def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
# feature edges are used to find any holes in the surface.
fedges = vtk.vtkFeatureEdges()
fedges.BoundaryEdgesOn()
fedges.FeatureEdgesOff()
fedges.ManifoldEdgesOff()
fedges.SetInputData(self.Surface)
fedges.Update()
ofedges = fedges.GetOutput()
# if numEdges is not 0, then there are holes which need to be capped
numEdges = ofedges.GetNumberOfPoints()
if numEdges != 0:
tempcapper = vmtksurfacecapper.vmtkSurfaceCapper()
tempcapper.Surface = self.Surface
tempcapper.Interactive = 0
tempcapper.Execute()
networkSurface = tempcapper.Surface
else:
networkSurface = self.Surface
# randomly select one cell to delete so that there is an opening for
# vmtkNetworkExtraction to use.
numCells = self.Surface.GetNumberOfCells()
cellToDelete = random.randrange(0, numCells-1)
networkSurface.BuildLinks()
networkSurface.DeleteCell(cellToDelete)
networkSurface.RemoveDeletedCells()
# extract the network of approximated centerlines
net = vmtknetworkextraction.vmtkNetworkExtraction()
net.Surface = networkSurface
net.AdvancementRatio = 1.001
net.Execute()
network = net.Network
convert = vmtkcenterlinestonumpy.vmtkCenterlinesToNumpy()
convert.Centerlines = network
convert.LogOn = False
convert.Execute()
ad = convert.ArrayDict
cellDataTopology = ad['CellData']['Topology']
# the network topology identifies an the input segment with the "0" id.
# since we artificially created this segment, we don't want to use the
# ends of the segment as source/target points of the centerline calculation
nodeIndexToIgnore = np.where(cellDataTopology[:,0] == 0)[0][0]
keepCellConnectivityList = []
pointIdxToKeep = np.array([])
# we remove the cell, points, and point data which are associated with the
# segment we want to ignore
for loopIdx, cellConnectivityList in enumerate(ad['CellData']['CellPointIds']):
if loopIdx == nodeIndexToIgnore:
removeCellStartIdx = cellConnectivityList[0]
removeCellEndIdx = cellConnectivityList[-1]
removeCellLength = cellConnectivityList.size
if (removeCellEndIdx + 1) - removeCellStartIdx != removeCellLength:
raise(ValueError)
continue
else:
rescaledCellConnectivity = np.subtract(cellConnectivityList, removeCellLength, where=cellConnectivityList >= removeCellLength)
keepCellConnectivityList.append(rescaledCellConnectivity)
pointIdxToKeep = np.concatenate((pointIdxToKeep, cellConnectivityList)).astype(np.int)
newPoints = ad['Points'][pointIdxToKeep]
newRadius = ad['PointData']['Radius'][pointIdxToKeep]
# precompute the delaunay tessellation for the whole surface.
tessalation = vmtkdelaunayvoronoi.vmtkDelaunayVoronoi()
tessalation.Surface = networkSurface
tessalation.Execute()
self.DelaunayTessellation = tessalation.DelaunayTessellation
self.VoronoiDiagram = tessalation.VoronoiDiagram
self.PoleIds = tessalation.PoleIds
# vtk objects cannot be serialized in python. Instead of converting the inputs to numpy arrays and having
# to reconstruct the vtk object each time the loop executes (a slow process), we can just pass in the
# memory address of the data objects as a string, and use the vtk python bindings to create a python name
# referring to the data residing at that memory address. This works because joblib executes each loop
# iteration in a fork of the original process, providing access to the original memory space.
# However, the process does not work for return arguments, since the original process will not have access to
# the memory space of the fork. To return results we use the vmtkCenterlinesToNumpy converter.
networkSurfaceMemoryAddress = networkSurface.__this__
delaunayMemoryAddress = tessalation.DelaunayTessellation.__this__
voronoiMemoryAddress = tessalation.VoronoiDiagram.__this__
poleIdsMemoryAddress = tessalation.PoleIds.__this__
# When using Joblib Under Windows, it is important to protect the main loop of code to avoid recursive spawning
# of subprocesses. Since we cannot guarantee no code will run outside of “if __name__ == ‘__main__’” blocks
# (only imports and definitions), we make Joblib execute each loop iteration serially on windows.
# On unix-like os's (linux, Mac) we execute each loop iteration independently on as many cores as the system has.
if (sys.platform == 'win32') or (sys.platform == 'win64') or (sys.platform == 'cygwin'):
self.PrintLog('Centerlines extraction on windows computer will execute serially.')
self.PrintLog('To speed up execution, please run vmtk on unix-like operating system')
numParallelJobs = 1
else:
numParallelJobs = -1
self.PrintLog('Computing Centerlines ...')
# note about the verbose function: while Joblib can print a progress bar output (set verbose = 20),
# it does not implement a callback function as of version 0.11, so we cannot report progress to the user
# if we are redirecting standard out with the self.PrintLog method.
outlist = Parallel(n_jobs=numParallelJobs, backend='multiprocessing', verbose=0)(
delayed(_compute_centerlines_network)(networkSurfaceMemoryAddress,
delaunayMemoryAddress,
voronoiMemoryAddress,
poleIdsMemoryAddress,
cell,
newPoints) for cell in keepCellConnectivityList)
out = []
for item in outlist:
npConvert = vmtknumpytocenterlines.vmtkNumpyToCenterlines()
npConvert.ArrayDict = item
npConvert.LogOn = 0
npConvert.Execute()
out.append(npConvert.Centerlines)
# Append each segment's polydata into a single polydata object
centerlineAppender = vtk.vtkAppendPolyData()
for data in out:
centerlineAppender.AddInputData(data)
centerlineAppender.Update()
# clean and strip the output centerlines so that redundant points are merged and tracts are combined
centerlineCleaner = vtk.vtkCleanPolyData()
centerlineCleaner.SetInputData(centerlineAppender.GetOutput())
centerlineCleaner.Update()
centerlineStripper = vtk.vtkStripper()
centerlineStripper.SetInputData(centerlineCleaner.GetOutput())
centerlineStripper.JoinContiguousSegmentsOn()
centerlineStripper.Update()
self.Centerlines = centerlineStripper.GetOutput()
def __init__(self, target_mesh):
self.point_locator = vtk.vtkPointLocator()
self.point_locator.SetDataSet(target_mesh)
self.point_locator.BuildLocator()
self.cell_locator = vtk.vtkCellLocator()
self.cell_locator.SetDataSet(target_mesh)
self.cell_locator.SetTolerance(0.0001)
self.cell_locator.BuildLocator()
edge_filter = vtk.vtkFeatureEdges()
edge_filter.SetInputData(target_mesh)
edge_filter.BoundaryEdgesOn()
edge_filter.FeatureEdgesOn()
edge_filter.SetFeatureAngle(90)
edge_filter.ManifoldEdgesOff()
edge_filter.NonManifoldEdgesOff()
edge_filter.Update()
edge_points = edge_filter.GetOutput().GetPoints()
self.edge_point_ids = []
for i in range(edge_points.GetNumberOfPoints()):
point_id = self.point_locator.FindClosestPoint(
edge_points.GetPoint(i))
self.edge_point_ids.append(point_id)
def GetEdgeMask(self, angle):
"""
Returns a mask of the points of a surface mesh that have a surface
angle greater than angle
Parameters
----------
angle : float
Angle to consider an edge.
"""
featureEdges = vtk.vtkFeatureEdges()
featureEdges.SetInputData(self)
featureEdges.FeatureEdgesOn()
featureEdges.BoundaryEdgesOff()
featureEdges.NonManifoldEdgesOff()
featureEdges.ManifoldEdgesOff()
featureEdges.SetFeatureAngle(angle)
featureEdges.Update()
edges = featureEdges.GetOutput()
origID = vtkInterface.GetPointScalars(edges, 'vtkOriginalPointIds')
return np.in1d(self.GetPointScalars('vtkOriginalPointIds'),
origID,
assume_unique=True)
def extractboundaryedge(polydata):
edge = vtk.vtkFeatureEdges()
edge.SetInputData(polydata)
edge.FeatureEdgesOff()
edge.NonManifoldEdgesOff()
edge.Update()
return edge.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkFeatureEdges(), 'Processing.',
('vtkPolyData',), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def vtk_extract_feature_edges(polydata,
compute_feature_edges=False,
compute_boundary_edges=True,
compute_non_manifold_edges=False):
"""Wrapper for vtkFeatureedges. Extracts the edges of the cells that are open.
