def ExtractGeometryZ(pd, nx, ny, nz, z0):
"""
cut the mesh using z > z0
could try vtkClipPolyData too
"""
filter = vtk.vtkExtractPolyDataGeometry()
function = vtk.vtkPlane()
function.SetNormal(nx, ny, nz)
function.SetOrigin(0, 0, z0)
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(pd)
triangleFilter.Update()
filter.SetImplicitFunction(function)
filter.SetInputData(triangleFilter.GetOutput())
filter.Update()
#geometryFilter = vtk.vtkGeometryFilter()
#geometryFilter.SetInputData(filter.GetOutput())
#geometryFilter.Update()
connectFilter = vtk.vtkPolyDataConnectivityFilter()
connectFilter.SetExtractionModeToLargestRegion()
connectFilter.SetInputData(filter.GetOutput())
connectFilter.Update()
return connectFilter.GetOutput()
def extractDataSetByBounds(fullvtkDataSet, boundvtkDataSet):
"""
Function to extract from a vtkDataSet within bounds of another vtkDataSet.
Returns a extrct filter
"""
# Define a bounding box implicit
if boundvtkDataSet.IsA('vtkDataSet'):
impFunc = vtk.vtkBox()
impFunc.SetBounds(boundvtkDataSet.GetBounds())
elif boundvtkDataSet.IsA('vtkImplicitFunction'):
impFunc = boundvtkDataSet
# Extract all inside and boundaries
if fullvtkDataSet.IsA('vtkPolyData'):
extractFilt = vtk.vtkExtractPolyDataGeometry()
else:
extractFilt = vtk.vtkExtractGeometry()
extractFilt.SetExtractInside(1)
extractFilt.SetExtractBoundaryCells(1)
extractFilt.SetInputData(fullvtkDataSet)
extractFilt.SetImplicitFunction(impFunc)
extractFilt.Update()
return extractFilt
def _ClipModel(self, plane, surface):
"""Clips surface and returns full cells on the plane i.e. does not produce flat output"""
clipper = vtk.vtkExtractPolyDataGeometry()
clipper.SetInputData(surface)
clipper.SetImplicitFunction(plane)
clipper.Update()
return clipper
def extractDataSetWithPolygon(vtkDataSet,
vtkPoly,
returnImpDist=False,
extInside=True,
extBoundaryCells=True,
extractBounds=False):
"""
Function to extract cells from a vtkDataSet, given polygon/s in a vtkPolyData.
Returns a full cells that fall fully inside/outside and/or on the polygon boundary.
"""
# Make a implicit function
impDist = convertToImplicitPolyDataDistance(vtkPoly)
# Reduce the data to the bounds
# Reduce the data to the bounds
if extractBounds:
extBoundsFilt = extractDataSetByBounds(vtkDataSet, vtkPoly)
else:
extBoundsFilt = extractDataSetByBounds(vtkDataSet, vtkDataSet)
# If input is a vtkPolyData
if vtkDataSet.IsA('vtkPolyData'):
extractFilt = vtk.vtkExtractPolyDataGeometry()
else:
extractFilt = vtk.vtkExtractGeometry()
extractFilt.SetExtractInside(extInside + 0)
extractFilt.SetExtractBoundaryCells(extBoundaryCells + 0)
extractFilt.SetInputConnection(extBoundsFilt.GetOutputPort())
extractFilt.SetImplicitFunction(impDist)
extractFilt.Update()
if returnImpDist:
return extractFilt.GetOutput(), impDist
else:
return extractFilt.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkExtractPolyDataGeometry(), 'Processing.',
('vtkPolyData',), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkExtractPolyDataGeometry(),
'Processing.', ('vtkPolyData', ),
('vtkPolyData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def __init__(self, size=4, color=(0.9, 0.9, 0.9), **kwargs):
kwargs["color"] = color
kwargs["size"] = size
self.poly_data = vtk.vtkPolyData()
self.extractor = vtk.vtkExtractPolyDataGeometry()
self.extractor.SetInput(self.poly_data)
self.constant_function = vtk.vtkQuadric()
self.constant_function.SetCoefficients(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0)
# Filter disabled by default
self.extractor.SetImplicitFunction(self.constant_function)
self.frustum = None
self.mapper = vtk.vtkPolyDataMapper()
self.mapper.SetInputConnection(self.extractor.GetOutputPort())
self.actor = vtk.vtkActor()
self.actor.SetMapper(self.mapper)
self._process_kwargs(**kwargs)
def __init__(self,
param_farplane_threshold=1.0,
param_convolution_threshold=0.01):
"""
Algorithm setup and define parameters.
