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find_distance_dental.py
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find_distance_dental.py
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# find_distance_dental.py
#
#
# This script performs ICP (iterative closest point) registration between two sets of STL
# files. The mean absolute distance is calculated and displayed between the two meshes.
# A screenshot and the distance mesh in the vtk format are currently saved to disk.
#
# Notes for resources:
# https://github.com/Kitware/VTK/blob/master/Examples/GUI/Python/ImplicitPlaneWidget.py
# https://github.com/Kitware/VTK/blob/master/Examples/VisualizationAlgorithms/Python/ClipCow.py
# https://gitlab.kitware.com/bxa/vtk/blob/a7996f418f2e1375aa91cbd98ab952a7162b4a26/Examples/Annotation/Python/annotatePick.py
# http://vtk.1045678.n5.nabble.com/Picking-and-moving-a-vertex-td1233640.html
# https://vtk.org/Wiki/VTK/Examples/Python/Visualization/AssignColorsCellFromLUT
# https://github.com/Kitware/VTK/blob/master/Examples/GUI/Python/BoxWidget.py
# https://python.hotexamples.com/examples/vtk/-/vtkPointPicker/python-vtkpointpicker-function-examples.html
#
#
# Deepa Krishnaswamy
# Brigham and Women's Hospital
# November 2021
#########################################################################
# -*- coding: utf-8 -*-
import numpy as np
import vtk
import sys
from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
print (str(vtk.VTK_MAJOR_VERSION) + '.' + str(vtk.VTK_MINOR_VERSION))
from PyQt5.QtWidgets import QApplication, QFileDialog
from vtk.util.colors import peacock, tomato
from vtk.util.colors import brown_ochre, tomato, banana, azure
import re
#########################################################################
def calculate_ICP(source, target):
icp = vtk.vtkIterativeClosestPointTransform()
icp.SetSource(source)
icp.SetTarget(target)
icp.GetLandmarkTransform().SetModeToRigidBody()
#icp.DebugOn()
# icp.SetMaximumNumberOfIterations(20)
icp.SetMaximumNumberOfIterations(150)
icp.StartByMatchingCentroidsOn()
icp.Modified()
icp.Update()
icpTransformFilter = vtk.vtkTransformPolyDataFilter()
if vtk.VTK_MAJOR_VERSION <= 5:
icpTransformFilter.SetInput(source)
else:
icpTransformFilter.SetInputData(source)
icpTransformFilter.SetTransform(icp)
icpTransformFilter.Update()
transformedSource = icpTransformFilter.GetOutput()
return transformedSource
def calculate_MAD(mesh_A, mesh_B):
'''Calculates the mean absolute distance (MAD) between two meshes'''
'''The distance is calculated between the cells'''
### calculate MAD metric ###
distance_filter = vtk.vtkDistancePolyDataFilter()
distance_filter.SetSignedDistance(0)
# added
distance_filter.ComputeSecondDistanceOff()
distance_filter.SetComputeSecondDistance(0)
# distance between ref and my mesh
if vtk.VTK_MAJOR_VERSION <= 5:
distance_filter.SetInput(0,mesh_A)
distance_filter.SetInput(1,mesh_B)
else:
distance_filter.SetInputData(0,mesh_A)
distance_filter.SetInputData(1,mesh_B)
distance_filter.Update()
# get distance
# distances = vtk_to_numpy(distance_filter.GetOutput().GetPointData().GetScalars())
distances = vtk_to_numpy(distance_filter.GetOutput().GetCellData().GetScalars())
mean_distance = np.mean(distances)
# get distance meshes
distance_mesh = vtk.vtkPolyData()
distance_mesh = distance_filter.GetOutput()
return distance_mesh, distances, mean_distance
#########################################################################