Args:
compute_non_manifold_edges (bool): Turn on/off the extraction of non-manifold edges.
compute_boundary_edges (bool): Turn on/off the extraction of boundary edges.
compute_feature_edges (bool): Turn on/off the extraction of feature edges.
polydata (vtkPolyData): surface to extract the openings from.
Returns:
feature_edges (vtkPolyData): The boundary edges of the surface.
"""
feature_edges = vtk.vtkFeatureEdges()
if compute_feature_edges:
feature_edges.FeatureEdgesOn()
else:
feature_edges.FeatureEdgesOff()
if compute_boundary_edges:
feature_edges.BoundaryEdgesOn()
else:
feature_edges.BoundaryEdgesOff()
if compute_non_manifold_edges:
feature_edges.NonManifoldEdgesOn()
else:
feature_edges.NonManifoldEdgesOff()
feature_edges.SetInputData(polydata)
feature_edges.Update()
return feature_edges.GetOutput()
def PlotBoundaries(mesh):
""" Plots boundaries of a mesh """
featureEdges = vtk.vtkFeatureEdges()
vtkInterface.SetVTKInput(featureEdges, mesh)
featureEdges.FeatureEdgesOff()
featureEdges.BoundaryEdgesOn()
featureEdges.NonManifoldEdgesOn()
featureEdges.ManifoldEdgesOff()
edgeMapper = vtk.vtkPolyDataMapper();
edgeMapper.SetInputConnection(featureEdges.GetOutputPort());
edgeActor = vtk.vtkActor();
edgeActor.GetProperty().SetLineWidth(5);
edgeActor.SetMapper(edgeMapper)
mapper = vtk.vtkDataSetMapper()
vtkInterface.SetVTKInput(mapper, mesh)
# Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().LightingOff()
# Render
pobj = PlotClass()
pobj.AddActor(actor)
pobj.AddActor(edgeActor)
pobj.Plot(); del pobj
def _SliceModel(self, plane):
"""cuts surface and returns polydata of the clipped surface and the clipped face"""
cutter = vtk.vtkCutter()
cutter.SetCutFunction(plane)
cutter.SetInputData(self.Surface)
cutter.Update()
FeatureEdges = vtk.vtkFeatureEdges()
FeatureEdges.SetInputConnection(cutter.GetOutputPort())
FeatureEdges.BoundaryEdgesOn()
FeatureEdges.FeatureEdgesOff()
FeatureEdges.NonManifoldEdgesOff()
FeatureEdges.ManifoldEdgesOff()
FeatureEdges.Update()
cutStrips = vtk.vtkStripper(
) # Forms loops (closed polylines) from cutter
cutStrips.SetInputConnection(cutter.GetOutputPort())
cutStrips.Update()
cutPoly = vtk.vtkPolyData(
) # This trick defines polygons as polyline loop
cutPoly.SetPoints((cutStrips.GetOutput()).GetPoints())
cutPoly.SetPolys((cutStrips.GetOutput()).GetLines())
return cutter.GetOutput(), cutPoly
def __init__(self, args):
self.Surface = None
self.InputFile = args.surface
self.OutputFile = args.file_out
self.FeatureAngle = 50.0 #args.feature_angle
self.NumberOfRegions = 0
self.RegionIdsArrayName = "RegionsId"
self.boundaries = vtk.vtkFeatureEdges()
self.NewScalars = vtk.vtkIntArray()
self.RegionAreas = vtk.vtkDoubleArray()
self.mesh = vtk.vtkPolyData()
self.BoundaryLines = vtk.vtkPolyData()
self.BoundaryPointArray = vtk.vtkIntArray()
self.BoundaryCellArray = vtk.vtkIntArray()
self.CheckCells = vtk.vtkIdList()
self.CheckCells2 = vtk.vtkIdList()
self.CheckCellsCareful = vtk.vtkIdList()
self.CheckCellsCareful2 = vtk.vtkIdList()
# dynamic alloated arrays
self.checked = None
self.checkedcarefully = None
self.pointMapper = None
#Feature edges options
self.BoundaryEdges = 0
self.ManifoldEdges = 0
self.NonManifoldEdges = 0
self.FeatureEdges = 1
self.ExtractLargestregion = 0
def Edges(self, opacity=1):
"""Create edges of polytopes."""
domain = vtk.vtkGeometryFilter()
domain.SetInput(self.vtkgrid[self.dim])
domain.Update()
normals = vtk.vtkPolyDataNormals()
normals.SetInput(domain.GetOutput())
edges = vtk.vtkFeatureEdges()
edges.SetInput(normals.GetOutput())
edges.ManifoldEdgesOff()
edges.BoundaryEdgesOn()
edges.NonManifoldEdgesOff()
edges.FeatureEdgesOff()
edges.SetFeatureAngle(1)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(edges.GetOutput())
# if self.mesh.topology().dim()==3:
mapper.ScalarVisibilityOff()
# else:
# mapper.SetLookupTable(self.lut)
# mapper.SetScalarRange(self.vmin, self.vmax)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(opacity)
return actor
def PlotBoundaries(mesh):
""" Plots boundaries of a mesh """
# Determine boundary edges
featureEdges = vtk.vtkFeatureEdges()
SetVTKInput(featureEdges, mesh)
featureEdges.FeatureEdgesOff()
featureEdges.BoundaryEdgesOn()
featureEdges.NonManifoldEdgesOff()
featureEdges.ManifoldEdgesOff()
edgeMapper = vtk.vtkPolyDataMapper()
edgeMapper.SetInputConnection(featureEdges.GetOutputPort())
# Create edge actor
edgeActor = vtk.vtkActor()
edgeActor.GetProperty().SetLineWidth(5)
edgeActor.SetMapper(edgeMapper)
# Render
plobj = PlotClass()
plobj.AddMesh(mesh)
plobj.AddActor(edgeActor)
# plobj.AddLegend([
# ['Mesh', [1, 1, 1]],
# ['Holes', [1, 0, 0]]
# ])
plobj.Plot('Plotting Degenerates Features')
del plobj
def vtk_read(path):
reader = vtk.vtkOBJReader()
reader.SetFileName(path)
reader.Update()
pdata = reader.GetOutput()
# check if the stl file is closed
featureEdge = vtk.vtkFeatureEdges()
featureEdge.FeatureEdgesOff()
featureEdge.BoundaryEdgesOn()
featureEdge.NonManifoldEdgesOn()
featureEdge.SetInputData(pdata)
featureEdge.Update()
# pass pdata through a triangle filter
tr = vtk.vtkTriangleFilter()
tr.SetInputData(pdata)
tr.PassVertsOff()
tr.PassLinesOff()
tr.Update()
# normals filter
pnormal = vtk.vtkPolyDataNormals()
pnormal.SetInputData(tr.GetOutput())
pnormal.AutoOrientNormalsOff()
pnormal.ComputePointNormalsOn()
pnormal.ComputeCellNormalsOff()
pnormal.SplittingOff()
pnormal.ConsistencyOn()
pnormal.FlipNormalsOn()
pnormal.Update()
pdata = pnormal.GetOutput()
# create a vtkSelectEnclosedPoints filter
filter = vtk.vtkSelectEnclosedPoints()
filter.SetSurfaceData(pdata)
print(pdata.GetNumberOfPoints())
print(pdata.GetPointData().GetNumberOfTuples())
# print(pdata)
obj_points = np.zeros([pdata.GetNumberOfPoints(), 3])
obj_normals = np.zeros([pdata.GetNumberOfPoints(), 3])
polydata = vtk.vtkPolyData()
polydata.ShallowCopy(pdata)
for i in range(pdata.GetNumberOfPoints()):
obj_points[i, :] = pdata.GetPoint(i)
obj_normals[i, :] = pdata.GetPointData().GetNormals().GetTuple(i)
obj_polygons = numpy.zeros([pdata.GetNumberOfCells(), 3]).astype(np.int)
for i in range(pdata.GetNumberOfCells()):
cell = vtk.vtkIdList()
pdata.GetCellPoints(i, cell)
for j in range(3):
obj_polygons[i, j] = cell.GetId(j)
# print(cell.GetId(j) )
return (obj_points, obj_normals, obj_polygons)
def extractboundaryedge(surface, feature_edges=False):
"""Extract boundary edges of a surface mesh."""
edge = vtk.vtkFeatureEdges()
edge.SetInput(surface)
if not feature_edges:
edge.FeatureEdgesOff()
edge.Update()
return edge.GetOutput()
def extractboundaryedge(polydata):
"""Extract boundary edges of a surface mesh."""
