@@ -349,7 +354,7 @@ if __name__ == '__main__':
renderer.AddActor(actor2)
renderer.AddActor(bone_actor)
# renderer.AddActor(spline_actor)
- renderer.AddActor(surf_actor)
+ # renderer.AddActor(surf_actor)
if not subject == 100 and not subject == 'S0':
renderer.AddActor(wire_actor)
# renderer.AddActor(wire_actor2)
@@ -377,23 +382,23 @@ if __name__ == '__main__':
renderWindowInteractor.Start()
-# polyData = vtk.vtkPolyData()
-# polyData.DeepCopy(surf_actor.GetMapper().GetInput())
-# transform = vtk.vtkTransform()
-# transform.SetMatrix(surf_actor.GetMatrix())
-# fil = vtk.vtkTransformPolyDataFilter()
-# fil.SetTransform(transform)
-# fil.SetInputDataObject(polyData)
-# fil.Update()
-# polyData.DeepCopy(fil.GetOutput())
-#
-# writer = vtk.vtkPLYWriter()
-# writer.SetFileTypeToASCII()
-# writer.SetColorModeToDefault()
-# filename = r'C:\Users\mariskawesseli\Documents\GitLab\tibia_surf_ply.ply'
-# writer.SetFileName(filename)
-# writer.SetInputData(polyData)
-# writer.Write()
+polyData = vtk.vtkPolyData()
+polyData.DeepCopy(actor2.GetMapper().GetInput())
+transform = vtk.vtkTransform()
+transform.SetMatrix(actor2.GetMatrix())
+fil = vtk.vtkTransformPolyDataFilter()
+fil.SetTransform(transform)
+fil.SetInputDataObject(polyData)
+fil.Update()
+polyData.DeepCopy(fil.GetOutput())
+
+writer = vtk.vtkPLYWriter()
+writer.SetFileTypeToASCII()
+writer.SetColorModeToDefault()
+filename = r'C:\Users\mariskawesseli\Documents\GitLab\femur_lig_ply_col2.ply'
+writer.SetFileName(filename)
+writer.SetInputData(polyData)
+writer.Write()
# import pandas as pd
# pd.DataFrame(color).to_clipboard()
\ No newline at end of file
diff --git a/LigamentStudy/VisualizeMeanSSM.ipynb b/LigamentStudy/VisualizeMeanSSM.ipynb
index 69fd983..b5e7158 100644
--- a/LigamentStudy/VisualizeMeanSSM.ipynb
+++ b/LigamentStudy/VisualizeMeanSSM.ipynb
@@ -21,7 +21,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"id": "0a85e4e1-b480-4f37-a5de-4d2098d01e66",
"metadata": {
"tags": []
@@ -45,14 +45,13 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 2,
"id": "9ad2e1fd-d4a4-48d2-8966-671b64ce093d",
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import vtk\n",
- "from numpy import random\n",
"import trimesh\n",
"import numpy as np\n",
"import seaborn as sns\n",
@@ -69,7 +68,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 3,
"id": "4efddfba-c04e-4023-8f6c-fdca0a5f25de",
"metadata": {},
"outputs": [],
@@ -120,7 +119,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 4,
"id": "8f40bba1-dcd8-4d37-9682-d7d19e21bea0",
"metadata": {},
"outputs": [],
@@ -159,7 +158,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 5,
"id": "77dfff23-beb1-413e-b73b-c20a9e00245f",
"metadata": {},
"outputs": [],
@@ -179,12 +178,12 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 6,
"id": "e418af21-2c51-441b-8e2c-94d800a1fd73",
"metadata": {},
"outputs": [],
"source": [
- "path = os.path.join(r'C:\\Users\\mariskawesseli\\Documents\\GitLab\\knee_ssm\\OAI\\Output/' + segment + r'_bone\\new_bone\\shape_models')"
+ "path = os.path.join(r'./data/' + segment)"
]
},
{
@@ -197,7 +196,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 7,