app = QApplication(sys.argv)
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
fnames = QFileDialog.getOpenFileNames(None,"Select STL File","","STL Files (*.stl);;All Files (*)", "", options)[0]
if len(fnames) == 2:
# Sort filenames so T1 is first, T2 is second
fnames.sort(key=lambda f: int(re.sub('\D', '', f)))
mesh1_filename = fnames[0]
mesh2_filename = fnames[1]
else:
sys.exit(app.exec_())
# Outputs
output_mesh_filename = 'distance_mesh.vtk'
output_jpg_filename = 'distance_mesh.jpg'
output_txt_filename = 'mean_absolute_distance_in_mm.txt'
print ('mesh1_filename: ' + str(mesh1_filename))
print ('mesh2_filename: ' + str(mesh2_filename))
#########################################################################
# read mesh
reader1 = vtk.vtkSTLReader()
reader1.SetFileName(mesh1_filename)
reader1.Update()
mesh1 = reader1.GetOutput()
# read gt mesh
reader2 = vtk.vtkSTLReader()
reader2.SetFileName(mesh2_filename)
reader2.Update()
mesh2 = reader2.GetOutput()
mapper1, mapper2, mapper1t = [vtk.vtkPolyDataMapper() for i in range(3)]
actor1, actor2, actor1t = [vtk.vtkActor() for i in range(3)]
mapper1.SetInputData(mesh1)
mapper2.SetInputData(mesh2)
actor1.SetMapper(mapper1)
actor2.SetMapper(mapper2)
actor1.GetProperty().SetColor(0.8,0.4,0.2) # orange = T1
actor2.GetProperty().SetColor(0.4,0.8,0.2) # green = T2
# calculate MAD
mesh1t = calculate_ICP(mesh1, mesh2)
distance_mesh, distances, mean_distance = calculate_MAD(mesh2, mesh1t)
# print maximum distance
print ('max distance: ' + str(np.max(distances)))
distance_meshb, distancesb, mean_distanceb = calculate_MAD(mesh1t, mesh2)
dist_min = distance_mesh.GetPointData().GetScalars().GetRange()[0]
dist_minb = distance_meshb.GetPointData().GetScalars().GetRange()[0]
dist_max = distance_mesh.GetPointData().GetScalars().GetRange()[1]
dist_maxb = distance_meshb.GetPointData().GetScalars().GetRange()[1]
# save distance mesh
polydata_writer = vtk.vtkPolyDataWriter()
polydata_writer.SetFileName(output_mesh_filename)
polydata_writer.SetInputData(distance_mesh)
polydata_writer.Write()
# save the MAD to a text file
with open(output_txt_filename, 'w') as f:
f.write(str(np.round(mean_distance,4)))
# Create renderers
renWin = vtk.vtkRenderWindow()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
mapper1t.SetInputData(mesh1t)
actor1t.SetMapper(mapper1t)
actor1t.GetProperty().SetColor(0.8,0.4,0.2)
mapper, mapperb = [vtk.vtkPolyDataMapper() for i in range(2)]
actor, actorb = [vtk.vtkActor() for i in range(2)]
ren1, ren1b, ren2, ren3 = [vtk.vtkRenderer() for i in range(4)]
if vtk.VTK_MAJOR_VERSION <= 5:
mapper.SetInput(distance_mesh)
mapperb.SetInput(distance_meshb)
else:
mapper.SetInputData(distance_mesh)
mapperb.SetInputData(distance_meshb)
# Set range between 0 and 3
# mapper.SetScalarRange(0, 3)
# mapper.SetScalarRange(0, 1)
# mapper.SetScalarRange(0, 1.6)
mapper.SetScalarRange(0, 2)
# mapper.SetScalarRange(0, 2.4)
# Create own look up table with set colors
hueLut = vtk.vtkLookupTable()
# hueLut.SetNumberOfTableValues(6)
hueLut.SetNumberOfTableValues(5)
hueLut.Build()
nc = vtk.vtkNamedColors()
# hueLut.SetTableValue(0,nc.GetColor4d("Blue"))
# hueLut.SetTableValue(1,nc.GetColor4d("Purple"))
# hueLut.SetTableValue(2,nc.GetColor4d("Green"))
# hueLut.SetTableValue(3,nc.GetColor4d("Yellow"))
# hueLut.SetTableValue(4,nc.GetColor4d("Orange"))
# hueLut.SetTableValue(5,nc.GetColor4d("Red"))
hueLut.SetTableValue(0,nc.GetColor4d("Blue"))