edge = vtk.vtkFeatureEdges()
edge.SetInput(polydata)
edge.FeatureEdgesOff()
edge.NonManifoldEdgesOff()
edge.Update()
return edge.GetOutput()
def get_vtk_actors(self):
if not self.enabled:
return []
else:
if self.solid_actor is None:
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.get_polydata())
self.solid_actor = vtk.vtkActor()
self.solid_actor.SetMapper(mapper)
# Make the edge actor if it doesn't already exist and is needed
if self.parent.edges and self.edge_actor is None:
if self.parent.status_callback is not None:
self.parent.status_callback('Detecting mesh edges...')
edge_finder = vtk.vtkFeatureEdges()
edge_finder.SetInputData(self.get_polydata())
edge_finder.ManifoldEdgesOff()
edge_finder.BoundaryEdgesOff()
edge_finder.NonManifoldEdgesOff()
edge_finder.SetFeatureAngle(20)
edge_finder.ColoringOff()
edge_finder.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(edge_finder.GetOutputPort())
self.edge_actor = vtk.vtkActor()
self.edge_actor.SetMapper(mapper)
self.edge_actor.GetProperty().SetLineWidth(self.linewidth)
if self.parent.status_callback is not None:
self.parent.status_callback(None)
# Make sure the colour and lighing are set appropriately
if self.parent.edges:
self.solid_actor.GetProperty().SetColor((0, 0, 0))
self.edge_actor.GetProperty().SetColor(self.colour)
else:
self.solid_actor.GetProperty().SetColor(self.colour)
if self.parent.flat_shading:
self.solid_actor.GetProperty().LightingOff()
if self.parent.edges:
return [self.solid_actor, self.edge_actor]
else:
return [self.solid_actor]
def getEdges(polydata):
featureEdges = vtk.vtkFeatureEdges()
featureEdges.SetInputData(polydata)
featureEdges.BoundaryEdgesOn()
featureEdges.FeatureEdgesOn()
featureEdges.ManifoldEdgesOn()
featureEdges.NonManifoldEdgesOn()
featureEdges.Update()
return featureEdges.GetOutput()
def n_open_edges(self):
"""Return the number of open edges on this mesh."""
alg = vtk.vtkFeatureEdges()
alg.FeatureEdgesOff()
alg.BoundaryEdgesOn()
alg.NonManifoldEdgesOn()
alg.SetInputDataObject(self)
alg.Update()
return alg.GetOutput().GetNumberOfCells()
def extractboundaryedge(polydata):
edge = vtk.vtkFeatureEdges()
if vtk.vtkVersion.GetVTKMajorVersion() > 5:
edge.SetInputData(polydata)
else:
edge.SetInput(polydata)
edge.FeatureEdgesOff()
edge.NonManifoldEdgesOff()
edge.Update()
return edge.GetOutput()
def _extract_boundary_data(self, internalData):
patchFeatureEdgesFilter = vtk.vtkFeatureEdges()
patchFeatureEdgesFilter.FeatureEdgesOff()
patchFeatureEdgesFilter.NonManifoldEdgesOff()
patchFeatureEdgesFilter.ManifoldEdgesOff()
patchFeatureEdgesFilter.SetInputData(internalData)
patchFeatureEdgesFilter.Update()
return patchFeatureEdgesFilter.GetOutput()
def PlotEdges(mesh, angle):
featureEdges = vtk.vtkFeatureEdges()
if vtk.vtkVersion().GetVTKMajorVersion() >5:
featureEdges.SetInputData(mesh)
else:
featureEdges.SetInput(mesh)
featureEdges.FeatureEdgesOn()
featureEdges.BoundaryEdgesOff()
featureEdges.NonManifoldEdgesOff()
featureEdges.ManifoldEdgesOff()
featureEdges.SetFeatureAngle(angle)
edgeMapper = vtk.vtkPolyDataMapper();
edgeMapper.SetInputConnection(featureEdges.GetOutputPort());
edgeActor = vtk.vtkActor();
edgeActor.GetProperty().SetLineWidth(5);
edgeActor.SetMapper(edgeMapper)
mapper = vtk.vtkDataSetMapper()
if vtk.vtkVersion().GetVTKMajorVersion() >5:
mapper.SetInputData(mesh)
else:
mapper.SetInput(mesh)
# Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().LightingOff()
###############################
# Display
###############################
# Render
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Allow user to interact
istyle = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(istyle)
ren.AddActor(actor)
ren.AddActor(edgeActor)
iren.Initialize()
renWin.Render()
iren.Start()
def extractfeatureedges(surface, boundary_edges=True,
feature_edges=False, feature_angle=30):
"""Extract feature edges of a surface mesh. Defaults to extracting boundary
edges."""
edge = vtk.vtkFeatureEdges()
edge.SetInput(surface)
edge.BoundaryEdgesOn() if boundary_edges else edge.BoundaryEdgesOff()
edge.FeatureEdgesOn() if feature_edges else edge.FeatureEdgesOff()
edge.SetFeatureAngle(feature_angle)
edge.Update()
return edge.GetOutput()
def extractfeatureedges(surface, boundary_edges=True,
feature_edges=False, feature_angle=30):
"""Extract feature edges of a surface mesh. Defaults to extracting boundary
edges."""
edge = vtk.vtkFeatureEdges()
edge.SetInputData(surface)
edge.BoundaryEdgesOn() if boundary_edges else edge.BoundaryEdgesOff()
edge.FeatureEdgesOn() if feature_edges else edge.FeatureEdgesOff()
edge.SetFeatureAngle(feature_angle)
edge.Update()
return edge.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No Input Surface.')
# Step 0: Check if the surface has any unfilled holes in it. if it does, cap them.
fedges = vtk.vtkFeatureEdges()
fedges.BoundaryEdgesOn()
fedges.FeatureEdgesOff()
fedges.ManifoldEdgesOff()
fedges.SetInputData(self.Surface)
fedges.Update()
ofedges = fedges.GetOutput()
# if the following is not == 0, then the surface contains unfilled holes.
numEdges = ofedges.GetNumberOfPoints()
if numEdges >= 1:
self.PrintLog('Capping unclosed holes in surface.')
tempcapper = vmtksurfacecapper.vmtkSurfaceCapper()
tempcapper.Surface = self.Surface
tempcapper.LogOn = 0
tempcapper.Interactive = 0
tempcapper.Execute()
self.Surface = tempcapper.Surface
# Step 1: Convert the input surface into an image mask of unsigned char type and spacing = PolyDataToImageDataSpacing
# Where voxels lying inside the surface are set to 255 and voxels outside the image are set to value 0.
# since we are creating a new image container from nothing, calculate the origin, extent, and dimensions for the
# vtkImageDataObject from the surface parameters.
self.PrintLog('Converting Surface to Image Mask')
binaryImageFilter = vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage()
binaryImageFilter.Surface = self.Surface
binaryImageFilter.InsideValue = 255
binaryImageFilter.LogOn = 0
binaryImageFilter.OutsideValue = 0
binaryImageFilter.PolyDataToImageDataSpacing = self.PolyDataToImageDataSpacing
binaryImageFilter.Execute()
# Step 2: Feed into the vtkvmtkMedialCurveFilter
# This takes the binary image and computes the average outward flux of the image. This is then
# used to compute the skeleton image. It returns a binary image where values of 1 are skeleton points
# and values of 0 are outside the skeleton. The execution speed of this algorithm is fairly sensetive to
# the extent of the input image.
self.PrintLog('Extracting Centerline Skeleton from Image Mask...')
medialCurveFilter = vtkvmtk.vtkvmtkMedialCurveFilter()
medialCurveFilter.SetInputData(binaryImageFilter.Image)
medialCurveFilter.SetThreshold(self.Threshold)
medialCurveFilter.SetSigma(self.Sigma)
medialCurveFilter.Update()
self.Image = medialCurveFilter.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No Input Surface.')