:param param_farplane_threshold: default=1.0
Values on the depth image range from 0.0-1.0. Points with depth values greater
than param_farplane_threshold will be thrown away.
:param param_convolution_threshold: default=0.01
Convolution is used to determine pixel neighbors with a large difference. If
there is one, the point will be thrown away. This threshold controls sensitivity.
"""
VTKPythonAlgorithmBase.__init__(self,
nInputPorts=1, inputType='vtkImageData',
nOutputPorts=1, outputType='vtkPolyData')
self._param_farplane_threshold = param_farplane_threshold
self.param_convolution_theshold = param_convolution_threshold
self._sizex = []
self._sizey = []
self._viewport = []
self._display_pts = []
self._viewport_pts = []
self._world_pts = []
self._points = vtk.vtkPoints()
self._polys = vtk.vtkCellArray()
self._polydata = vtk.vtkPolyData()
self._polydata.SetPoints(self._points)
self._polydata.SetPolys(self._polys)
self._extract = vtk.vtkExtractPolyDataGeometry()
DebugTimeVTKFilter(self._extract)
self._extract.SetInputData(self._polydata)
planefunc = vtk.vtkPlane()
planefunc.SetNormal(0.0, -1.0, 0.0)
planefunc.SetOrigin(0.0, -1.0, 0.0)
self._extract.SetImplicitFunction(planefunc)
def __init__(self, size=4, color=(0.9, 0.9, 0.9), **kwargs):
kwargs["color"] = color
kwargs["size"] = size
self.poly_data = vtk.vtkPolyData()
self.extractor = vtk.vtkExtractPolyDataGeometry()
self.extractor.SetInput(self.poly_data)
self.constant_function = vtk.vtkQuadric()
self.constant_function.SetCoefficients(0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, -1.0)
# Filter disabled by default
self.extractor.SetImplicitFunction(self.constant_function)
self.frustum = None
self.mapper = vtk.vtkPolyDataMapper()
self.mapper.SetInputConnection(self.extractor.GetOutputPort())
self.actor = vtk.vtkActor()
self.actor.SetMapper(self.mapper)
self._process_kwargs(**kwargs)
def runGeoJSONCropExample(input_filename, bbox_filename):
inputDataset = loadGeoJSONData(input_filename)
bboxDataset = loadGeoJSONData(bbox_filename)
# Use the bounds from the bounding box to create an implicit function
queryBounds = list(bboxDataset.GetBounds())
bbox = vtk.vtkPlanes()
bbox.SetBounds(queryBounds)
# This filter uses the implicit function to extract the data
bboxFilter = vtk.vtkExtractPolyDataGeometry()
bboxFilter.SetInputData(inputDataset)
bboxFilter.SetImplicitFunction(bbox)
# Exclude (set to 0) or include (set to 1) districts on the boundary
bboxFilter.SetExtractBoundaryCells(0)
# Get the cropped region and write it to disk
bboxFilter.Update()
croppedDataset = bboxFilter.GetOutput()
outputWriter = vtk.vtkGeoJSONWriter()
outputWriter.SetFileName('cropped_output.geojson')
outputWriter.SetInputData(croppedDataset)
outputWriter.Write()
renderer = init()
inputActor = renderPolyData(renderer, inputDataset)
bboxActor = renderPolyData(renderer, bboxDataset)
cropActor = renderPolyData(renderer, croppedDataset)
# Set rendering type and color on the actors
inputActor.GetProperty().SetRepresentationToWireframe()