hueLut.SetTableValue(1,nc.GetColor4d("Green"))
hueLut.SetTableValue(2,nc.GetColor4d("Yellow"))
hueLut.SetTableValue(3,nc.GetColor4d("Orange"))
hueLut.SetTableValue(4,nc.GetColor4d("Red"))
mapper.SetLookupTable(hueLut)
# Set the scalar bar
scalarBar = vtk.vtkScalarBarActor()
scalarBar.SetLookupTable(hueLut)
scalarBar.SetTitle("mean distance")
# scalarBar.SetMaximumNumberOfColors(6); # 0.5 between each
# scalarBar.SetNumberOfLabels(7);
scalarBar.SetMaximumNumberOfColors(5) # 0.2 between each
scalarBar.SetNumberOfLabels(6)
# Set range between 0 and 3 for b
# mapperb.SetScalarRange(0, 3)
# mapperb.SetScalarRange(0, 1)
# mapperb.SetScalarRange(0, 1.6)
mapperb.SetScalarRange(0, 2)
# mapperb.SetScalarRange(0, 2.4)
# Create own look up table with set colors for b
hueLutb = vtk.vtkLookupTable()
# hueLutb.SetNumberOfTableValues(6)
hueLutb.SetNumberOfTableValues(5)
hueLutb.Build()
nc = vtk.vtkNamedColors()
# hueLutb.SetTableValue(0,nc.GetColor4d("Blue"))
# hueLutb.SetTableValue(1,nc.GetColor4d("Purple"))
# hueLutb.SetTableValue(2,nc.GetColor4d("Green"))
# hueLutb.SetTableValue(3,nc.GetColor4d("Yellow"))
# hueLutb.SetTableValue(4,nc.GetColor4d("Orange"))
# hueLutb.SetTableValue(5,nc.GetColor4d("Red"))
hueLutb.SetTableValue(0,nc.GetColor4d("Blue"))
hueLutb.SetTableValue(1,nc.GetColor4d("Green"))
hueLutb.SetTableValue(2,nc.GetColor4d("Yellow"))
hueLutb.SetTableValue(3,nc.GetColor4d("Orange"))
hueLutb.SetTableValue(4,nc.GetColor4d("Red"))
mapperb.SetLookupTable(hueLutb)
# Set the scalar bar b
scalarBarb = vtk.vtkScalarBarActor()
scalarBarb.SetLookupTable(hueLutb)
scalarBarb.SetTitle("mean distance")
# scalarBarb.SetMaximumNumberOfColors(6); # 0.5 between each
# scalarBarb.SetNumberOfLabels(7);
scalarBarb.SetMaximumNumberOfColors(5); # 0.2 between each
scalarBarb.SetNumberOfLabels(6);
# Add both actors to renderer
ren1.AddActor2D(scalarBar)
ren1b.AddActor2D(scalarBarb)
#####################################################
### Set up cutting box - 3 planes and the clipper ###
#####################################################
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(distance_mesh)
normals.Update()
points = vtk_to_numpy(distance_mesh.GetPoints().GetData())
bounds_min = np.min(points,axis=0)
bounds_max = np.max(points,axis=0)
planes = vtk.vtkPlanes()
planes.SetBounds(bounds_min[0], bounds_max[0], bounds_min[1], bounds_max[1], bounds_min[2], bounds_max[2])
clipper = vtk.vtkClipPolyData()
clipper.SetInputData(distance_mesh)
clipper.SetClipFunction(planes)
clipper.InsideOutOn()
clipper.GenerateClippedOutputOn()
clipMapper = vtk.vtkPolyDataMapper()
clipMapper.SetInputConnection(clipper.GetOutputPort())
clipMapper.ScalarVisibilityOn()
# clipMapper.SetScalarRange(0, 3)
# clipMapper.SetScalarRange(0, 1)
# clipMapper.SetScalarRange(0, 1.6)
clipMapper.SetScalarRange(0, 2)
# clipMapper.SetScalarRange(0, 2.4)
clipMapper.SetLookupTable(hueLut)
clipActor = vtk.vtkActor()
clipActor.SetMapper(clipMapper)
# create a MAD annotation
corner_MAD = vtk.vtkCornerAnnotation()
corner_MAD.SetMinimumFontSize(16)
corner_MAD.SetMaximumFontSize(16)
corner_MAD.SetText(7, "MAD: " + str(np.round(mean_distance,4)))
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetCurrentRenderer(ren1)
boxWidget.SetInteractor(iren)
boxWidget.SetPlaceFactor(1.25)
def myCallback(obj, event):
'''Callback function for the plane'''
global clipActor, planes
obj.GetPlanes(planes)
clipActor.VisibilityOn()