# Step 0: Check if the surface has any unfilled holes in it. if it does, cap them.
fedges = vtk.vtkFeatureEdges()
fedges.BoundaryEdgesOn()
fedges.FeatureEdgesOff()
fedges.ManifoldEdgesOff()
fedges.SetInputData(self.Surface)
fedges.Update()
ofedges = fedges.GetOutput()
# if the following is not == 0, then the surface contains unfilled holes.
numEdges = ofedges.GetNumberOfPoints()
if numEdges >= 1:
self.PrintLog('Capping unclosed holes in surface.')
tempcapper = vmtksurfacecapper.vmtkSurfaceCapper()
tempcapper.Surface = self.Surface
tempcapper.LogOn = 0
tempcapper.Interactive = 0
tempcapper.Execute()
self.Surface = tempcapper.Surface
# Step 1: Convert the input surface into an image mask of unsigned char type and spacing = PolyDataToImageDataSpacing
# Where voxels lying inside the surface are set to 255 and voxels outside the image are set to value 0.
# since we are creating a new image container from nothing, calculate the origin, extent, and dimensions for the
# vtkImageDataObject from the surface parameters.
self.PrintLog('Converting Surface to Image Mask')
binaryImageFilter = vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage()
binaryImageFilter.Surface = self.Surface
binaryImageFilter.InsideValue = 255
binaryImageFilter.LogOn = 0
binaryImageFilter.OutsideValue = 0
binaryImageFilter.PolyDataToImageDataSpacing = self.PolyDataToImageDataSpacing
binaryImageFilter.Execute()
# Step 2: Feed into the vtkvmtkMedialCurveFilter
# This takes the binary image and computes the average outward flux of the image. This is then
# used to compute the skeleton image. It returns a binary image where values of 1 are skeleton points
# and values of 0 are outside the skeleton. The execution speed of this algorithm is fairly sensetive to
# the extent of the input image.
self.PrintLog('Extracting Centerline Skeleton from Image Mask...')
medialCurveFilter = vtkvmtk.vtkvmtkMedialCurveFilter()
medialCurveFilter.SetInputData(binaryImageFilter.Image)
medialCurveFilter.SetThreshold(self.Threshold)
medialCurveFilter.SetSigma(self.Sigma)
medialCurveFilter.Update()
self.Image = medialCurveFilter.GetOutput()
def boundaries(actor, c='p', lw=5, legend=None):
'''Build a copy of actor that shows the boundary lines of its surface.'''
fe = vtk.vtkFeatureEdges()
vu.setInput(fe, vu.polydata(actor))
fe.BoundaryEdgesOn()
fe.FeatureEdgesOn()
fe.ManifoldEdgesOn()
fe.NonManifoldEdgesOn()
fe.ColoringOff()
fe.Update()
bactor = vu.makeActor(fe.GetOutput(), c=c, alpha=1, legend=legend)
bactor.GetProperty().SetLineWidth(lw)
return bactor
def getSurfaceData(a_FileName, a_InputLegacyDataType = 'none'):
#------------------
# Get geometry data
#------------------
geoFilter = vtk.vtkGeometryFilter()
geoFilter.SetInputData(a_Data)
geoFilter.Update()
#--------------------------
# Extract domain boundaries
#--------------------------
featureEdges = vtk.vtkFeatureEdges()
featureEdges.SetInputConnection(geo_filter.GetOutputPort())
featureEdges.BoundaryEdgesOn()
featureEdges.FeatureEdgesOff()
featureEdges.Update()
edgeData = featureEdges.GetOutput()
numCells = edgeData.GetNumberOfCells()
numNodes = edgeData.GetNumberOfPoints()
#-------------------------------------------------------------------
# Get connectivity data
#
# NOTE: Turning on ScalarConnectivity (not shown) will exclude holes
# in the mesh
#-------------------------------------------------------------------
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInputConnection(featureEdges.GetOutputPort())
connectivity.Update()
connectivityData = connectivity.GetOutput()
#----------------------------------------------
# VTK List object for storing boundary node IDs
#----------------------------------------------
nodeList = vtk.vtkIdList()
connectivityArray = np.zeros((numCells, 2), dtype=np.int32, order='F')
for cellID in range(numCells):
connectivityData.GetCellPoints(cellID, nodeList)
connectivityArray[cellID,0] = nodeList.GetId(0)
connectivityArray[cellID,1] = nodeList.GetId(1)
coordinatesArray = np.zeros((numNodes, 3), dtype=np.float64, order='F')
for nodeID in range(numNodes):
coordinatesArray[p,:] = connectivityData.GetPoint(p)[0], connectivityData.GetPoint(p)[1], \
connectivityData.GetPoint(p)[2]
return coordinatesArray, connectivityArray
def PlotEdges(mesh, angle):
featureEdges = vtk.vtkFeatureEdges()
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
featureEdges.SetInputData(mesh)
else:
featureEdges.SetInput(mesh)
featureEdges.FeatureEdgesOn()
featureEdges.BoundaryEdgesOff()
featureEdges.NonManifoldEdgesOff()
featureEdges.ManifoldEdgesOff()
featureEdges.SetFeatureAngle(angle)
edgeMapper = vtk.vtkPolyDataMapper()
edgeMapper.SetInputConnection(featureEdges.GetOutputPort())
edgeActor = vtk.vtkActor()
edgeActor.GetProperty().SetLineWidth(5)
edgeActor.SetMapper(edgeMapper)
mapper = vtk.vtkDataSetMapper()
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
mapper.SetInputData(mesh)
else:
mapper.SetInput(mesh)
# Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().LightingOff()
###############################
# Display
###############################
# Render
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Allow user to interact
istyle = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(istyle)
ren.AddActor(actor)
ren.AddActor(edgeActor)
iren.Initialize()
renWin.Render()
iren.Start()
def extractBoundaryEdges(inputModel, outputModel, boundary=False, feature=False, nonManifold=False, manifold=False, featureAngle=20):
"""Extract edges of a model.
"""
boundaryEdges = vtk.vtkFeatureEdges()
boundaryEdges.SetInputData(inputModel.GetPolyData())
boundaryEdges.ExtractAllEdgeTypesOff()
boundaryEdges.SetBoundaryEdges(boundary)
boundaryEdges.SetFeatureEdges(feature)
if feature:
boundaryEdges.SetFeatureAngle(featureAngle)
boundaryEdges.SetNonManifoldEdges(nonManifold)
boundaryEdges.SetManifoldEdges(manifold)
boundaryEdges.Update()
outputModel.SetAndObservePolyData(boundaryEdges.GetOutput())
def ExtractEdges(self,
feature_angle=30,
boundary_edges=True,
non_manifold_edges=True,
feature_edges=True,
manifold_edges=True):
"""
Extracts edges from a surface. From vtk documentation, the edges are
one of the following
1) boundary (used by one polygon) or a line cell
2) non-manifold (used by three or more polygons)
3) feature edges (edges used by two triangles and whose
dihedral angle > feature_angle)
4) manifold edges (edges used by exactly two polygons).
Parameters
----------
feature_angle : float, optional
Defaults to 30 degrees.
boundary_edges : bool, optional
Defaults to True
non_manifold_edges : bool, optional
Defaults to True
feature_edges : bool, optional
Defaults to True
manifold_edges : bool, optional
Defaults to True
Returns
-------
edges : vtkInterface.vtkPolyData
Extracted edges
"""
featureEdges = vtk.vtkFeatureEdges()
featureEdges.SetInputData(self)
featureEdges.SetFeatureAngle(feature_angle)
featureEdges.SetManifoldEdges(manifold_edges)
featureEdges.SetNonManifoldEdges(non_manifold_edges)
featureEdges.SetBoundaryEdges(non_manifold_edges)
featureEdges.SetFeatureEdges(feature_edges)
featureEdges.SetColoring(False)
featureEdges.Update()
return PolyData(featureEdges.GetOutput())
def PlotBoundaries(mesh, **args):
""" Plots boundaries of a mesh """
featureEdges = vtk.vtkFeatureEdges()
featureEdges.SetInputData(mesh)
featureEdges.FeatureEdgesOff()
featureEdges.BoundaryEdgesOn()
featureEdges.NonManifoldEdgesOn()
featureEdges.ManifoldEdgesOff()
featureEdges.Update()
edges = vtkInterface.PolyData(featureEdges.GetOutput())
plobj = PlotClass()
plobj.AddMesh(edges, 'r', style='wireframe')
plobj.AddMesh(mesh)
plobj.Plot()
def GetWholeConnectedRegions(poly, coord):