inputActor.GetProperty().SetColor(0.0, 1.0, 0.0)
bboxActor.GetProperty().SetRepresentationToWireframe()
bboxActor.GetProperty().SetColor(1.0, 0.0, 0.0)
cropActor.GetProperty().SetRepresentationToWireframe()
cropActor.GetProperty().SetColor(1.0, 0.0, 1.0)
run()
# Demonstrate how to extract polygonal cells with an implicit function # get the interactor ui # create a sphere source and actor # sphere = vtk.vtkSphereSource() sphere.SetThetaResolution(8) sphere.SetPhiResolution(16) sphere.SetRadius(1.5) # Extraction stuff t = vtk.vtkTransform() t.RotateX(90) cylfunc = vtk.vtkCylinder() cylfunc.SetRadius(0.5) cylfunc.SetTransform(t) extract = vtk.vtkExtractPolyDataGeometry() extract.SetInputConnection(sphere.GetOutputPort()) extract.SetImplicitFunction(cylfunc) extract.ExtractBoundaryCellsOn() extract.PassPointsOn() sphereMapper = vtk.vtkPolyDataMapper() sphereMapper.SetInputConnection(extract.GetOutputPort()) sphereMapper.GlobalImmediateModeRenderingOn() sphereActor = vtk.vtkActor() sphereActor.SetMapper(sphereMapper) # Extraction stuff - now cull points extract2 = vtk.vtkExtractPolyDataGeometry() extract2.SetInputConnection(sphere.GetOutputPort()) extract2.SetImplicitFunction(cylfunc) extract2.ExtractBoundaryCellsOn()
def om_display_vtp(f, n = 0):
"""
This function displays a VTK::vtp file generated with OpenMEEG.
Such a file defines a polydata, containing points and triangles of several
meshes which are labelled through a vtkAbstractArray (Strings) associated to
the cells (mesh names).
Results of the forward problem (or a cortical mapping) can be seen thanks to
arrays associated to points and cells (respectively potentials and normals
currents).
"""
welcome = """Welcome\n\n
Switch the button: To either see Potentials (on points) or Currents (on triangles)\n
Move the slider to see all sources (columns of the input matrix)\n
Press 'r': To select points/cells.\n"""
# This callback function does updates the mappers for where n is the slider value
def CleanPickData(object, event):
for i in range(4):
rens[i].RemoveActor(selactor)
if buttonWidget.GetRepresentation().GetState():
PickData(object, event, selactor, 1, view, text_init)
else:
PickData(object, event, selactor, 0, view, text_init)
def SelectSource(object, event): # object will be the slider2D
slidervalue = int(round(object.GetRepresentation().GetValue()))
for i in range(4):
mappers[i].GetInput().GetPointData().SetActiveScalars("Potentials-"+str(slidervalue))
mappers[i].GetInput().GetCellData().SetActiveScalars("Currents-"+str(slidervalue))
renWin.SetWindowName(renWin.GetWindowName()[0:(renWin.GetWindowName().find('-')+1)]+str(slidervalue))
UpdateColorBar(colorBars[i], mappers[i])
# This callback function does updates the Scalar Mode To Use
def SelectMode(object, event):
# object will be the buttonWidget
for i in range(4):
if (object.GetRepresentation().GetState()):
mappers[i].SetScalarModeToUseCellData()
renWin.SetWindowName(renWin.GetWindowName().replace('Potentials','Currents'))
else:
mappers[i].SetScalarModeToUsePointData()
