def convert_cluster_to_volume_with_sz(inpd, volume, sampling_size=0.5):
volume_shape = volume.get_data().shape
new_voxel_data = numpy.zeros(volume_shape)
resampler = vtk.vtkPolyDataPointSampler()
resampler.GenerateEdgePointsOn()
resampler.GenerateVertexPointsOff()
resampler.GenerateInteriorPointsOff()
resampler.GenerateVerticesOff()
resampler.SetDistance(sampling_size)
inpoints = inpd.GetPoints()
inpd.GetLines().InitTraversal()
for lidx in range(0, inpd.GetNumberOfLines()):
ptids = vtk.vtkIdList()
inpd.GetLines().GetNextCell(ptids)
tmpPd = vtk.vtkPolyData()
tmpPoints = vtk.vtkPoints()
tmpCellPtIds = vtk.vtkIdList()
tmpLines = vtk.vtkCellArray()
for pidx in range(0, ptids.GetNumberOfIds()):
point = inpoints.GetPoint(ptids.GetId(pidx))
idx_ = tmpPoints.InsertNextPoint(point)
tmpCellPtIds.InsertNextId(idx_)
tmpLines.InsertNextCell(tmpCellPtIds)
tmpPd.SetLines(tmpLines)
tmpPd.SetPoints(tmpPoints)
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
resampler.SetInputData(tmpPd)
else:
resampler.SetInput(tmpPd)
resampler.Update()
sampledCellPts = resampler.GetOutput().GetPoints()
sampledNpts = resampler.GetOutput().GetNumberOfPoints()
line_tmp_voxel_data = numpy.zeros(volume_shape)
for pidx in range(0, sampledNpts):
point = sampledCellPts.GetPoint(pidx)
point_ijk = apply_affine(numpy.linalg.inv(volume.affine), point)
point_ijk = numpy.rint(point_ijk).astype(numpy.int32)
line_tmp_voxel_data[(point_ijk[0], point_ijk[1],
point_ijk[2])] += 1
new_voxel_data = new_voxel_data + line_tmp_voxel_data
return new_voxel_data
def vtk_mesh_sampling(inputdata,
distance=150,
generate_vertex_points=True,
generate_edge_points=True,
generate_face_points=True,
verbose=False):
"""Sample points on a mesh from vertices, edges and faces in a given distance
Arguments:
inputdata (vtk.vtkPolyData): ytk object containing vertices and simplices
distance (float): Set the approximate distance between points. This is an absolute distance measure (default here 150 for safety reasons).
generate_vertex_points (bool): Indicating whether cell vertex points should be output (default True).
generate_edge_points (bool): Indicating whether cell edges should be sampled to produce output points (default True).
generate_face_points (bool): Indicating whether cell interiors should be sampled to produce output points (default True).
verbose (bool): Print out basic statistics (default False).
Returns:
decimatedPoly: vtkPolyData object or pandas.DataFrame of xyz coordinates (depends on input)
"""
if not isinstance(inputdata, vtkPolyData):
raise TypeError(
'Unknown dtype for inputdata! vtk.vtkPolyData expected.')
inputPoly = vtkPolyData()
inputPoly.ShallowCopy(inputdata)
sampler = vtkPolyDataPointSampler()
sampler.SetInputData(inputPoly)
# set parameters
sampler.SetDistance(distance)
sampler.SetGenerateVertexPoints(generate_vertex_points)
sampler.SetGenerateEdgePoints(generate_edge_points)
sampler.SetGenerateInteriorPoints(generate_face_points)
sampler.Update()
sampler_poly = vtkPolyData()
sampler_poly.ShallowCopy(sampler.GetOutput())
if verbose:
print('Points sampled:', sampler_poly.GetNumberOfPoints())
return sampler_poly
def __init__(self, parent=None):
super(VTKFrame, self).__init__(parent)
self.vtkWidget = QVTKRenderWindowInteractor(self)
vl = QtGui.QVBoxLayout(self)
vl.addWidget(self.vtkWidget)
vl.setContentsMargins(0, 0, 0, 0)
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.1, 0.2, 0.4)
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
# Create source
sphereSource = vtk.vtkSphereSource()
sphereSource.SetPhiResolution(50)
sphereSource.SetThetaResolution(50)
sphereSource.Update()
# Sample the sphere
pointSampler = vtk.vtkPolyDataPointSampler()
pointSampler.SetDistance(0.01)
pointSampler.SetInputConnection(sphereSource.GetOutputPort())
pointSampler.Update()
# Visualize
sphereMapper = vtk.vtkPolyDataMapper()
sphereMapper.SetInputConnection(sphereSource.GetOutputPort())
sphereActor = vtk.vtkActor()
sphereActor.SetMapper(sphereMapper)
sampleMapper = vtk.vtkPolyDataMapper()
sampleMapper.SetInputConnection(pointSampler.GetOutputPort())
sampleActor = vtk.vtkActor()
sampleActor.SetMapper(sampleMapper)
sampleActor.GetProperty().SetColor(1, 0, 0)
self.ren.AddActor(sphereActor)
self.ren.AddActor(sampleActor)
self.ren.ResetCamera()
self._initialized = False
def __init__(self, parent = None):
super(VTKFrame, self).__init__(parent)