# for each of the connected regions, make a (likely non-convex)
# whole polygon, divided at the self intersections.
# for small image, reduces by 4.975
# big image improves by 3.918
numCells = poly.GetNumberOfCells()
#print "numcells before", numCells
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInput(poly)
connectivity.SetExtractionModeToAllRegions()
connectivity.Update()
numRegions = connectivity.GetNumberOfExtractedRegions()
connectivity.SetExtractionModeToSpecifiedRegions()
featureEdges = vtk.vtkFeatureEdges()
featureEdges.BoundaryEdgesOn()
numResult = 0
for r in range(numRegions):
numResult += 1
connectivity.InitializeSpecifiedRegionList()
connectivity.AddSpecifiedRegion(r)
region = connectivity.GetOutput()
region.Update()
#print "region has ", region.GetNumberOfCells(), " cells"
featureEdges.SetInput(region)
edges = featureEdges.GetOutput()
edges.Update()
edges.BuildLinks(0)
#print "edges has", edges.GetNumberOfCells(), " cells"
numCells = edges.GetNumberOfCells()
# for i in xrange(numCells):
# print edges.GetCell(i).GetPoints().GetPoint(0), edges.GetCell(i).GetPoints().GetPoint(1)
# edges not given in order, we need to traverse
# first look for self intersections
points = edges.GetPoints()
selfIntersections = []
cellIds = vtk.vtkIdList()
for p in range(points.GetNumberOfPoints()):
edges.GetPointCells(p,cellIds)
if cellIds.GetNumberOfIds() == 4:
selfIntersections.append(p)
numResult += 1
#print selfIntersections
## if not selfIntersections:
## selfIntersections.append(edges.GetCell(0).GetPointIds().GetId(0))
# for now just return number of cells in result
return numResult
def GetWholeConnectedRegions(poly, coord):
# for each of the connected regions, make a (likely non-convex)
# whole polygon, divided at the self intersections.
# for small image, reduces by 4.975
# big image improves by 3.918
numCells = poly.GetNumberOfCells()
#print "numcells before", numCells
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInput(poly)
connectivity.SetExtractionModeToAllRegions()
connectivity.Update()
numRegions = connectivity.GetNumberOfExtractedRegions()
connectivity.SetExtractionModeToSpecifiedRegions()
featureEdges = vtk.vtkFeatureEdges()
featureEdges.BoundaryEdgesOn()
numResult = 0
for r in range(numRegions):
numResult += 1
connectivity.InitializeSpecifiedRegionList()
connectivity.AddSpecifiedRegion(r)
region = connectivity.GetOutput()
region.Update()
#print "region has ", region.GetNumberOfCells(), " cells"
featureEdges.SetInput(region)
edges = featureEdges.GetOutput()
edges.Update()
edges.BuildLinks(0)
#print "edges has", edges.GetNumberOfCells(), " cells"
numCells = edges.GetNumberOfCells()
# for i in xrange(numCells):
# print edges.GetCell(i).GetPoints().GetPoint(0), edges.GetCell(i).GetPoints().GetPoint(1)
# edges not given in order, we need to traverse
# first look for self intersections
points = edges.GetPoints()
selfIntersections = []
cellIds = vtk.vtkIdList()
for p in range(points.GetNumberOfPoints()):
edges.GetPointCells(p, cellIds)
if cellIds.GetNumberOfIds() == 4:
selfIntersections.append(p)
numResult += 1
#print selfIntersections
## if not selfIntersections:
## selfIntersections.append(edges.GetCell(0).GetPointIds().GetId(0))
# for now just return number of cells in result
return numResult
def identify_caps(model):
#print("========== identify_caps ==========")
face_caps = []
face_ids = model.get_face_ids()
for face_id in face_ids:
#print("----- face {0:d} -----".format(face_id))
face_polydata = model.get_face_polydata(face_id=face_id)
feature_edges = vtk.vtkFeatureEdges()
feature_edges.SetInputData(face_polydata)
feature_edges.BoundaryEdgesOn()
feature_edges.ManifoldEdgesOff()
feature_edges.NonManifoldEdgesOff()
feature_edges.FeatureEdgesOff()
feature_edges.ColoringOn()
#feature_edges.SetFeatureAngle(self.params.angle);
feature_edges.Update()
boundary_edges = feature_edges.GetOutput()
clean_filter = vtk.vtkCleanPolyData()
boundary_edges_clean = clean_filter.SetInputData(boundary_edges)
clean_filter.Update()
cleaned_edges = clean_filter.GetOutput()
conn_filter = vtk.vtkPolyDataConnectivityFilter()
conn_filter.SetInputData(cleaned_edges)
conn_filter.SetExtractionModeToSpecifiedRegions()
boundary_edge_components = list()
rid = 0
while True:
conn_filter.AddSpecifiedRegion(rid)
conn_filter.Update()
component = vtk.vtkPolyData()
component.DeepCopy(conn_filter.GetOutput())
if component.GetNumberOfCells() <= 0:
break
#print("{0:d}: Number of boundary lines: {1:d}".format(rid, component.GetNumberOfCells()))
boundary_edge_components.append(component)
conn_filter.DeleteSpecifiedRegion(rid)
rid += 1
if rid == 1:
face_caps.append(True)
else:
face_caps.append(False)
print("Done.")
return face_caps
def preprocess_mesh(mesh, num_patches=10):
"""
This function...
:param mesh:
:param num_patches:
:return:
"""
# run patching
for i in range(num_patches):
mesh = patch(mesh)
edges2 = vtk.vtkFeatureEdges()
edges2.SetInputData(mesh)
edges2.FeatureEdgesOff()
edges2.NonManifoldEdgesOn()
edges2.ManifoldEdgesOff()
edges2.BoundaryEdgesOn()
edges2.Update()
edgesPd = edges2.GetOutput()
print(
"{0} cells and {1} points".format(
edgesPd.GetNumberOfCells(), edgesPd.GetNumberOfPoints()
)
)
toDelete = vtk.vtkFloatArray()
toDelete.SetNumberOfComponents(1)
toDelete.SetNumberOfValues(mesh.GetNumberOfPoints())
for i in range(mesh.GetNumberOfPoints()):
toDelete.SetValue(i, 0)
for i in range(edgesPd.GetNumberOfPoints()):
edgePnt = edgesPd.GetPoint(i)
meshVertId = mesh.FindPoint(edgePnt)
toDelete.SetValue(meshVertId, 1)
mesh.GetPointData().SetScalars(toDelete)
clipper = vtk.vtkClipPolyData()
clipper.SetValue(0.5)
clipper.SetInputData(mesh)
clipper.InsideOutOn()
clipper.Update()
return clipper.GetOutput()
def main():
fn = get_program_parameters()
polyData = ReadPolyData(fn)
featureEdges = vtk.vtkFeatureEdges()
featureEdges.FeatureEdgesOff()
featureEdges.BoundaryEdgesOn()
featureEdges.NonManifoldEdgesOn()
featureEdges.SetInputData(polyData)
featureEdges.Update()
numberOfOpenEdges = featureEdges.GetOutput().GetNumberOfCells()
if numberOfOpenEdges > 0:
print(fn, ': Surface is not closed')
else:
print(fn, ': Surface is closed')
def boundaries(actor, c='p', lw=5, legend=None):
'''Build a copy of actor that shows the boundary lines of its surface.
[**Example**](https://github.com/marcomusy/vtkplotter/blob/master/examples/tutorial.py)
'''
fe = vtk.vtkFeatureEdges()
fe.SetInputData(actor.polydata())
fe.BoundaryEdgesOn()
fe.FeatureEdgesOn()
fe.ManifoldEdgesOn()
fe.NonManifoldEdgesOn()
fe.ColoringOff()
fe.Update()
bactor = Actor(fe.GetOutput(), c=c, alpha=1, legend=legend)
bactor.GetProperty().SetLineWidth(lw)
return bactor
def featureEdgeView(self):
if not self.featureEdge:
feature_edge = vtk.vtkFeatureEdges()
feature_edge.SetInputConnection(self.filter.GetOutputPort())
self.mapper.SetInputConnection(feature_edge.GetOutputPort())
self.featureEdge = True
prop = self.actor.GetProperty()
prop.SetColor(0, 0, 0)
prop.SetLineWidth(2)
prop.SetRepresentationToSurface()
self.interRender.ReInitialize()
else:
self.mapper.SetInputConnection(self.filter.GetOutputPort())
self.mapper.SetScalarModeToUseCellFieldData()
self.vtkWindow.interRender()
self.featureEdge = False
def CloseSurface( shape, output ):
"""
Closes holes in a surface with a flat cover
shape vtkPolyData: input shape
output vtkPolyData: output shape
Return nothing.
"""
fe = vtk.vtkFeatureEdges()
fe.SetInputData( shape )
fe.BoundaryEdgesOn()
fe.NonManifoldEdgesOff()
fe.FeatureEdgesOff()
fe.ManifoldEdgesOff()
fe.Update()
connect = vtk.vtkPolyDataConnectivityFilter()
connect.SetInputData(fe.GetOutput())
connect.Update()
ncontours = connect.GetNumberOfExtractedRegions()
append = vtk.vtkAppendPolyData()
append.AddInput(shape)
for i in range(ncontours):
connect.AddSpecifiedRegion(i)
connect.SetExtractionModeToSpecifiedRegions()
connect.Update()
edges = connect.GetOutput()
cover = vtk.vtkPolyData()
GenerateHoleCover(edges, cover)
append.AddInput(cover)
connect.DeleteSpecifiedRegion(i)
append.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(append.GetOutput())
cleaner.Update()
output.DeepCopy(cleaner.GetOutput())
def patch(mesh):
"""
This function...