renWin.SetWindowName(renWin.GetWindowName().replace('Currents','Potentials'))
UpdateColorBar(colorBars[i], mappers[i])
# A window with an interactor
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600, 600)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.SetInteractorStyle(vtk.vtkInteractorStyleRubberBandPick())
# A picker (to pick points/cells)
picker = vtk.vtkRenderedAreaPicker()
iren.SetPicker(picker)
# Read the input file
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(f); reader.Update()
poly = reader.GetOutput()
renWin.SetWindowName(f+' Potentials-'+str(n))
# determine the number of sources
nb_sources = 0
for i in range(poly.GetPointData().GetNumberOfArrays()):
if poly.GetPointData().GetGlobalIds('Potentials-'+str(i)):
nb_sources += 1
if n < nb_sources:
poly.GetPointData().SetActiveScalars('Potentials-'+str(n))
poly.GetCellData().SetActiveScalars('Currents-'+str(n))
# Get the mesh names
cell_labels = poly.GetCellData().GetAbstractArray(0)
assert(cell_labels.GetName()=='Names')
s = set(); nb_meshes = 0; cell_ids = list()
for i in range(cell_labels.GetNumberOfValues()):
s.add(cell_labels.GetValue(i))
if len(s)>nb_meshes:
# if a label is added, store the ID for the connectivity filter
cell_ids.append(i)
nb_meshes += 1
# Number of meshes
assert(nb_meshes<=4)
# Multiple viewports: 4
xmins = [0,.5,0,.5]; xmaxs = [0.5,1,0.5,1]; ymins = [0,0,.5,.5]; ymaxs = [0.5,0.5,1,1]
mappers = [vtk.vtkPolyDataMapper() for i in range(4)]
colorBars = [vtk.vtkScalarBarActor() for i in range(4)]
actors = [vtk.vtkActor() for i in range(4)]
rens = [vtk.vtkRenderer() for i in range(4)]
for i in range(4):
rens[i].SetViewport(xmins[i],ymins[i],xmaxs[i],ymaxs[i]);
# Display the meshes
if (i < nb_meshes):
# Create a connectivity filter based on cell seeded region (to display
# only one mesh per viewport)
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetInput(poly)
conn.SetExtractionModeToCellSeededRegions()
conn.AddSeed(cell_ids[i]); conn.Update()
actor_meshname = vtk.vtkTextActor();
actor_meshname.SetInput(cell_labels.GetValue(cell_ids[i]));
actor_meshname.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport();
actor_meshname.SetPosition(0.5, 0.85); tprop = actor_meshname.GetTextProperty(); tprop.SetFontSize(30)
tprop.SetFontFamilyToArial(); tprop.SetColor(1, 1, 1); tprop.SetJustificationToCentered()
mappers[i].SetInputConnection(conn.GetOutputPort())
mappers[i].SetScalarModeToUsePointData(); mappers[i].Update()
if nb_sources:
rens[i].AddActor2D(colorBars[i])
actors[i].SetMapper(mappers[i])
rens[i].AddActor2D(actor_meshname)
rens[i].AddActor(actors[i])
if (i == 0):
cam = rens[i].GetActiveCamera()
rens[i].ResetCamera()
else:
# Create a plane to cut
plane = vtk.vtkPlane(); plane.SetOrigin(0,0,0); plane.SetNormal(1,0,0);
# Create cutter
extract = vtk.vtkExtractPolyDataGeometry(); extract.SetInput(poly)
extract.SetImplicitFunction(plane); extract.ExtractBoundaryCellsOff()
mappers[i].SetInputConnection(extract.GetOutputPort())
mappers[i].SetScalarModeToUsePointData(); mappers[i].Update()
