def removeOutliers(points, radius, c='k', alpha=1, legend=None):
'''
Remove outliers from a cloud of points within radius search
'''
isactor = False
if isinstance(points, vtk.vtkActor):
isactor = True
poly = vu.polydata(points)
else:
src = vtk.vtkPointSource()
src.SetNumberOfPoints(len(points))
src.Update()
vpts = src.GetOutput().GetPoints()
for i, p in enumerate(points):
vpts.SetPoint(i, p)
poly = src.GetOutput()
removal = vtk.vtkRadiusOutlierRemoval()
vu.setInput(removal, poly)
removal.SetRadius(radius)
removal.SetNumberOfNeighbors(5)
removal.GenerateOutliersOff()
removal.Update()
rpoly = removal.GetOutput()
print("# of removed outlier points: ", removal.GetNumberOfPointsRemoved(),
'/', poly.GetNumberOfPoints())
outpts = []
for i in range(rpoly.GetNumberOfPoints()):
outpts.append(list(rpoly.GetPoint(i)))
outpts = np.array(outpts)
if not isactor: return outpts
actor = vs.points(outpts, c=c, alpha=alpha, legend=legend)
return actor # return same obj for concatenation
def showPointCloud(modelNodeID):
model = slicer.mrmlScene.GetNodeByID(modelNodeID)
polydata = model.GetPolyData()
# Reuse the locator
locator = vtk.vtkStaticPointLocator()
locator.SetDataSet(polydata)
locator.BuildLocator()
# Remove isolated points
removal = vtk.vtkRadiusOutlierRemoval()
removal.SetInputData(polydata)
removal.SetLocator(locator)
removal.SetRadius(10)
removal.SetNumberOfNeighbors(2)
removal.GenerateOutliersOn()
# Time execution
timer = vtk.vtkTimerLog()
timer.StartTimer()
removal.Update()
timer.StopTimer()
time = timer.GetElapsedTime()
print("Time to remove points: {0}".format(time))
print(" Number removed: {0}".format(removal.GetNumberOfPointsRemoved()),
" (out of: {}".format(polydata.GetNumberOfPoints()))
# First output are the non-outliers
remMapper = vtk.vtkPointGaussianMapper()
remMapper.SetInputConnection(removal.GetOutputPort())
remMapper.EmissiveOff()
remMapper.SetScaleFactor(0.0)
remActor = vtk.vtkActor()
remActor.SetMapper(remMapper)
lm = slicer.app.layoutManager()
tdWidget = lm.threeDWidget(0)
tdView = tdWidget.threeDView()
rWin = tdView.renderWindow()
rCollection = rWin.GetRenderers()
renderer = rCollection.GetItemAsObject(0)
# Add the actors to the renderer, set the background and size
#
renderer.AddActor(remActor)
def showPointCloud(modelNodeID):
model = slicer.mrmlScene.GetNodeByID(modelNodeID)
polydata = model.GetPolyData()
# Reuse the locator
locator = vtk.vtkStaticPointLocator()
locator.SetDataSet(polydata)
locator.BuildLocator()
# Remove isolated points
removal = vtk.vtkRadiusOutlierRemoval()
removal.SetInputData(polydata)
removal.SetLocator(locator)
removal.SetRadius(10)
removal.SetNumberOfNeighbors(2)
removal.GenerateOutliersOn()
# Time execution
timer = vtk.vtkTimerLog()
timer.StartTimer()
removal.Update()
timer.StopTimer()
time = timer.GetElapsedTime()
print("Time to remove points: {0}".format(time))
print(" Number removed: {0}".format(removal.GetNumberOfPointsRemoved()),
" (out of: {}".format(polydata.GetNumberOfPoints()))
# First output are the non-outliers
remMapper = vtk.vtkPointGaussianMapper()
remMapper.SetInputConnection(removal.GetOutputPort())
remMapper.EmissiveOff()
remMapper.SetScaleFactor(0.0)
remActor = vtk.vtkActor()
remActor.SetMapper(remMapper)
lm = slicer.app.layoutManager()
tdWidget = lm.threeDWidget(0)
tdView = tdWidget.threeDView()
rWin = tdView.renderWindow()
rCollection = rWin.GetRenderers()
renderer = rCollection.GetItemAsObject(0)
# Add the actors to the renderer, set the background and size
#
renderer.AddActor(remActor)
# create pipeline
#
points = vtk.vtkBoundedPointSource()
points.SetNumberOfPoints(NPts)
points.ProduceRandomScalarsOn()
points.ProduceCellOutputOff()
points.Update()
# Reuse the locator
locator = vtk.vtkStaticPointLocator()
locator.SetDataSet(points.GetOutput())
locator.BuildLocator()
# Remove isolated points
removal = vtk.vtkRadiusOutlierRemoval()
removal.SetInputConnection(points.GetOutputPort())
removal.SetLocator(locator)
removal.SetRadius(0.1)
removal.SetNumberOfNeighbors(2)
removal.GenerateOutliersOn()
# Time execution
timer = vtk.vtkTimerLog()
timer.StartTimer()
removal.Update()
timer.StopTimer()
time = timer.GetElapsedTime()
print("Time to remove points: {0}".format(time))
print(" Number removed: {0}".format(removal.GetNumberOfPointsRemoved()))
print(" Original number of points: {0}".format(NPts))
# create pipeline
#
points = vtk.vtkBoundedPointSource()
points.SetNumberOfPoints(NPts)
points.ProduceRandomScalarsOn()
points.ProduceCellOutputOff()
points.Update()
# Reuse the locator
locator = vtk.vtkStaticPointLocator()
locator.SetDataSet(points.GetOutput())
locator.BuildLocator()
# Remove isolated points
removal = vtk.vtkRadiusOutlierRemoval()
removal.SetInputConnection(points.GetOutputPort())
removal.SetLocator(locator)
removal.SetRadius(0.1)
removal.SetNumberOfNeighbors(2)
removal.GenerateOutliersOn()
# Time execution
timer = vtk.vtkTimerLog()
timer.StartTimer()
removal.Update()
timer.StopTimer()
time = timer.GetElapsedTime()
print("Time to remove points: {0}".format(time))
print(" Number removed: {0}".format(removal.GetNumberOfPointsRemoved()))
print(" Original number of points: {0}".format(NPts))