"id": "154780b1-e011-4a8c-8935-03900ef064d2",
"metadata": {},
"outputs": [],
@@ -312,14 +311,14 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 11,
"id": "c98f226f-a28a-4e44-a342-5771f4984d63",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "21bc484f709e4c0091acadc04799fac6",
+ "model_id": "dd208c6057af4d6696067520b403e9ee",
"version_major": 2,
"version_minor": 0
},
@@ -347,6 +346,63 @@
"plotter.show()"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "id": "cd376163",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "aee45e50ed6746e69e7e02c8392f989a",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "ViewInteractiveWidget(height=768, layout=Layout(height='auto', width='100%'), width=1024)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "spheres=[]\n",
+ "plotter = pv.Plotter()\n",
+ "for i in range(0,len(points_lig)):\n",
+ " spheres.append(pv.Sphere(center=points_lig[i], radius=0.25))\n",
+ " cols = np.tile(rgb_col[i], (spheres[i].number_of_points,1))\n",
+ " spheres[i][\"colors\"] = cols\n",
+ " plotter.add_mesh(spheres[i])\n",
+ "\n",
+ "plotter.add_actor(bone_actor)\n",
+ "plotter.add_actor(legend)\n",
+ "pv.set_plot_theme(\"document\")\n",
+ "plotter.show() # show the two spheres from two PolyData\n",
+ "\n",
+ "plotter.export_html(r\"C:\\Users\\mariskawesseli\\Documents\\GitLab\\2022_JCWMSK_tutorials\\SSMfemur.html\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "id": "990d654f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# plotter = pv.Plotter(window_size=(900, 900),notebook=True)\n",
+ "# mesh= pv.read(r\"C:\\Users\\mariskawesseli\\Documents\\GitLab\\femur_lig_ply_col.ply\")\n",
+ "# scalars = mesh['RGBA']\n",
+ "# plotter.add_actor(bone_actor)\n",
+ "# plotter.add_mesh(mesh, show_scalar_bar=False, scalars=scalars[:,0:3])\n",
+ "# plotter.add_actor(legend)\n",
+ "# pv.set_plot_theme(\"document\")\n",
+ "# plotter.show()\n",
+ "\n",
+ "# plotter.export_html(r\"C:\\Users\\mariskawesseli\\Documents\\GitLab\\2022_JCWMSK_tutorials\\SSMfemur.html\")"
+ ]
+ },
{
"cell_type": "markdown",
"id": "9ae0ddf1-b716-4e73-ab28-06015b2a8bc7",
@@ -367,7 +423,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 15,
"id": "dedd30e3-4598-4b88-9d0d-e8b4b6fe5f26",
"metadata": {},
"outputs": [],
@@ -387,12 +443,12 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 16,
"id": "eeb6abea-1e7c-42a3-be1c-6a0d1730ff58",
"metadata": {},
"outputs": [],
"source": [
- "path = os.path.join(r'C:\\Users\\mariskawesseli\\Documents\\GitLab\\knee_ssm\\OAI\\Output/' + segment + r'_bone\\new_bone\\shape_models')"
+ "path = os.path.join(r'./data/' + segment)"
]
},
{
@@ -405,7 +461,7 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": 17,
"id": "2445f518-0319-4075-800b-d35bdabe434a",
"metadata": {},
"outputs": [],
@@ -431,7 +487,7 @@
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": 18,
"id": "606f3104-8996-4529-b101-796ac53e00c2",
"metadata": {},
"outputs": [],
@@ -455,14 +511,14 @@
},
{
"cell_type": "code",
- "execution_count": 20,
+ "execution_count": 19,