### Update the distance mesh here by the new clip plane ###
# Don't need to update scalar bars since they are set always
# from 0 to 3.
# Clip mesh2 and mesh1t using the same clip plane and
# calculate a new distance mesh
global mesh2
global mesh1t
global distance_mesh
clipper_mesh2 = vtk.vtkClipPolyData()
clipper_mesh2.SetInputData(mesh2)
clipper_mesh2.SetClipFunction(planes)
# clipper_mesh2.InsideOutOn()
clipper_mesh2.GenerateClippedOutputOn()
clipper_mesh2.Update()
mesh2_clipped = vtk.vtkPolyData()
mesh2_clipped = clipper_mesh2.GetClippedOutput()
clipper_mesh1t = vtk.vtkClipPolyData()
clipper_mesh1t.SetInputData(mesh1t)
clipper_mesh1t.SetClipFunction(planes)
# clipper_mesh1t.InsideOutOn()
clipper_mesh1t.GenerateClippedOutputOn()
clipper_mesh1t.Update()
mesh1t_clipped = vtk.vtkPolyData()
mesh1t_clipped = clipper_mesh1t.GetClippedOutput()
distance_mesh, distances, mean_distance = calculate_MAD(mesh2_clipped, mesh1t_clipped)
global corner_MAD
corner_MAD.SetMinimumFontSize(14)
corner_MAD.SetMaximumFontSize(14)
corner_MAD.SetText(7, "MAD: " + str(np.round(mean_distance,4)))
# save distance mesh that has been clipped
polydata_writer = vtk.vtkPolyDataWriter()
polydata_writer.SetFileName(output_mesh_filename)
polydata_writer.SetInputData(distance_mesh)
polydata_writer.Write()
# save the MAD to a text file
with open(output_txt_filename, 'w') as f:
f.write(str(np.round(mean_distance,4)))
# Interaction event
boxWidget.SetInputData(distance_mesh)
boxWidget.PlaceWidget()
boxWidget.On()
boxWidget.AddObserver("EndInteractionEvent", myCallback) # should be faster compared to "InteractionEvent"
##############################################################
### Set up the clicking of a point to display the distance ###
##############################################################
# # Create the point picker
# picker = vtk.vtkPointPicker()
# # create a text actor
# txt1 = vtk.vtkTextActor()
#
# def annotate_pick(obj, event):
# '''Callback function for displaying the scalar value of a clicked point'''
#
# global ren1
# global iren
# global txt_actor
# global distance_mesh
#
# pointPicker = vtk.vtkPointPicker()
# eventPosition = obj.GetEventPosition()
# result = picker.Pick(float(eventPosition[0]),float(eventPosition[1]),0.0,ren1)
# pickId = picker.GetPointId()
#
# # Get scalar that is associated with this pickId
# scalars = vtk_to_numpy(distance_mesh.GetPointData().GetScalars())
# dist_value = scalars[pickId]
#
# # Set as input to text actor
# txt1.SetInput("Picked point distance value: " + str(np.round(dist_value,4)))
# Create the cell picker
picker = vtk.vtkCellPicker()
# create a text actor
txt1 = vtk.vtkTextActor()
def annotate_pick(obj, event):
'''Callback function for displaying the scalar value of a clicked point'''
global ren1
global iren
global txt_actor
global distance_mesh