:param mesh:
:return:
"""
edges = vtk.vtkFeatureEdges()
edges.SetInputData(mesh)
edges.FeatureEdgesOff()
edges.NonManifoldEdgesOn()
edges.ManifoldEdgesOff()
edges.BoundaryEdgesOn()
edges.Update()
print(
"{0} cells and {1} points".format(
edges.GetOutput().GetNumberOfCells(), edges.GetOutput().GetNumberOfPoints()
)
)
if edges.GetOutput().GetNumberOfPoints() == 0:
print("No defects")
return mesh
patchSkel = vtk.vtkStripper()
patchSkel.SetInputData(edges.GetOutput())
patchSkel.Update()
patchPoly = vtk.vtkPolyData()
patchPoly.Initialize()
patchPoly.SetPoints(patchSkel.GetOutput().GetPoints())
patchPoly.SetPolys(patchSkel.GetOutput().GetLines())
patchTri = vtk.vtkTriangleFilter()
patchTri.SetInputData(patchPoly)
patchTri.Update()
meshAppend = vtk.vtkAppendPolyData()
meshAppend.AddInputData(patchTri.GetOutput())
meshAppend.AddInputData(mesh)
meshAppend.Update()
poly = vtk.vtkCleanPolyData()
poly.SetInputData(meshAppend.GetOutput())
poly.Update()
return poly.GetOutput()
def conditionImp(self):
featureEdges = vtk.vtkFeatureEdges();
featureEdges.FeatureEdgesOff();
featureEdges.BoundaryEdgesOn();
featureEdges.NonManifoldEdgesOn();
featureEdges.SetInputData(self.data);
featureEdges.Update();
numberOfOpenEdges = featureEdges.GetOutput().GetNumberOfCells();
if numberOfOpenEdges > 0:
if not self.failed:
self.failed = True;
return False;
else:
return False;
else:
self.failed = False;
return True;
def makeBorderPD(ipw):
# setup source
ps = vtk.vtkPlaneSource()
ps.SetOrigin(ipw.GetOrigin())
ps.SetPoint1(ipw.GetPoint1())
ps.SetPoint2(ipw.GetPoint2())
fe = vtk.vtkFeatureEdges()
fe.SetInput(ps.GetOutput())
tubef = vtk.vtkTubeFilter()
tubef.SetNumberOfSides(12)
tubef.SetRadius(0.5)
tubef.SetInput(fe.GetOutput())
return tubef.GetOutput()
def Domain(self, opacity=1, mesh=False):
domain = vtk.vtkGeometryFilter()
domain.SetInput(self.vtkgrid)
domain.Update()
normals = vtk.vtkPolyDataNormals()
normals.SetInput(domain.GetOutput())
# edges
edges = vtk.vtkFeatureEdges()
edges.SetInput(normals.GetOutput())
edges.ManifoldEdgesOff()
if mesh:
edges.ManifoldEdgesOn()
edges.BoundaryEdgesOn()
edges.NonManifoldEdgesOff()
edges.FeatureEdgesOff()
edges.SetFeatureAngle(1)
# mapper for domain
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(normals.GetOutput())
mapper.SetLookupTable(self.lut)
mapper.SetScalarRange(self.vmin, self.vmax)
# actor for domain
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(opacity)
# mapper for edges
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(edges.GetOutput())
if self.mesh.topology().dim() == 3:
mapper.ScalarVisibilityOff()
else:
mapper.SetLookupTable(self.lut)
mapper.SetScalarRange(self.vmin, self.vmax)
# actor for domain
actor2 = vtk.vtkActor()
actor2.SetMapper(mapper)
actor2.GetProperty().SetOpacity((1 + opacity) / 2)
if mesh:
actor2.GetProperty().SetOpacity(opacity)
return [actor, actor2]
def _Execute(self, *args):
input = self.GetPolyDataInput()
# Gets any edges of the mesh
edger = vtkFeatureEdges()
edger.BoundaryEdgesOn()
edger.FeatureEdgesOff()
edger.NonManifoldEdgesOff()
edger.ManifoldEdgesOff()
edger.SetInputData(input)
# Converts the edges to a polyline
stripper = vtkStripper()
stripper.SetInputConnection(edger.GetOutputPort())
stripper.Update()
# Change the polylines into polygons
boundaryPoly = vtkPolyData()
boundaryPoly.SetPoints(stripper.GetOutput().GetPoints())
boundaryPoly.SetPolys(stripper.GetOutput().GetLines())
# Triangulate
tri = vtkTriangleFilter()
tri.SetInputData(boundaryPoly)
tri.Update()
# Join to the input
merger = vtkAppendPolyData()
merger.AddInputData(input)
merger.AddInputData(tri.GetOutput())
# Clean up by merging duplicate points
cleaner = vtkCleanPolyData()
cleaner.SetInputConnection(merger.GetOutputPort())
cleaner.Update()
# Set output
output = self.GetPolyDataOutput()
output.ShallowCopy(cleaner.GetOutput())
return
def boundaries_create(clean,arg_boundaries_color,arg_boundaries_width): boundariespolydata = vtk.vtkFeatureEdges() boundariespolydata.SetInputConnection(clean.GetOutputPort()) boundariespolydata.SetBoundaryEdges(1) boundariespolydata.SetFeatureEdges(0) boundariespolydata.SetNonManifoldEdges(0) boundariespolydata.SetColoring(1) boundariesmapper = vtk.vtkPolyDataMapper() boundariesmapper.SetInputConnection(boundariespolydata.GetOutputPort()) boundariesmapper.SetScalarVisibility(0) boundariesactor = vtk.vtkActor() boundariesactor.SetMapper(boundariesmapper) boundariesactor.GetProperty().SetLineWidth(arg_boundaries_width) boundariesactor.GetProperty().SetColor(arg_boundaries_color) boundariesactor.GetProperty().SetAmbient(1) boundariesactor.GetProperty().SetDiffuse(0) boundariesactor.PickableOff() return(boundariesactor,boundariespolydata)
input_file = 'spatial_data_%03d.d' % int(options.frame)
#input_file = 'v6brivers.14_fort.74_%03d.vtu' % int(frame)
#input_file = 'v6brivers.14_fort.74.pvd'
#input_file = 'femar3_irene30_maxwvel.vtu'
meshReader.SetFileName(input_file)
meshReader.SetScalarsName("WindSpeed")
meshReader.SetVectorsName("WindVelocity")
#meshReader.SetPointArrayStatus("WindVelocity",1)
##meshReader.SetPointArrayStatus("MaximumWindSpeed",1)
meshReader.Update()
# create actor for unstructured grid outline
#outlineMesh = vtk.vtkOutlineFilter()
meshGeometryFilter = vtk.vtkGeometryFilter()
meshGeometryFilter.SetInput(meshReader.GetOutput())
outlineMesh = vtk.vtkFeatureEdges()
outlineMesh.SetInputConnection(meshGeometryFilter.GetOutputPort())
outlineMesh.BoundaryEdgesOn()
outlineMeshMapper = vtk.vtkPolyDataMapper()
outlineMeshMapper.SetInputConnection(outlineMesh.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMeshMapper)
outlineActor.GetProperty().SetColor(1,1,1)
# create a color scale (color lookup table)
refLut = vtk.vtkLookupTable()
lut = vtk.vtkLookupTable()
refLut.SetNumberOfColors(256)
lut.SetNumberOfColors(256)
refLut.SetHueRange(0.0, 0.667)
refLut.Build()
def renderthis(self,warunek):
# open a window and create a renderer
self.widget.GetRenderWindow().AddRenderer(self.ren)
# open file
openFileDialog = wx.FileDialog(self, "Open STL file", "", self.filename,
"*.stl", wx.FD_OPEN | wx.FD_FILE_MUST_EXIST)
if openFileDialog.ShowModal() == wx.ID_CANCEL:
return
self.filename = openFileDialog.GetPath()
# render the data
reader = vtk.vtkSTLReader()
reader.SetFileName(self.filename)
reader.Update()
mesh = reader.GetOutput()