"id": "cd8b342b-39bd-4bcb-b0f6-f25d6d3edc2e",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "f21bda3655db48ddae6deabeb32d58a3",
+ "model_id": "278f323878ef45eba11f5d340b212af3",
"version_major": 2,
"version_minor": 0
},
@@ -484,13 +540,71 @@
"plotter.add_actor(legend)\n",
"\n",
"pv.set_plot_theme(\"document\")\n",
+ "\n",
"plotter.show()"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "id": "944d007a",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "85366469fecb4683975db877749f97ed",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "ViewInteractiveWidget(height=768, layout=Layout(height='auto', width='100%'), width=1024)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "spheres=[]\n",
+ "plotter = pv.Plotter()\n",
+ "for i in range(0,len(points_lig)):\n",
+ " spheres.append(pv.Sphere(center=points_lig[i], radius=0.25))\n",
+ " cols = np.tile(rgb_col[i], (spheres[i].number_of_points,1))\n",
+ " spheres[i][\"colors\"] = cols\n",
+ " plotter.add_mesh(spheres[i])\n",
+ "\n",
+ "plotter.add_actor(bone_actor)\n",
+ "plotter.add_actor(legend)\n",
+ "pv.set_plot_theme(\"document\")\n",
+ "plotter.show() # show the two spheres from two PolyData\n",
+ "\n",
+ "plotter.export_html(r\"C:\\Users\\mariskawesseli\\Documents\\GitLab\\2022_JCWMSK_tutorials\\SSMtibia.html\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "id": "0b196960-88d0-471c-9bec-a7231a969c85",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# plotter = pv.Plotter(window_size=(900, 900),notebook=True)\n",
+ "# mesh= pv.read(r\"C:\\Users\\mariskawesseli\\Documents\\GitLab\\tibia_lig_ply_col.ply\")\n",
+ "# scalars = mesh['RGBA']\n",
+ "# plotter.add_actor(bone_actor)\n",
+ "# plotter.add_mesh(mesh, show_scalar_bar=False, scalars=scalars[:,0:3])\n",
+ "# plotter.add_actor(legend)\n",
+ "# pv.set_plot_theme(\"document\")\n",
+ "# plotter.show()\n",
+ "\n",
+ "# plotter.export_html(r\"C:\\Users\\mariskawesseli\\Documents\\GitLab\\2022_JCWMSK_tutorials\\SSMtibia.html\")"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
- "id": "7a65e4e1-74df-4b42-a3b2-e865922dd018",
+ "id": "3c364012",
"metadata": {},
"outputs": [],
"source": []
@@ -513,6 +627,37 @@
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.12"
+ },
+ "latex_envs": {
+ "LaTeX_envs_menu_present": true,
+ "autoclose": false,
+ "autocomplete": true,
+ "bibliofile": "biblio.bib",
+ "cite_by": "apalike",
+ "current_citInitial": 1,
+ "eqLabelWithNumbers": true,
+ "eqNumInitial": 1,
+ "hotkeys": {
+ "equation": "Ctrl-E",
+ "itemize": "Ctrl-I"
+ },
+ "labels_anchors": false,
+ "latex_user_defs": false,
+ "report_style_numbering": false,
+ "user_envs_cfg": false
+ },
+ "toc": {
+ "base_numbering": 1,
+ "nav_menu": {},
+ "number_sections": true,
+ "sideBar": true,
+ "skip_h1_title": false,
+ "title_cell": "Table of Contents",
+ "title_sidebar": "Contents",
+ "toc_cell": false,
+ "toc_position": {},
+ "toc_section_display": true,
+ "toc_window_display": false
}
},
"nbformat": 4,
diff --git a/LigamentStudy/testVisualizeSSM.py b/LigamentStudy/testVisualizeSSM.py
new file mode 100644
index 0000000..d3273f9
--- /dev/null
+++ b/LigamentStudy/testVisualizeSSM.py