# pointPicker = vtk.vtkPointPicker()
cellPicker = vtk.vtkCellPicker()
eventPosition = obj.GetEventPosition()
result = picker.Pick(float(eventPosition[0]),float(eventPosition[1]),0.0,ren1)
pickId = picker.GetCellId()
# Get scalar that is associated with this pickId
scalars = vtk_to_numpy(distance_mesh.GetCellData().GetScalars())
dist_value = scalars[pickId]
# Set as input to text actor
txt1.SetInput("Picked point distance value: " + str(np.round(dist_value,4)))
iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
iren.AddObserver("RightButtonPressEvent", annotate_pick)
# Text actor properties
txtprop=txt1.GetTextProperty()
txtprop.SetFontFamilyToArial()
txtprop.SetFontSize(14)
txtprop.SetColor(1,1,1)
txt1.SetTextProperty(txtprop)
txt1.SetPosition2(20,30)
corner1 = vtk.vtkCornerAnnotation()
corner1.SetMinimumFontSize(14)
corner1.SetMaximumFontSize(14)
corner1.SetText(2, "Mean absolute distance \n Rotate with left mouse \n Move object or box planes by middle mouse button \n Turn on/off box planes by pressing i \n Move planes with left mouse \n Select cell on condyle with right mouse")
corner2 = vtk.vtkCornerAnnotation()
corner2.SetMinimumFontSize(14)
corner2.SetMaximumFontSize(14)
# corner2.SetText(2,"Before alignment \n T1 (orange) and T2 (green)")
corner2.SetText(2,"Before alignment \n scan 1 (orange) and scan 2 (green)")
corner3 = vtk.vtkCornerAnnotation()
corner3.SetMinimumFontSize(14)
corner3.SetMaximumFontSize(14)
# corner3.SetText(2,"After alignment \n T1 (orange) and T2 (green)")
corner3.SetText(2,"After alignment \n scan 1 (orange) and scan 2 (green)")
#################
### Rendering ###
#################
# actor.SetMapper(mapper)
# ren1.AddActor(actor) # This is the original distance mesh
ren1.AddActor(clipActor)
ren1.AddActor2D(txt1)
ren1.AddActor2D(corner1)
ren1.AddActor2D(corner_MAD)
ren1.SetViewport(0.5, 0.5, 1.0, 1.0)
actorb.SetMapper(mapperb)
ren1b.AddActor(actorb)
ren1b.SetViewport(0.5, 0.0, 1.0, 0.5)
ren2.AddActor(actor1)
ren2.AddActor(actor2)
ren2.AddActor2D(corner2)
ren2.SetViewport(0.0, 0.5, 0.5, 1.0)
ren3.AddActor(actor1t)
ren3.AddActor(actor2)
ren3.AddActor2D(corner3)
ren3.SetViewport(0.0, 0.0, 0.5, 0.5)
ren1b.SetBackground(0.05, 0.05, 0.05)
ren3.SetBackground(0.1, 0.1, 0.1)
ren2.SetBackground(0.15, 0.15, 0.15)
renWin.AddRenderer(ren1)
renWin.AddRenderer(ren1b)
renWin.AddRenderer(ren2)
renWin.AddRenderer(ren3)
renWin.Render()
renWin.SetSize(1920,1080)
renWin.Render()
# write out screenshot
w2if = vtk.vtkWindowToImageFilter()
w2if.SetInput(renWin)
w2if.Update()
writer = vtk.vtkJPEGWriter()
writer.SetFileName(output_jpg_filename)
writer.SetInputConnection(w2if.GetOutputPort())
writer.Write()
# iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
# added
# iren.SetPicker(picker)
iren.Initialize()
iren.Start()
# sys.exit(app.exec_())