# To take the polygonal data from the vtkConeSource and
# create a rendering for the renderer.
coneMapper = vtk.vtkPolyDataMapper()
coneMapper.SetInput(reader.GetOutput())
# create an actor for our scene
if self.isploted:
coneActor=self.ren.GetActors().GetLastActor()
self.ren.RemoveActor(coneActor)
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMapper)
# Add actor
self.ren.AddActor(coneActor)
# print self.ren.GetActors().GetNumberOfItems()
#addPoint(self.ren, pSource, color=[1.0,0.0,0.0])
#addPoint(self.ren, pTarget, color=[1.0,0.0,1.0])
addLine(self.ren, pp1, pp2)
addLine(self.ren, pp3, pp4)
addLine(self.ren, pp5, pp6)
addLine(self.ren, pp7, pp8)
addLine(self.ren, pp1, pp7)
addLine(self.ren, pp3, pp5)
addLine(self.ren, pp4, pp6)
addLine(self.ren, pp2, pp8)
addLine(self.ren, pp1, pp3)
addLine(self.ren, pp7, pp5)
addLine(self.ren, pp4, pp2)
addLine(self.ren, pp6, pp8)
if warunek==1:
addEdges(self.ren)
#####################################################################################
featureEdge=vtk.vtkFeatureEdges()
featureEdge.FeatureEdgesOff()
featureEdge.BoundaryEdgesOn()
featureEdge.NonManifoldEdgesOn()
featureEdge.SetInput(mesh)
featureEdge.Update()
openEdges = featureEdge.GetOutput().GetNumberOfCells()
if openEdges != 0:
print "the stl file is not closed"
select = vtk.vtkSelectEnclosedPoints()
select.SetSurface(mesh)
inside_polydat = vtk.vtkPolyData()
forcing_polydat = vtk.vtkPolyData()
interpolation_polydat = vtk.vtkPolyData()
inside_points = vtk.vtkPoints()
forcing_points = vtk.vtkPoints()
interpolation_points = vtk.vtkPoints()
# for i in range(11):
#IsInside(i-5,0.1,0.1,mesh)
global licz
global licz2
global licznik
for j in range(1,lwY+1):
for i in range(1,lwX+1):
licz += 1
print (licz/float(stoProcent))*100.0
for k in range(1,lwZ+1):
sprawdzenie = 0
siatkaX[1]=xmin+0.001
siatkaX[lwX]=xmax-0.001
siatkaY[1]=ymin+0.001
siatkaY[lwY]=ymax-0.001
siatkaZ[1]=zmin+0.001
siatkaZ[lwZ]=zmax-0.001
sprawdzenie = IsInsideCheck(siatkaX[i],siatkaY[j],siatkaZ[k],mesh)
siatkaX[1]=xmin
siatkaX[lwX]=xmax
siatkaY[1]=ymin
siatkaY[lwY]=ymax
siatkaZ[1]=zmin
siatkaZ[lwZ]=zmax
mesh_point_inside = [siatkaX[i],siatkaY[j],siatkaZ[k]]
#mesh_point_forcing = [siatkaX[i]+1.0,siatkaY[j],siatkaZ[k]]
maska[licznik] = sprawdzenie
licznik=licznik+1
if sprawdzenie == 1:
inside_points.InsertNextPoint(mesh_point_inside)
#forcing_points.InsertNextPoint(mesh_point_forcing)
licznik=0
licznik_forcing=0
for j in range(0,lwY):
for i in range(0,lwX):
for k in range(0,lwZ):
#print j,i,k
maska3D[j][i][k]=maska[licznik]
licznik=licznik+1
#print maska3D
find_forcing_points(lwY,lwX,lwZ,maska3D,forcing_points,siatkaX,siatkaY,siatkaZ,boundary_points,mesh,intersection,maska3D_forcing,interpolation_points,fnix,fniy,fniz,fncx,fncy,fncz)
for j in range(0,lwY):
for i in range(0,lwX):
for k in range(0,lwZ):
if maska3D_forcing[j][i][k] > 0:
licznik_forcing = licznik_forcing+maska3D_forcing[j][i][k]
for i in range(0,licznik_forcing):
print i,fnix[i],fniy[i],fniz[i],fncx[i],fncy[i],fncz[i]
odczyt_STL(self.filename,normals,licznik_forcing,fnix,fniy,fniz,fncx,fncy,fncz)
zp = [0,0,0]
for i in range(0,licznik_forcing):
if fncx[i]>0 and normals[i][0]<0:
normals[i][0]=normals[i][0]*(-1.0)
if fncx[i]<0 and normals[i][0]>0:
normals[i][0]=normals[i][0]*(-1.0)
if fncy[i]>0 and normals[i][1]<0:
normals[i][1]=normals[i][1]*(-1.0)
if fncy[i]<0 and normals[i][1]>0:
normals[i][1]=normals[i][1]*(-1.0)
if fncz[i]>0 and normals[i][2]<0:
normals[i][2]=normals[i][2]*(-1.0)
if fncz[i]<0 and normals[i][2]>0:
normals[i][2]=normals[i][2]*(-1.0)
for i in range(0,licznik_forcing):
zp1 = [fncx[i],fncy[i],fncz[i]]
zp2 = [normals[i][0]+fncx[i],normals[i][1]+fncy[i],normals[i][2]+fncz[i]]
#normals[i][0]=normals[i][0]+fncx[i]
#normals[i][1]=normals[i][1]+fncy[i]
#normals[i][2]=normals[i][2]+fncz[i]
addLine(self.ren, zp1, zp2)
print i,normals[i],zp1,zp2
#print intersection
#print "+++++++++++++++++++="
#print maska3D_forcing
"""
licznik=0
for j in range(0,lwY):
for i in range(0,lwX-1):
for k in range(0,lwZ):
mesh_point_forcing = [siatkaX[i+1],siatkaY[j+1],siatkaZ[k+1]]
if (maska3D[j][i][k] == 0) and (maska3D[j][i+1][k] == 1):
forcing_points.InsertNextPoint(mesh_point_forcing)
licznik=licznik+1
"""
zapis = open('Maska.txt', 'w')
for i in range(0,lwX*lwY*lwZ):
zapis.write(str(maska[i]))
zapis.write('\n')
zapis.close()
print "zapisano Maske"
inside_polydat.SetPoints(inside_points)
inside = vtk.vtkSphereSource()
inside.SetRadius(0.02)
inside.SetPhiResolution(8)
inside.SetThetaResolution(8)
ballGlyph = vtkGlyph3D()
ballGlyph.SetColorModeToColorByScalar()
ballGlyph.SetSourceConnection(inside.GetOutputPort())
ballGlyph.SetInput(inside_polydat)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(ballGlyph.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor([1.0,0.0,0.0])
self.ren.AddActor(actor)
######################################################################################
forcing_polydat.SetPoints(forcing_points)
forcing = vtk.vtkSphereSource()
#point.SetCenter(pS)
forcing.SetRadius(0.02)
forcing.SetPhiResolution(8)
forcing.SetThetaResolution(8)
forcingGlyph = vtkGlyph3D()
forcingGlyph.SetColorModeToColorByScalar()
forcingGlyph.SetSourceConnection(forcing.GetOutputPort())
forcingGlyph.SetInput(forcing_polydat)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(forcingGlyph.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor([0.0,1.0,0.0])
self.ren.AddActor(actor)
#####################################################################################
"""
interpolation_polydat.SetPoints(interpolation_points)
interpolation = vtk.vtkSphereSource()
#point.SetCenter(pS)
interpolation.SetRadius(0.02)
interpolation.SetPhiResolution(8)
interpolation.SetThetaResolution(8)
interpolationGlyph = vtkGlyph3D()
interpolationGlyph.SetColorModeToColorByScalar()
interpolationGlyph.SetSourceConnection(interpolation.GetOutputPort())
interpolationGlyph.SetInput(interpolation_polydat)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(interpolationGlyph.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor([0.0,0.0,1.0])
self.ren.AddActor(actor)
"""
#####################################################################################
obbTree = vtk.vtkOBBTree()
obbTree.SetDataSet(mesh)
obbTree.BuildLocator()
pointsVTKintersection = vtk.vtkPoints()
obbTree.IntersectWithLine(pSource, pTarget, pointsVTKintersection, None)
pointsVTKIntersectionData = pointsVTKintersection.GetData()
noPointsVTKIntersection = pointsVTKIntersectionData.GetNumberOfTuples()
pointsIntersection = []
for idx in range(noPointsVTKIntersection):