@@ -0,0 +1,441 @@
+# import pyvista as pv
+# mesh= pv.read(r"C:\Users\mariskawesseli\Documents\GitLab\femur_lig_ply_col.ply")
+# mesh.plot()
+
+# import pyvista as pv
+# import numpy as np
+# # Re cast PolyData because file was not properly saved
+# bad = pv.read(r"C:\Users\mariskawesseli\Documents\GitLab\femur_lig_ply_col.ply")
+# bad.plot()
+# mesh = pv.PolyData(bad.points)
+# # Plot it
+# scalars = bad['RGBA']
+# # mesh.plot(scalars=scalars)
+# mesh.plot(scalars=scalars[:,0:3])
+# mesh.plot(scalars=scalars)
+# mesh.plot(scalars=scalars, rgba=True)
+
+import sys
+import os
+import vtk
+from numpy import random
+import trimesh
+import numpy as np
+import seaborn as sns
+
+
+class VtkPointCloud:
+ def __init__(self, zMin=-10.0, zMax=10.0, maxNumPoints=1e6):
+ self.maxNumPoints = maxNumPoints
+ self.vtkPolyData = vtk.vtkPolyData()
+ self.clearPoints()
+ mapper = vtk.vtkPolyDataMapper()
+ mapper.SetInputData(self.vtkPolyData)
+ mapper.SetColorModeToDefault()
+ mapper.SetScalarRange(zMin, zMax)
+ mapper.SetScalarVisibility(1)
+ self.vtkActor = vtk.vtkActor()
+ self.vtkActor.SetMapper(mapper)
+
+ def addPoint(self, point):
+ if (self.vtkPoints.GetNumberOfPoints() < self.maxNumPoints):
+ pointId = self.vtkPoints.InsertNextPoint(point[:])
+ self.vtkDepth.InsertNextValue(point[2])
+ self.vtkCells.InsertNextCell(1)
+ self.vtkCells.InsertCellPoint(pointId)
+ else:
+ r = random.randint(0, self.maxNumPoints)
+ self.vtkPoints.SetPoint(r, point[:])
+ self.vtkCells.Modified()
+ self.vtkPoints.Modified()
+ self.vtkDepth.Modified()
+
+ def clearPoints(self):
+ self.vtkPoints = vtk.vtkPoints()
+ self.vtkCells = vtk.vtkCellArray()
+ self.vtkDepth = vtk.vtkDoubleArray()
+ self.vtkDepth.SetName('DepthArray')
+ self.vtkPolyData.SetPoints(self.vtkPoints)
+ self.vtkPolyData.SetVerts(self.vtkCells)
+ self.vtkPolyData.GetPointData().SetScalars(self.vtkDepth)
+ self.vtkPolyData.GetPointData().SetActiveScalars('DepthArray')
+
+
+def load_data(data, pointCloud):
+ # data = genfromtxt(filename, dtype=float, usecols=[0, 1, 2])
+ for k in range(size(data, 0)):
+ point = data[k] # 20*(random.rand(3)-0.5)
+ pointCloud.addPoint(point)
+
+ return pointCloud
+
+
+def load_stl(filename):
+ reader = vtk.vtkSTLReader()
+ reader.SetFileName(filename)
+
+ mapper = vtk.vtkPolyDataMapper()
+ if vtk.VTK_MAJOR_VERSION <= 5:
+ mapper.SetInput(reader.GetOutput())
+ else:
+ mapper.SetInputConnection(reader.GetOutputPort())
+
+ actor = vtk.vtkActor()
+ actor.SetMapper(mapper)
+
+ return actor
+
+
+def create_pointcloud_polydata(points, colors=None, seg=None):
+ """https://github.com/lmb-freiburg/demon
+ Creates a vtkPolyData object with the point cloud from numpy arrays
+
+ points: numpy.ndarray
+ pointcloud with shape (n,3)
+
+ colors: numpy.ndarray
+ uint8 array with colors for each point. shape is (n,3)
+
+ Returns vtkPolyData object
+ """
+ vpoints = vtk.vtkPoints()
+ vpoints.SetNumberOfPoints(points.shape[0])
+ for i in range(points.shape[0]):
+ vpoints.SetPoint(i, points[i])
+ # vpoints.SetMarkerStyle(vtk.vtkPlotPoints.CIRCLE)
+
+ vpoly = vtk.vtkPolyData()
+
