def getPatch(self, inputModel, inputCurve):
# Clip model with curve
loop = vtk.vtkSelectPolyData()
loop.SetLoop(inputCurve)
loop.GenerateSelectionScalarsOn()
loop.SetInputData(inputModel)
loop.SetSelectionModeToLargestRegion()
clip = vtk.vtkClipPolyData()
clip.InsideOutOn()
clip.SetInputConnection(loop.GetOutputPort())
clip.GenerateClippedOutputOn()
clip.Update()
extractLargestPart = False
clippedOutput = clip.GetOutput(
) if extractLargestPart else clip.GetClippedOutput()
connectivity = vtk.vtkConnectivityFilter()
connectivity.SetInputData(clippedOutput)
connectivity.Update()
clippedOutput2 = connectivity.GetOutput()
# Remove unused points
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(clippedOutput2)
cleaner.Update()
return cleaner.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkSelectPolyData(), 'Processing.',
('vtkPolyData',), ('vtkPolyData', 'vtkPolyData', 'vtkPolyData'),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def LeftButtonRelease(obj, ev):
global pickedPoint
pickedPoint = -1
#Select Polydata
loop = vtk.vtkSelectPolyData()
loop.SetInputData(target)
loop.SetLoop(landmark)
loop.GenerateSelectionScalarsOn()
# loop.SetSelectionModeToLargestRegion()
loop.SetSelectionModeToSmallestRegion()
loop.Update()
outputScalar = loop.GetOutput().GetPointData().GetScalars()
#Add
if outputScalar == None:
for i in range(landmark.GetNumberOfPoints()):
print(landmark.GetPoint(i), end=" ")
print()
# return
target.GetPointData().SetScalars(outputScalar)
target.GetPointData().Modified()
targetActor.GetMapper().SetScalarRange(outputScalar.GetRange())
def ScalarsCallback(self, obj):
rep = vtk.vtkOrientedGlyphContourRepresentation.SafeDownCast(
self.ContourWidget.GetRepresentation())
pointIds = vtk.vtkIdList()
self.Interpolator.GetContourPointIds(rep, pointIds)
points = vtk.vtkPoints()
points.SetNumberOfPoints(pointIds.GetNumberOfIds())
for i in range(pointIds.GetNumberOfIds()):
pointId = pointIds.GetId(i)
point = self.Surface.GetPoint(pointId)
points.SetPoint(i, point)
selectionFilter = vtk.vtkSelectPolyData()
selectionFilter.SetInputData(self.Surface)
selectionFilter.SetLoop(points)
selectionFilter.GenerateSelectionScalarsOn()
selectionFilter.SetSelectionModeToSmallestRegion()
selectionFilter.Update()
selectionScalars = selectionFilter.GetOutput().GetPointData(
).GetScalars()
contourScalars = self.Surface.GetPointData().GetArray(
self.ContourScalarsArrayName)
for i in range(contourScalars.GetNumberOfTuples()):
selectionValue = selectionScalars.GetTuple1(i)
if self.Binary:
if selectionValue < 0.0:
contourScalars.SetTuple1(i, self.InsideValue)
else:
contourValue = contourScalars.GetTuple1(i)
if (not contourValue < 0.0 and selectionValue < 0.0) or (
contourValue < 0.0 and selectionValue < contourValue):
contourScalars.SetTuple1(i, selectionValue)
self.Actor.GetMapper().SetScalarRange(contourScalars.GetRange(0))
self.Surface.Modified()
self.ContourWidget.Initialize()
def ScalarsCallback(self, obj):
rep = vtk.vtkOrientedGlyphContourRepresentation.SafeDownCast(self.ContourWidget.GetRepresentation())
pointIds = vtk.vtkIdList()
self.Interpolator.GetContourPointIds(rep,pointIds)
points = vtk.vtkPoints()