# Create plane actor
actors[i].SetMapper(mappers[i])
rens[i].AddActor(actors[i])
rens[i].SetActiveCamera(cam)
if nb_sources:
UpdateColorBar(colorBars[i], mappers[i])
renWin.AddRenderer(rens[i])
renWin.Render();
if nb_sources > 1:
# Slider
sliderWidget = vtk.vtkSliderWidget()
slider = vtk.vtkSliderRepresentation2D(); slider.SetMaximumValue(nb_sources-1)
slider.SetValue(n); slider.SetEndCapLength(0.01); slider.SetLabelFormat('%1.0f')
slider.SetSliderWidth(0.05); slider.SetSliderLength(1./nb_sources)
slider.GetPoint1Coordinate().SetCoordinateSystemToNormalizedViewport()
slider.GetPoint1Coordinate().SetValue(.0 ,0.02)
slider.GetPoint2Coordinate().SetCoordinateSystemToNormalizedViewport()
slider.GetPoint2Coordinate().SetValue(1. ,0.02);
sliderWidget.SetInteractor(iren); sliderWidget.SetRepresentation(slider);
sliderWidget.SetAnimationModeToAnimate(); sliderWidget.EnabledOn();
sliderWidget.AddObserver("InteractionEvent", SelectSource);
if not nb_sources == 0:
# The button for choosing Potentials/Currents
buttonWidget = vtk.vtkButtonWidget()
button = vtk.vtkTexturedButtonRepresentation2D(); button.SetNumberOfStates(2)
tex1r = vtk.vtkImageData(); tex2r = vtk.vtkImageData();
prop = vtk.vtkTextProperty(); prop.SetFontSize(24);
prop.SetColor(1,0,0); prop.SetBold(2); prop.SetShadow(2);
str2im = vtk.vtkFreeTypeStringToImage()
str2im.RenderString(prop,'Potentials',tex1r)
str2im.RenderString(prop,'Currents',tex2r)
button.SetButtonTexture(0, tex1r)
button.SetButtonTexture(1, tex2r)
buttonWidget.SetInteractor(iren);
buttonWidget.SetRepresentation(button);
button.SetPlaceFactor(1);
button.PlaceWidget([0., 100, 50, 500, 0, 0]);
buttonWidget.On()
buttonWidget.AddObserver(vtk.vtkCommand.StateChangedEvent,SelectMode);
# Selection
selactor = vtk.vtkActor()
view = vtk.vtkContextView(); view.GetRenderWindow().SetWindowName('Plot')
view.GetRenderWindow().SetPosition(600, 0); view.GetRenderWindow().SetSize(600, 600)
# Welcome text
text_init = vtk.vtkTextActor()
text_init.SetPosition(10, 300)
text_init.SetInput(welcome)
text_init.GetTextProperty().SetColor(1.0, 0.0, 0.0)
view.GetRenderer().AddActor2D(text_init)
view.GetInteractor().Initialize()
iren.AddObserver(vtk.vtkCommand.EndPickEvent,CleanPickData)
iren.Initialize()
iren.Start()
def doWrap(Act,wc,wrap=[0.,360], fastClip=True):
if wrap is None:
return Act
Mapper = Act.GetMapper()
data = Mapper.GetInput()
xmn=min(wc[0],wc[1])
xmx=max(wc[0],wc[1])
if numpy.allclose(xmn,1.e20) or numpy.allclose(xmx,1.e20):
xmx = abs(wrap[1])
xmn = -wrap[1]
ymn=min(wc[2],wc[3])
ymx=max(wc[2],wc[3])
if numpy.allclose(ymn,1.e20) or numpy.allclose(ymx,1.e20):
ymx = abs(wrap[0])
ymn = -wrap[0]
## Prepare MultiBlock and puts in oriinal data
appendFilter =vtk.vtkAppendPolyData()
appendFilter.AddInputData(data)
appendFilter.Update()
## X axis wrappping
Amn,Amx = Act.GetXRange()
if wrap[1]!=0.:
i=0
while Amn>xmn:
i+=1
Amn-=wrap[1]
Tpf = vtk.vtkTransformPolyDataFilter()
Tpf.SetInputData(data)
T=vtk.vtkTransform()
T.Translate(-i*wrap[1],0,0)
Tpf.SetTransform(T)
Tpf.Update()