+ appendFilter = vtk.vtkAppendPolyData()
+ for i in range(points.shape[0]):
+ sphereSource = vtk.vtkSphereSource()
+ # spheres.SetThetaResolution(1)
+ # spheres.SetPhiResolution(1)
+ sphereSource.SetRadius(1)
+ sphereSource.SetCenter(vpoints.GetPoint(i))
+ sphereSource.Update()
+
+ appendFilter.AddInputData(sphereSource.GetOutput())
+
+ # vpoly.SetPoints(vpoints)
+ rgb_col = []
+ if not colors is None:
+ if seg == 'femur':
+ max_val = 8
+ color[112:len(color)] = (color[112:len(color)] / max_val) * 10
+ vcolors = vtk.vtkUnsignedCharArray()
+ vcolors.SetNumberOfComponents(3)
+ vcolors.SetName("Colors")
+ vcolors.SetNumberOfTuples(points.shape[0])
+ rgb_col = []
+ for i in range(points.shape[0]):
+ c = sns.color_palette("viridis_r", n_colors=101, as_cmap=False)
+ vcolors.SetTuple3(i, c[int(colors[i] * 10)][0] * 255, c[int(colors[i] * 10)][1] * 255,
+ c[int(colors[i] * 10)][2] * 255)
+ rgb_col.append(
+ [c[int(colors[i] * 10)][0] * 255, c[int(colors[i] * 10)][1] * 255, c[int(colors[i] * 10)][2] * 255])
+ # print(i, c[int(colors[i] - 1)][0], c[int(colors[i] - 1)][1], c[int(colors[i] - 1)][2])
+ # c = rgb(1,10,colors[i])
+ # vcolors.SetTuple3(i, c[0], c[1], c[2])
+ vpoly.GetPointData().SetScalars(vcolors)
+
+ actor.GetProperty().SetColor(color)
+
+ vcells = vtk.vtkCellArray()
+
+ for i in range(points.shape[0]):
+ vcells.InsertNextCell(1)
+ vcells.InsertCellPoint(i)
+
+ vpoly.SetVerts(vcells)
+
+ return vpoly, rgb_col
+
+
+def rgb(minimum, maximum, value):
+ minimum, maximum = float(minimum), float(maximum)
+ ratio = (value - minimum) / (maximum - minimum) # 2 *
+ g = int(max(0, 255 * (1 - ratio)))
+ r = int(max(0, 255 * (ratio - 0)))
+ b = 0 # 255 - b - r
+ return r, g, b
+
+
+def createSpline(points):
+ vpoints = vtk.vtkPoints()
+ vpoints.SetNumberOfPoints(points.shape[0])
+ for i in range(points.shape[0]):
+ vpoints.SetPoint(i, points[i])
+
+ spline = vtk.vtkParametricSpline()
+ spline.SetPoints(vpoints)
+
+ functionSource = vtk.vtkParametricFunctionSource()
+ functionSource.SetParametricFunction(spline)
+ functionSource.Update()
+
+ # Create a mapper
+ mapper = vtk.vtkPolyDataMapper()
+ mapper.SetInputConnection(functionSource.GetOutputPort())
+
+ # Create an actor
+ actor = vtk.vtkActor()
+ actor.SetMapper(mapper)
+
+ return actor
+
+
+if __name__ == '__main__':
+ center_tibia = np.concatenate((np.arange(131), np.arange(470 - 341) + 341)) # PCL + ACL
+ center_femur = np.concatenate((np.arange(112), np.arange(341 - 263) + 263)) # PCL + ACL
+ # center_femur = np.concatenate((np.arange(64), np.arange(101 - 68) + 68)) # PCL + ACL
+ center_only = 1
+ subjects = [100] # [100] # ['9','13','19','23','26','29','32','35','37','41'] #, S0 [100]
+
+ segments = ['femur'] # 'femur',
+ ligaments_fem = [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+ [6, 5, 6, 6, 6, 6, 4, 4, 5, 5],
+ [3, 2, 5, 3, 3, 2, 2, 0, 3, 3],
+ [0, 8, 0, 0, 0, 0, 0, 0, 0, 0], # MCLd2
+ [7, 3, 7, 7, 7, 5, 7, 6, 7, 0],
+ [0, 0, 8, 0, 0, 0, 0, 0, 0, 0], # POL2
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # POL3
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # POL4
+ [4, 6, 3, 5, 4, 0, 0, 3, 4, 4],