_tup = pointsVTKIntersectionData.GetTuple3(idx)
pointsIntersection.append(_tup)
print pointsIntersection
if not self.isploted:
axes = vtk.vtkAxesActor()
self.marker = vtk.vtkOrientationMarkerWidget()
self.marker.SetInteractor( self.widget._Iren )
self.marker.SetOrientationMarker( axes )
self.marker.SetViewport(0.75,0,1,0.25)
self.marker.SetEnabled(1)
self.ren.ResetCamera()
self.ren.ResetCameraClippingRange()
#cam = self.ren.GetActiveCamera()
self.cam.Elevation(50)
self.cam.Azimuth(40)
#cam.SetPosition(0,0,1)
#cam.SetFocalPoint(0,0,-50)
self.isploted = True
self.ren.Render()
clipper.SetValue(0)
clipMapper = vtk.vtkPolyDataMapper()
clipMapper.SetInputConnection(clipper.GetOutputPort())
clipMapper.ScalarVisibilityOff()
backProp = vtk.vtkProperty()
backProp.SetDiffuseColor(GetRGBColor('tomato'))
clipActor = vtk.vtkActor()
clipActor.SetMapper(clipMapper)
clipActor.GetProperty().SetColor(GetRGBColor('peacock'))
clipActor.SetBackfaceProperty(backProp)
# now extract feature edges
boundaryEdges = vtk.vtkFeatureEdges()
boundaryEdges.SetInputConnection(clipper.GetOutputPort())
boundaryEdges.BoundaryEdgesOn()
boundaryEdges.FeatureEdgesOff()
boundaryEdges.NonManifoldEdgesOff()
boundaryClean = vtk.vtkCleanPolyData()
boundaryClean.SetInputConnection(boundaryEdges.GetOutputPort())
boundaryStrips = vtk.vtkStripper()
boundaryStrips.SetInputConnection(boundaryClean.GetOutputPort())
boundaryStrips.Update()
boundaryPoly = vtk.vtkPolyData()
boundaryPoly.SetPoints(boundaryStrips.GetOutput().GetPoints())
boundaryPoly.SetPolys(boundaryStrips.GetOutput().GetLines())
foldingNormals.SetInputData(folding)
else:
foldingNormals.SetInput(folding)
foldingNormals.SplittingOff()
foldingMapper.SetInputConnection(foldingNormals.GetOutputPort())
foldingMapper.SetScalarRange(0, 24)
foldingMapper.SetLookupTable(lut)
foldingMapper.SetScalarModeToUseCellData()
foldingActor.SetMapper(foldingMapper)
# foldingActor.GetProperty().EdgeVisibilityOn()
# foldingActor.GetProperty().SetOpacity(0.7)
ren.AddActor(foldingActor)
kq_to_folding = [[a for a in folding_to_kq if folding_to_kq[a] == i] for i in range(surface.GetNumberOfPoints())]
boundary_extractor = vtk.vtkFeatureEdges()
boundary_extractor.FeatureEdgesOff()
if vtk.vtkVersion.GetVTKMajorVersion() >= 6:
boundary_extractor.SetInputData(folding)
else:
boundary_extractor.SetInput(folding)
boundary_extractor.Update()
boundary_scalars = vtk.vtkIntArray()
for iEdge in range(boundary_extractor.GetOutput().GetNumberOfCells()):
boundary_scalars.InsertNextValue(iEdge)
boundary_extractor.GetOutput().GetCellData().SetScalars(boundary_scalars)
show_boundary = True
boundary = vtk.vtkPolyData()
if show_boundary:
cutter = vtk.vtkCutter()
cutter.SetCutFunction(p)
cutter.SetInput(data)
cutter.Update()
out = cutter.GetOutput()
# Save cut data to file
# Comment this if you dont want the cut-plane data
cfile = "cut" + str(int(ncut)) + ".vtp"
w = vtk.vtkXMLPolyDataWriter()
w.SetFileName(cfile)
w.SetInput(out)
w.Write()
# Extract boundary, includes outer boundary
bd = vtk.vtkFeatureEdges()
bd.BoundaryEdgesOn()
bd.ColoringOff()
bd.FeatureEdgesOff()
bd.ManifoldEdgesOff()
bd.AddInput(out)
bd.Update()
shape = bd.GetOutput()
if shape.GetNumberOfPoints() == 0:
print "No points found, something wrong !!!"
# Now extract only the shape not the outer boundary
g = vtk.vtkGeometryFilter()
g.ExtentClippingOn()
g.SetExtent(xmin, xmax, ymin, ymax, zmin, zmax)
g.SetInput(shape)
def testICPTransform(self):
renWin = vtk.vtkRenderWindow()
#iren = vtk.vtkRenderWindowInteractor()
#iren.SetRenderWindow(renWin)
# Create objects
sscale = {2:[0.7, 0.7, 0.7],
3:[0.5, 0.5, 0.5]}
scenter = {2:[-0.25, 0.25, 0.0],
3:[ 0.4, -0.3, 0.0]}
scolors = {2:[0.2, 0.6, 0.1],
3:[0.1, 0.2, 0.6]}
s = dict() # The super quadric sources
for sidx in range(1, 4):
s.update({sidx:vtk.vtkSuperquadricSource()})
s[sidx].ToroidalOff()
s[sidx].SetThetaResolution(20)
s[sidx].SetPhiResolution(20)
s[sidx].SetPhiRoundness(0.7 + (sidx - 2) * 0.4)
s[sidx].SetThetaRoundness(0.85 + (sidx - 1) * 0.4)
if sidx in sscale:
s[sidx].SetScale(sscale[sidx])
if sidx in scenter:
s[sidx].SetCenter(scenter[sidx])
s[sidx].Update()
ren = dict() # Renderers
sm = dict() # Mappers for the super quadric source
sa = dict() # Actors for the super quadric source
fe = dict() # Feature edges
fem = dict() # Feature edges mappers
fea = dict() # Feature edges actors
icp = dict() # Iterated closest point transforms
# Create the renderers
for ridx in range(1, 4):
ren.update({ridx: vtk.vtkRenderer()})
ren[ridx].SetViewport((ridx - 1) / 3.0, 0.0, ridx / 3.0, 1.0)
ren[ridx].SetBackground(0.7, 0.8, 1.0)
cam = ren[ridx].GetActiveCamera()
cam.SetPosition(1.7, 1.4, 1.7)
renWin.AddRenderer(ren[ridx])
# renderer 1 has all 3 objects, render i has object 1 and i (i=2, 3)
# add actors (corresponding to the objects) to each renderer
# and ICP transforms from objects i or to 1.
# object 1 has feature edges too.
for sidx in range(1, 4):
if ridx == 1 or sidx == 1 or ridx == sidx:
sm.update({ridx:{sidx:vtk.vtkPolyDataMapper()}})
sm[ridx][sidx].SetInputConnection(s[sidx].GetOutputPort())
sa.update({ridx:{sidx:vtk.vtkActor()}})
sa[ridx][sidx].SetMapper(sm[ridx][sidx])
prop = sa[ridx][sidx].GetProperty()
if sidx in scolors:
prop.SetColor(scolors[sidx])
if sidx == 1:
prop.SetOpacity(0.2)
fe.update({ridx:{sidx:vtk.vtkFeatureEdges()}})
src = s[sidx]
fe[ridx][sidx].SetInputConnection(src.GetOutputPort())
fe[ridx][sidx].BoundaryEdgesOn()
fe[ridx][sidx].ColoringOff()
fe[ridx][sidx].ManifoldEdgesOff()
fem.update({ridx:{sidx:vtk.vtkPolyDataMapper()}})
fem[ridx][sidx].SetInputConnection(fe[ridx][sidx].GetOutputPort())
fem[ridx][sidx].SetResolveCoincidentTopologyToPolygonOffset()
fea.update({ridx:{sidx:vtk.vtkActor()}})
fea[ridx][sidx].SetMapper(fem[ridx][sidx])
ren[ridx].AddActor(fea[ridx][sidx])
ren[ridx].AddActor(sa[ridx][sidx])
if ridx > 1 and ridx == sidx:
icp.update({ridx:{sidx:vtk.vtkIterativeClosestPointTransform()}})
icp[ridx][sidx].SetSource(s[sidx].GetOutput())
icp[ridx][sidx].SetTarget(s[1].GetOutput())
icp[ridx][sidx].SetCheckMeanDistance(1)
icp[ridx][sidx].SetMaximumMeanDistance(0.001)
icp[ridx][sidx].SetMaximumNumberOfIterations(30)
icp[ridx][sidx].SetMaximumNumberOfLandmarks(50)
sa[ridx][sidx].SetUserTransform(icp[ridx][sidx])
icp[3][3].StartByMatchingCentroidsOn()
renWin.SetSize(400, 100)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin);
renWin.Render()
img_file = "TestICPTransform.png"
vtk.test.Testing.compareImage(iRen.GetRenderWindow(), vtk.test.Testing.getAbsImagePath(img_file), threshold=25)
vtk.test.Testing.interact()