points.SetNumberOfPoints(pointIds.GetNumberOfIds())
for i in range(pointIds.GetNumberOfIds()):
pointId = pointIds.GetId(i)
point = self.Surface.GetPoint(pointId)
points.SetPoint(i,point)
selectionFilter = vtk.vtkSelectPolyData()
selectionFilter.SetInputData(self.Surface)
selectionFilter.SetLoop(points)
selectionFilter.GenerateSelectionScalarsOn()
selectionFilter.SetSelectionModeToSmallestRegion()
selectionFilter.Update()
selectionScalars = selectionFilter.GetOutput().GetPointData().GetScalars()
contourScalars = self.Surface.GetPointData().GetArray(self.ContourScalarsArrayName)
for i in range(contourScalars.GetNumberOfTuples()):
selectionValue = selectionScalars.GetTuple1(i)
if self.Binary:
if selectionValue < 0.0:
contourScalars.SetTuple1(i,self.InsideValue)
else:
contourValue = contourScalars.GetTuple1(i)
if (not contourValue < 0.0 and selectionValue < 0.0) or (contourValue < 0.0 and selectionValue < contourValue):
contourScalars.SetTuple1(i,selectionValue)
self.Actor.GetMapper().SetScalarRange(contourScalars.GetRange(0))
self.Surface.Modified()
self.ContourWidget.Initialize()
selectionPoints.InsertPoint(20, 0.263789, 0.174982, 0.387308) selectionPoints.InsertPoint(21, 0.213034, 0.175485, 0.417142) selectionPoints.InsertPoint(22, 0.169113, 0.261974, 0.390286) selectionPoints.InsertPoint(23, 0.102552, 0.25997, 0.414814) selectionPoints.InsertPoint(24, 0.131512, 0.161254, 0.454705) selectionPoints.InsertPoint(25, 0.000192443, 0.156264, 0.475307) selectionPoints.InsertPoint(26, -0.0392091, 0.000251724, 0.499943) selectionPoints.InsertPoint(27, -0.096161, 0.159646, 0.46438) sphere = vtk.vtkSphereSource() sphere.SetPhiResolution(50) sphere.SetThetaResolution(100) sphere.SetStartPhi(0) sphere.SetEndPhi(90) loop = vtk.vtkSelectPolyData() loop.SetInputConnection(sphere.GetOutputPort()) loop.SetLoop(selectionPoints) loop.GenerateSelectionScalarsOn() # negative scalars inside loop.SetSelectionModeToSmallestRegion() # clips out positive region clip = vtk.vtkClipPolyData() clip.SetInputConnection(loop.GetOutputPort()) clipMapper = vtk.vtkPolyDataMapper() clipMapper.SetInputConnection(clip.GetOutputPort()) clipActor = vtk.vtkLODActor() clipActor.SetMapper(clipMapper)
def extractSurfaceByBoundary(self):
"""
Update model to enclose all points in the input markup list
"""
inputMarkup = self.surfaceBoundary.controlPointsMarkupNode
numberOfPoints = self.getNumberOfControlPoints(inputMarkup)
fullLeafletPolydata = self.getLeafletPolydata()
if not fullLeafletPolydata or fullLeafletPolydata.GetNumberOfCells(
) == 0 or not inputMarkup or numberOfPoints < 3:
# empty input mesh
if self.surfaceModelNode.GetPolyData(
) and self.surfaceModelNode.GetPolyData().GetNumberOfCells() > 0:
# existing mesh is not empty
emptyPolyData = vtk.vtkPolyData()
self.surfaceModelNode.SetAndObservePolyData(emptyPolyData)
return None
selectionPoints = vtk.vtkPoints()
new_coord = [0.0, 0.0, 0.0]
for i in range(numberOfPoints):
inputMarkup.GetNthFiducialPosition(i, new_coord)
selectionPoints.InsertPoint(i, new_coord)
loop = vtk.vtkSelectPolyData()
loop.SetLoop(selectionPoints)
loop.GenerateSelectionScalarsOn()
loop.SetInputData(fullLeafletPolydata)