+ [5, 7, 4, 4, 5, 7, 6, 5, 6, 6],
+ [2, 4, 2, 2, 2, 3, 3, 2, 2, 2]]
+
+ ligaments_tib = [[5, 7, 6, 5, 3, 4, 4, 5, 5, 4],
+ [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+ [3, 3, 8, 3, 5, 3, 5, 0, 3, 3],
+ [0, 4, 0, 0, 0, 0, 0, 0, 0, 0], # MCLd2
+ [4, 5, 3, 4, 4, 5, 3, 2, 4, 0],
+ [0, 6, 4, 0, 0, 0, 0, 0, 0, 0], # POL2
+ [0, 0, 5, 0, 0, 0, 0, 0, 0, 0], # POL3
+ [0, 0, 7, 0, 0, 0, 0, 0, 0, 0], # POL4
+ [6, 8, 9, 6, 6, 6, 6, 6, 6, 5],
+ [2, 2, 2, 2, 2, 2, 2, 3, 2, 2],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
+
+ ligaments_fib = [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # PCL
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # MCLp
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # MCLd
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # MCLd2
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # POL
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # POL2
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # POL3
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # POL4
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # ACL
+ [2, 2, 2, 2, 2, 2, 2, 3, 2, 2], # LCL
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]] # POP
+
+ for segment in segments:
+ SSMpoints = [[] for i in range(11)]
+ if segment == 'tibia':
+ center = center_tibia
+ elif segment == 'femur':
+ center = center_femur
+
+ for ind in range(0, 11):
+ SSMpoints[ind] = [[] for i in range(10)]
+
+ for ind, subject in enumerate(subjects):
+ if subject == 100:
+ path = os.path.join(
+ r'C:\Users\mariskawesseli\Documents\GitLab\knee_ssm\OAI\Output/' + segment + r'_bone\new_bone\shape_models')
+ elif subject == 'S0':
+ path = os.path.join(r'C:\Users\mariskawesseli\Documents\LigamentStudy\MRI\S0_prelim')
+ else:
+ path = os.path.join(r"C:\Users\mariskawesseli\Documents\LigamentStudy\ImageData", str(subject))
+
+ if subject in [9, 13, 26, 29, 32]:
+ side = 'R'
+ reflect = ''
+ else:
+ side = 'L'
+ reflect = '.reflect'
+
+ # points = trimesh.load_mesh(r'C:\Users\mariskawesseli\Documents\GitLab\knee_ssm\OAI\Output\femur_bone\new_bone\shape_models\meanshape_bone_no_lig.xyz')
+ # point_cloud = create_pointcloud_polydata(points)
+ # pointCloud = VtkPointCloud()
+ # pointCloud = load_data(point_cloud, pointCloud)
+ # points_lig = trimesh.load_mesh(r'C:\Users\mariskawesseli\Documents\GitLab\knee_ssm\OAI\Output\femur_bone\new_bone\shape_models\meanshape_ligs.xyz')
+ if subject == 100:
+ # points_lig = trimesh.load_mesh(path + '\meanshape_ligs.xyz')
+ # point_cloud_lig = create_pointcloud_polydata(points_lig)
+ points_lig = trimesh.load_mesh(path + '\meanshape_ligs_color.xyz')
+ color = np.loadtxt(path + r'\meanshape_ligs_color.xyz')[:, 3]
+
+ if center_only == 1:
+ points_lig = points_lig[center]
+ color = color[center]
+ point_cloud_lig, rgb_col = create_pointcloud_polydata(points_lig, colors=color, seg=segment)
+ bone_actor = load_stl(path + '/mean_shape.stl')
+ bone_actor.GetProperty().SetOpacity(1.0)
+
+ mesh = trimesh.load_mesh(path + '/mean_shape.stl')
+ # dist = trimesh.proximity.nearby_faces(mesh, np.squeeze(np.asarray(points_lig[np.argwhere(color >= 8)])))