appendFilter.AddInputData(Tpf.GetOutput())
appendFilter.Update()
i=0
while Amx<xmx:
i+=1
Amx+=wrap[1]
Tpf = vtk.vtkTransformPolyDataFilter()
Tpf.SetInputData(data)
T = vtk.vtkTransform()
T.Translate(i*wrap[1],0,0)
Tpf.SetTransform(T)
Tpf.Update()
appendFilter.AddInputData(Tpf.GetOutput())
appendFilter.Update()
# Y axis wrapping
Amn,Amx = Act.GetYRange()
if wrap[0]!=0.:
i=0
while Amn>ymn:
i+=1
Amn-=wrap[0]
Tpf = vtk.vtkTransformPolyDataFilter()
Tpf.SetInputData(data)
T = vtk.vtkTransform()
T.Translate(0,i*wrap[0],0)
Tpf.SetTransform(T)
Tpf.Update()
appendFilter.AddInputData(Tpf.GetOutput())
appendFilter.Update()
i=0
while Amx<ymx:
i+=1
Amx+=wrap[0]
Tpf = vtk.vtkTransformPolyDataFilter()
Tpf.SetInputData(data)
T = vtk.vtkTransform()
T.Translate(0,-i*wrap[0],0)
Tpf.SetTransform(T)
Tpf.Update()
appendFilter.AddInputData(Tpf.GetOutput())
appendFilter.Update()
# Clip the data to the final window:
clipBox = vtk.vtkBox()
clipBox.SetXMin(xmn, ymn, -1.0)
clipBox.SetXMax(xmx, ymx, 1.0)
if fastClip:
clipper = vtk.vtkExtractPolyDataGeometry()
clipper.ExtractInsideOn()
clipper.SetImplicitFunction(clipBox)
clipper.ExtractBoundaryCellsOn()
clipper.PassPointsOff()
else:
clipper = vtk.vtkClipPolyData()
clipper.InsideOutOn()
clipper.SetClipFunction(clipBox)
clipper.SetInputConnection(appendFilter.GetOutputPort())
clipper.Update()
Mapper.SetInputData(clipper.GetOutput())
return Act
def _extract_polygon(self, PolyData, is_clean):
self._contour_widget.EnabledOff()
print "Init Extracting"
self.setCursor(QCursor(Qt.WaitCursor))
QApplication.processEvents()
polydata_rep = self._contour_representation.GetContourRepresentationAsPolyData()
planes = self.get_frustrum()
normal = planes.GetNormals()
nor = np.array([0,0,0])
normal.GetTuple(5, nor)
#progressBar.setValue(10)
#QApplication.processEvents()
selection = vtkImplicitSelectionLoop()
selection.SetLoop(polydata_rep.GetPoints())
selection.SetNormal(nor[0], nor[1], nor[2])
#progressBar.setValue(20)
#QApplication.processEvents()
tip = vtkImplicitBoolean()
tip.AddFunction(selection)
tip.AddFunction(planes)
tip.SetOperationTypeToIntersection()
tip.Modified()
#progressBar.setValue(40)
#QApplication.processEvents()
if is_clean:
extractGeometry = vtkExtractPolyDataGeometry()
else:
extractGeometry = vtkExtractGeometry()
extractGeometry.SetInput(PolyData)
extractGeometry.SetImplicitFunction(tip)
if is_clean:
extractGeometry.ExtractInsideOff()
extractGeometry.Update()
if is_clean:
clean = vtkCleanPolyData()
clean.SetInputConnection(extractGeometry.GetOutputPort())
clean.Update()
#progressBar.setValue(80)
#QApplication.processEvents()
filter = vtkDataSetSurfaceFilter()
if is_clean:
filter.SetInputConnection(clean.GetOutputPort())
else:
filter.SetInputConnection(extractGeometry.GetOutputPort())
filter.Update()
#progressBar.setValue(90)
#QApplication.processEvents()
self.setCursor(QCursor(Qt.ArrowCursor))
QApplication.processEvents()
self.extract_action.setEnabled(False)
self.clean_action.setEnabled(False)
print "End Extracting"
return filter.GetOutput()