# loop.SetSelectionModeToClosestPointRegion() does not seem to work
# (always extracts the same side of the mesh, regardless of what
# point is set in loop.SetClosestPoint(...)
# Therefore, we extract both sides of the surface and choose the one
# that is closer to the requested closestPoint.
closestPoint = None
valvePlaneNormal = self.getValvePlaneNormal()
valvePlanePosition = self.getValvePlanePosition()
if valvePlaneNormal is not None and valvePlanePosition is not None:
# we go 30mm opposite to the valve plane normal direction from the center of the plane
# to make sure we pick a point on the inflow side
closestPoint = valvePlanePosition - valvePlaneNormal * 30.0
loop.SetSelectionModeToLargestRegion()
clip = vtk.vtkClipPolyData()
clip.InsideOutOn()
clip.SetInputConnection(loop.GetOutputPort())
clip.GenerateClippedOutputOn()
# attributes = vtk.vtkDataSetAttributes()
# attributes.SetInputConnection(clip.GetOutputPort())
# attributes.CopyScalarsOff()
clip.Update()
clippedOutput = clip.GetOutput()
if closestPoint is not None:
clippedOutputs = [clip.GetOutput(), clip.GetClippedOutput()]
closestDistances = []
for part in clippedOutputs:
cleaner = vtk.vtkCleanPolyData() # removeUnusedPoints
cleaner.SetInputData(part)
cleaner.Update()
cleanedPart = cleaner.GetOutput()
loc = vtk.vtkPointLocator()
loc.SetDataSet(cleanedPart)
foundClosestPointId = loc.FindClosestPoint(closestPoint)
if foundClosestPointId >= 0 and foundClosestPointId < cleanedPart.GetPoints(
).GetNumberOfPoints():
nearestPointOnLeafletSurface = np.array(
cleanedPart.GetPoints().GetPoint(foundClosestPointId))
closestDistances.append(
np.linalg.norm(nearestPointOnLeafletSurface -
closestPoint))
else:
# empty mesh, use some large number to not find it as the closest distance
closestDistances.append(1e6)
if self.getSelectLargestRegion():
# inflow side
minimumClosestDistanceIndex = closestDistances.index(
min(closestDistances))
else:
# outflow side
minimumClosestDistanceIndex = closestDistances.index(
max(closestDistances))
clippedOutput = clippedOutputs[minimumClosestDistanceIndex]
else:
if self.getSelectLargestRegion():
clippedOutput = clip.GetClippedOutput()
else:
clippedOutput = clip.GetOutput()
#print("Result: {0} points, {1} cells".format(clippedOutput.GetNumberOfPoints(), clippedOutput.GetNumberOfCells()))
self.surfaceModelNode.SetAndObservePolyData(clippedOutput)
if self.surfaceModelNode.GetDisplayNode():
self.surfaceModelNode.GetDisplayNode().SetActiveScalarName("")
selectionPoints.InsertPoint(20, 0.263789, 0.174982, 0.387308) selectionPoints.InsertPoint(21, 0.213034, 0.175485, 0.417142) selectionPoints.InsertPoint(22, 0.169113, 0.261974, 0.390286) selectionPoints.InsertPoint(23, 0.102552, 0.25997, 0.414814) selectionPoints.InsertPoint(24, 0.131512, 0.161254, 0.454705) selectionPoints.InsertPoint(25, 0.000192443, 0.156264, 0.475307) selectionPoints.InsertPoint(26, -0.0392091, 0.000251724, 0.499943) selectionPoints.InsertPoint(27, -0.096161, 0.159646, 0.46438) sphere = vtk.vtkSphereSource() sphere.SetPhiResolution(50) sphere.SetThetaResolution(100) sphere.SetStartPhi(0) sphere.SetEndPhi(90) loop = vtk.vtkSelectPolyData() loop.SetInputConnection(sphere.GetOutputPort()) loop.SetLoop(selectionPoints) loop.GenerateSelectionScalarsOn() # negative scalars inside loop.SetSelectionModeToSmallestRegion() # clips out positive region clip = vtk.vtkClipPolyData() clip.SetInputConnection(loop.GetOutputPort()) clipMapper = vtk.vtkPolyDataMapper() clipMapper.SetInputConnection(clip.GetOutputPort()) clipActor = vtk.vtkLODActor() clipActor.SetMapper(clipMapper)
[ 3.4850955 , 1.784371 , -0.3970445 ],
[ 3.6015983 , 1.8645154 , -0.41358784],
[ 3.731929 , 1.9395119 , -0.43495524],
[ 3.8700097 , 2.0061252 , -0.4594413 ],
[ 4.0097623 , 2.0611203 , -0.48534057],
[ 4.145108 , 2.1012616 , -0.5109477 ],
[ 4.2699695 , 2.1233141 , -0.5345572 ],
[ 4.3782682 , 2.1240425 , -0.55446374],
[ 4.463926 , 2.1002119 , -0.5689619 ],
[ 4.5208645 , 2.0485868 , -0.5763462 ]]
loopPoints = vtk.vtkPoints()
for xyz in loopPointPositions:
loopPoints.InsertNextPoint(xyz)
selectionFilter = vtk.vtkSelectPolyData()
selectionFilter.SetInputConnection(reader.GetOutputPort())
selectionFilter.SetLoop(loopPoints)
selectionFilter.GenerateSelectionScalarsOn()
selectionFilter.SetSelectionModeToSmallestRegion()
# Run selection filter using greedy method (expected to fail)
# Add error observer to catch the expected error (uncaught error would make the test fail)
cb = callback()
cb.CallDataType = vtk.VTK_STRING
observerId = selectionFilter.AddObserver(vtk.vtkCommand.ErrorEvent, cb)
# Run the computation
selectionFilter.SetEdgeSearchModeToGreedy()
selectionFilter.Update()
# Remove the error observer
def main(): # pragma: no cover
sphere_source = vtk.vtkSphereSource()
sphere_source.Update()
selection_points = vtk.vtkPoints()
selection_points.InsertPoint(0, -0.16553, 0.135971, 0.451972)
selection_points.InsertPoint(1, -0.0880123, -0.134952, 0.4747)
selection_points.InsertPoint(2, 0.00292618, -0.134604, 0.482459)
selection_points.InsertPoint(3, 0.0641941, 0.067112, 0.490947)
selection_points.InsertPoint(4, 0.15577, 0.0734765, 0.469245)
selection_points.InsertPoint(5, 0.166667, -0.129217, 0.454622)
selection_points.InsertPoint(6, 0.241259, -0.123363, 0.420581)
selection_points.InsertPoint(7, 0.240334, 0.0727106, 0.432555)
selection_points.InsertPoint(8, 0.308529, 0.0844311, 0.384357)
selection_points.InsertPoint(9, 0.32672, -0.121674, 0.359187)
selection_points.InsertPoint(10, 0.380721, -0.117342, 0.302527)
selection_points.InsertPoint(11, 0.387804, 0.0455074, 0.312375)
selection_points.InsertPoint(12, 0.43943, -0.111673, 0.211707)
selection_points.InsertPoint(13, 0.470984, -0.0801913, 0.147919)
selection_points.InsertPoint(14, 0.436777, 0.0688872, 0.233021)
selection_points.InsertPoint(15, 0.44874, 0.188852, 0.109882)
selection_points.InsertPoint(16, 0.391352, 0.254285, 0.176943)
selection_points.InsertPoint(17, 0.373274, 0.154162, 0.294296)
selection_points.InsertPoint(18, 0.274659, 0.311654, 0.276609)