+ dist3 = trimesh.proximity.closest_point_naive(mesh, np.squeeze(
+ np.asarray(points_lig[np.argwhere(color >= 7)])), tol=1.0)
+
+ # faces = np.unique(np.asarray([item for sublist in dist for item in sublist]))
+ faces = np.unique(np.asarray([item for sublist in dist3[3] for item in sublist]))
+ mesh.update_faces(faces)
+ mesh.export(path + '/mean_shape_80percsurf.stl')
+ surf_actor = load_stl(path + '/mean_shape_80percsurf.stl')
+ else:
+ # points_lig = trimesh.load_mesh(path + '\SSM_' + segment + '_areas.xyz') #_pred_points_color
+ # point_cloud_lig = create_pointcloud_polydata(points_lig)
+ points_lig = trimesh.load_mesh(
+ path + '\SSM_' + segment + '_pred_points_color.xyz') # _pred_points_color
+ color = np.loadtxt(path + '\SSM_' + segment + '_pred_points_color.xyz')[:,
+ 3] # _areas _short_areas _pred_points
+ if center_only == 1:
+ points_lig = points_lig[center]
+ # color = color[center]
+ point_cloud_lig = create_pointcloud_polydata(points_lig, seg=segment) # ,color colors=color,
+ if subject == 'S0':
+ # bone_actor = load_stl(path + '/bone_femur2_2_bone_rot.stl')
+ # bone_actor = load_stl(path + '/bone_tibia_2_bone_rot.stl')
+ bone_actor = load_stl(path + '/bone_fibula_1_tissue_rot.stl')
+ else:
+ bone_actor = load_stl(
+ path + '/Segmentation_' + segment + '_resample.stl') # '/SSM_' + segment + '_reconstruct_transform_icp.stl'
+ if segment == 'fibula':
+ segment_temp = 'tibia'
+ else:
+ segment_temp = segment
+ # if center_only == 1:
+ # wire_actor = load_stl(path + '/Segmentation_' + segment_temp + '_wires1.stl')
+ # wire_actor2 = load_stl(path + '/Segmentation_' + segment_temp + '_wires3.stl')
+ # wire_actor2.GetProperty().SetColor(1, 1, 0)
+ # else:
+ wire_actor = load_stl(path + '/Segmentation_' + segment_temp + '_wires.stl')
+ wire_actor.GetProperty().SetColor(1, 1, 0)
+ bone_actor.GetProperty().SetOpacity(0.75)
+
+ points_bone = trimesh.load_mesh(path + '\SSM_' + segment + '_transform_icp.xyz')
+ point_cloud_bone = create_pointcloud_polydata(points_bone)
+
+ # orders = np.load(r'C:\Users\mariskawesseli\Documents\LigamentStudy\ImageData\occurances_order.npy')
+
+ mapper = vtk.vtkPolyDataMapper()
+ mapper.SetInputData(point_cloud_bone)
+ actor = vtk.vtkActor()
+ actor.SetMapper(mapper)
+ actor.GetProperty().SetColor(0, 0, 0)
+ actor.GetProperty().SetPointSize(2)
+ # actor.GetProperty().SetOpacity(1.0)
+
+ # spline_actor = createSpline(np.squeeze(np.asarray(points_lig[np.argwhere(color >= 8)])))
+ bone_actor.GetProperty().SetColor(0.89, 0.85, 0.79)
+ # bone_actor.GetProperty().LightingOff()
+ mapper2 = vtk.vtkPolyDataMapper()
+ mapper2.SetInputData(point_cloud_lig)
+ actor2 = vtk.vtkActor()
+ actor2.SetMapper(mapper2)
+ actor2.GetProperty().RenderPointsAsSpheresOn()
+ actor2.GetProperty().SetColor(1, 0, 0)
+ actor2.GetProperty().SetPointSize(7.5)
+
+ c = sns.color_palette("viridis_r", n_colors=101, as_cmap=False)
+ lut = vtk.vtkLookupTable()
+ lut.SetNumberOfColors(11)
+ lut.SetTableRange(1, 11)
+ for j in range(0, 11):
+ lut.SetTableValue(int(j * 1), c[j * 10][0], c[j * 10][1], c[j * 10][2])