selection_points.InsertPoint(19, 0.206068, 0.31396, 0.329702)
selection_points.InsertPoint(20, 0.263789, 0.174982, 0.387308)
selection_points.InsertPoint(21, 0.213034, 0.175485, 0.417142)
selection_points.InsertPoint(22, 0.169113, 0.261974, 0.390286)
selection_points.InsertPoint(23, 0.102552, 0.25997, 0.414814)
selection_points.InsertPoint(24, 0.131512, 0.161254, 0.454705)
selection_points.InsertPoint(25, 0.000192443, 0.156264, 0.475307)
selection_points.InsertPoint(26, -0.0392091, 0.000251724, 0.499943)
selection_points.InsertPoint(27, -0.096161, 0.159646, 0.46438)
loop = vtk.vtkSelectPolyData()
loop.SetInputConnection(sphere_source.GetOutputPort())
loop.SetLoop(selection_points)
loop.GenerateSelectionScalarsOn()
loop.SetSelectionModeToSmallestRegion() # negative scalars inside
clip = vtk.vtkClipPolyData() # clips out positive region
clip.SetInputConnection(loop.GetOutputPort())
clip_mapper = vtk.vtkPolyDataMapper()
clip_mapper.SetInputConnection(clip.GetOutputPort())
clip_actor = vtk.vtkLODActor()
clip_actor.SetMapper(clip_mapper)
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(render_window)
# Add the actors to the renderer, set the background and size
renderer.AddActor(clip_actor)
renderer.SetBackground(.1, .2, .4)
render_window.SetSize(500, 250)
render_window.Render()
interactor.Start()
def drawingMakeROI(obj, ev):
if obj.inDrawMode == 1:
print('closing and filling ROI')
# get the required surface
currPolyData = obj.GetPicker().GetActor().GetMapper().GetInput()
# ... and points
currPoints = obj.pickedPoints
# we're not actually going to change the original: we're going to clip out the region we want and
# show it as a separate surface "patch" - this allows easy control of transparency/colour etc
# a vtk selection tool that loops around our points
if debug: print "before select polydata"
selecta = vtk.vtkSelectPolyData()
selecta.SetInputData(currPolyData)
selecta.SetLoop(currPoints)
selecta.GenerateSelectionScalarsOn()
## selecta.SetSelectionModeToSmallestRegion()
selecta.SetSelectionModeToLargestRegion()
selecta.Update()
if debug: print "after select polydata"
## TODO - consider a different clipping function
## the one below appears to clip front AND back surfaces?
#loop = vtk.vtkImplicitSelectionLoop()
#loop.SetLoop(currPoints)
#clipROI = vtk.vtkExtractPolyDataGeometry()
#clipROI.SetInputData(currPolyData)
#clipROI.SetImplicitFunction(loop)
#clipROI.ExtractBoundaryCellsOn()
#clipROI.PassPointsOff()
#clipROI.Update()
# the tool that actually clips out the selected region
clipROI = vtk.vtkClipPolyData()
clipROI.SetInputConnection(selecta.GetOutputPort())
clipROI.Update()
if debug: print(clipROI.GetOutput())
# --- try to get an ROI
if clipROI.GetOutput().GetNumberOfPoints() == 0:
#loop could not clip data for some reason - we need to clean up
obj.pickedPoints = vtk.vtkPoints() #new
#stop drawing mode and reset the interactor to normal behaviour
obj.inDrawMode = 0
print 'Error while trying to close the ROI loop - resetting colours - please try again.'
print obj.ScalarsCopyForRevert
tmpScalarsCopyForRevert = vtk.vtkUnsignedCharArray()
tmpScalarsCopyForRevert.DeepCopy(obj.ScalarsCopyForRevert)
obj.curr_polydata.GetPointData().SetScalars(obj.ScalarsCopyForRevert)
obj.curr_polydata.Modified()
obj.ScalarsCopyForRevert = tmpScalarsCopyForRevert; #AND LOCK IN CURRENT STATE
obj.curr_smoother.Update()
obj.curr_mapper.SetColorModeToDefault()
obj.curr_mapper.Modified()
style = vtk.vtkInteractorStyleTrackballCamera()
obj.SetInteractorStyle(style)
obj.ren.Render()
obj.Render()
obj.parent_ui.statusbar.showMessage("Failed to close and fill ROI! Perhaps the surface is too spikey? - try smoothing.")
else:
## -- track the point IDs
# unfortunately the clip tool does not keep a reference of the original surface
# point IDs (that we need to send bakc to other programs later
# -- we need a pretty nasty bit or code to track the xyz positions extracted
# so that we can go back to the original surface and label these
# first, get the xyz position of all points in original surface
origDat = currPolyData.GetPoints().GetData()
origArr = []
for i in range(currPolyData.GetNumberOfPoints()):
origArr.append(origDat.GetTuple(i))
# next get the xyz position of select points
selectedDat = clipROI.GetOutput().GetPoints().GetData()
selectedArr = [] #place holder for loop
if debug: print(selectedDat)
for i in range(clipROI.GetOutput().GetNumberOfPoints()):
selectedArr.append(selectedDat.GetTuple(i)) #xyz
## now find matching indices in original using numpy manipulation
numpyOrigArr = array(origArr)
numpySelectedArr = array(selectedArr)
#if debug:
# numpyOrigArr.tofile('orig.txt',',')
# numpySelectedArr.tofile('new.txt',',')
# TODO - we only check the first 6 characters of the coordinate data - this may cause precision issues later - check
origAll = char.array(numpyOrigArr[:,0],'S6') + '-' + char.array(numpyOrigArr[:,1],'S6') + '-' + char.array(numpyOrigArr[:,2],'S6')
selectedAll = char.array(numpySelectedArr[:,0],'S6') + '-' + char.array(numpySelectedArr[:,1],'S6') + '-' + char.array(numpySelectedArr[:,2],'S6')
# and pipe it back to the original
obj.filledROIPoints = where(in1d(origAll, selectedAll))[0]
obj.ROI_ready = 1
if debug: print(obj.filledROIPoints)
if debug: print(size(obj.filledROIPoints))
## -- back to drawing
# draw the new surface
roiMapper = vtk.vtkPolyDataMapper()
roiMapper.SetInputConnection(clipROI.GetOutputPort())
roiMapper.ScalarVisibilityOff()
roiMapper.Update()
roiActor = vtk.vtkActor()
roiActor.SetVisibility(1)
roiActor.SetMapper(roiMapper)
roiActor.GetProperty().SetOpacity(0.5)
roiActor.GetProperty().SetColor(1.0,1.0,1.0)
obj.roiActor = roiActor;
obj.ren.AddActor(obj.roiActor)
obj.Render()
#stop drawing mode and reset hte interactor to normal behaviour
obj.inDrawMode = 0
#remove our black dots
tmpScalarsCopyForRevert = vtk.vtkUnsignedCharArray()
tmpScalarsCopyForRevert.DeepCopy(obj.ScalarsCopyForRevert)
obj.curr_polydata.GetPointData().SetScalars(obj.ScalarsCopyForRevert)
obj.curr_polydata.Modified()
obj.ScalarsCopyForRevert = tmpScalarsCopyForRevert; #AND LOCK IN CURRENT STATE
obj.curr_smoother.Update()
obj.curr_mapper.SetColorModeToDefault()
obj.curr_mapper.Modified()
style = vtk.vtkInteractorStyleTrackballCamera()
obj.SetInteractorStyle(style)
# and clean up for the next loop? TODO? - or button to reset?
obj.pickedPoints = vtk.vtkPoints() #new
else:
if debug: print('ignored right mouse click - not in draw mode')
pass