+ # print(int(j*1), c[j*10-1][0], c[j*10-1][1], c[j*10-1][2])
+
+ j = 10 - 1
+ surf_col = [c[j][0], c[j][1], c[j][2]]
+ surf_col = [169 / 255, 169 / 255, 169 / 255]
+ surf_actor.GetProperty().SetColor(surf_col)
+ surf_actor.GetProperty().SetOpacity(1.0)
+
+ legend = vtk.vtkScalarBarActor()
+ legend.SetOrientationToHorizontal()
+ labelFormat = vtk.vtkTextProperty()
+ labelFormat.SetFontSize(16)
+ titleFormat = vtk.vtkTextProperty()
+ titleFormat.SetFontSize(8)
+ legend.SetLabelTextProperty(labelFormat)
+ # legend.SetTitleTextProperty(titleFormat)
+
+ legend.SetNumberOfLabels(11)
+ lut.SetTableRange(0, 100)
+ legend.SetLookupTable(lut)
+ # pos = legend.GetPositionCoordinate()
+ # pos.SetCoordinateSystemToNormalizedViewport()
+
+ legend.SetTitle("% of specimens \n")
+ legend.SetLabelFormat("%1.0f")
+ legend.SetUnconstrainedFontSize(1)
+
+ text_prop_cb = legend.GetLabelTextProperty()
+ text_prop_cb.SetFontFamilyAsString('Arial')
+ text_prop_cb.SetFontFamilyToArial()
+ text_prop_cb.SetColor(0, 0, 0)
+ # text_prop_cb.SetFontSize(500)
+ text_prop_cb.ShadowOff()
+ legend.SetLabelTextProperty(text_prop_cb)
+ # legend.SetMaximumWidthInPixels(75)
+ # legend.SetMaximumHeightInPixels(300)
+ legend.SetMaximumWidthInPixels(300)
+ legend.SetMaximumHeightInPixels(75)
+ legend.SetTitleTextProperty(text_prop_cb)
+ # legend.SetPosition(0.85,0.5)
+ legend.SetPosition(0.5, 0.85)
+
+ # Renderer
+ renderer = vtk.vtkRenderer()
+ # renderer.AddActor(actor)
+ renderer.AddActor(actor2)
+ renderer.AddActor(bone_actor)
+ # renderer.AddActor(spline_actor)
+ # renderer.AddActor(surf_actor)
+ if not subject == 100 and not subject == 'S0':
+ renderer.AddActor(wire_actor)
+ # renderer.AddActor(wire_actor2)
+ renderer.AddActor(legend)
+ # renderer.SetBackground(.2, .3, .4)
+ renderer.SetBackground(1.0, 1.0, 1.0)
+ renderer.ResetCamera()
+ # light = vtk.vtkLight()
+ # light.SetIntensity(1)
+ # renderer.AddLight(light)
+
+ # Render Window
+ renderWindow = vtk.vtkRenderWindow()
+ renderWindow.AddRenderer(renderer)
+ renderWindow.SetSize(750, 750)
+
+ # Interactor
+ renderWindowInteractor = vtk.vtkRenderWindowInteractor()
+ renderWindowInteractor.SetRenderWindow(renderWindow)
+ renderWindowInteractor.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
+
+ # Begin Interaction
+ renderWindow.Render()
+ renderWindow.SetWindowName("XYZ Data Viewer " + str(subject))
+ renderWindowInteractor.Start()
+
+polyData = vtk.vtkPolyData()
+polyData.DeepCopy(actor2.GetMapper().GetInput())
+transform = vtk.vtkTransform()
+transform.SetMatrix(actor2.GetMatrix())
+fil = vtk.vtkTransformPolyDataFilter()
+fil.SetTransform(transform)
+fil.SetInputDataObject(polyData)
+fil.Update()
+polyData.DeepCopy(fil.GetOutput())
+
+writer = vtk.vtkPLYWriter()
+writer.SetFileTypeToASCII()
+writer.SetColorModeToDefault()
+filename = r'C:\Users\mariskawesseli\Documents\GitLab\femur_lig_ply_col2.ply'
+writer.SetFileName(filename)
+writer.SetInputData(polyData)
+writer.Write()
+
+# import pandas as pd
+# pd.DataFrame(color).to_clipboard()
\ No newline at end of file
--
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