self.vtkWidget = QVTKRenderWindowInteractor(self)
vl = QtGui.QVBoxLayout(self)
vl.addWidget(self.vtkWidget)
vl.setContentsMargins(0, 0, 0, 0)
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.1, 0.2, 0.4)
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
# Create source
sphereSource = vtk.vtkSphereSource()
sphereSource.SetPhiResolution(50)
sphereSource.SetThetaResolution(50)
sphereSource.Update()
# Sample the sphere
pointSampler = vtk.vtkPolyDataPointSampler()
pointSampler.SetDistance(0.01)
pointSampler.SetInputConnection(sphereSource.GetOutputPort())
pointSampler.Update()
# Visualize
sphereMapper = vtk.vtkPolyDataMapper()
sphereMapper.SetInputConnection(sphereSource.GetOutputPort())
sphereActor = vtk.vtkActor()
sphereActor.SetMapper(sphereMapper)
sampleMapper = vtk.vtkPolyDataMapper()
sampleMapper.SetInputConnection(pointSampler.GetOutputPort())
sampleActor = vtk.vtkActor()
sampleActor.SetMapper(sampleMapper)
sampleActor.GetProperty().SetColor(1, 0, 0)
self.ren.AddActor(sphereActor)
self.ren.AddActor(sampleActor)
self.ren.ResetCamera()
self._initialized = False
# Create a sphere implicit function sphere = vtk.vtkSphereSource() sphere.SetCenter(2, 0, 0) sphere.SetRadius(0.8) sphere.SetThetaResolution(96) sphere.SetPhiResolution(48) # Boolean (union) these together append = vtk.vtkAppendPolyData() append.AddInputConnection(cyl.GetOutputPort()) append.AddInputConnection(plane.GetOutputPort()) append.AddInputConnection(sphere.GetOutputPort()) # Extract points along sphere surface pts = vtk.vtkPolyDataPointSampler() pts.SetInputConnection(append.GetOutputPort()) pts.SetDistance(0.01) pts.Update() # Now generate normals from resulting points curv = vtk.vtkPCACurvatureEstimation() curv.SetInputConnection(pts.GetOutputPort()) curv.SetSampleSize(20) # Time execution timer = vtk.vtkTimerLog() timer.StartTimer() curv.Update() timer.StopTimer() time = timer.GetElapsedTime()
def compute_stat(inpd, volume, sampling_size=None):
volume_data = volume.get_data()
volume_shape = volume.get_data().shape
voxel_size = volume.header.get_zooms()
new_voxel_data = numpy.zeros(volume_shape)
if sampling_size is not None:
resampler = vtk.vtkPolyDataPointSampler()
resampler.GenerateEdgePointsOn()
resampler.GenerateVertexPointsOff()
resampler.GenerateInteriorPointsOff()
resampler.GenerateVerticesOff()
resampler.SetDistance(sampling_size)
value_list = []
inpoints = inpd.GetPoints()
inpd.GetLines().InitTraversal()
for lidx in range(0, inpd.GetNumberOfLines()):
ptids = vtk.vtkIdList()
inpd.GetLines().GetNextCell(ptids)
if sampling_size is not None:
# print '-- sampling with size', sampling_size
tmpPd = vtk.vtkPolyData()
tmpPoints = vtk.vtkPoints()
tmpCellPtIds = vtk.vtkIdList()
tmpLines = vtk.vtkCellArray()
for pidx in range(0, ptids.GetNumberOfIds()):
point = inpoints.GetPoint(ptids.GetId(pidx))
idx_ = tmpPoints.InsertNextPoint(point)
tmpCellPtIds.InsertNextId(idx_)
tmpLines.InsertNextCell(tmpCellPtIds)
tmpPd.SetLines(tmpLines)
tmpPd.SetPoints(tmpPoints)
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
resampler.SetInputData(tmpPd)
else:
resampler.SetInput(tmpPd)
resampler.Update()
sampledCellPts = resampler.GetOutput().GetPoints()
sampledNpts = resampler.GetOutput().GetNumberOfPoints()
else:
# print '-- No sampling'
sampledCellPts = inpoints
sampledNpts = inpd.GetNumberOfPoints()
for pidx in range(0, sampledNpts):
point = sampledCellPts.GetPoint(pidx)
point_ijk = apply_affine(numpy.linalg.inv(volume.affine),
point)
point_ijk = numpy.rint(point_ijk).astype(numpy.int32)
if point_ijk[0] > new_voxel_data.shape[0] or point_ijk[
1] > new_voxel_data.shape[1] or point_ijk[
2] > new_voxel_data.shape[2]:
print('Warning: point', point_ijk,
'is outside the input volumetric map.')
continue
if new_voxel_data[(point_ijk[0], point_ijk[1],
point_ijk[2])] == 0:
new_voxel_data[(point_ijk[0], point_ijk[1],
point_ijk[2])] = 1
value_list.append(volume_data[(point_ijk[0], point_ijk[1],
point_ijk[2])])
if len(value_list) > 0:
mean_v = numpy.mean(value_list)
var_v = numpy.var(value_list)
max_v = numpy.max(value_list)
min_v = numpy.min(value_list)
median_v = numpy.median(value_list)
else:
mean_v = numpy.nan
var_v = numpy.nan
max_v = numpy.nan
min_v = numpy.nan
median_v = numpy.nan
num_voxels = len(value_list)
volume_size = voxel_size[0] * voxel_size[1] * voxel_size[2] * num_voxels
return new_voxel_data, mean_v, var_v, max_v, min_v, median_v, num_voxels, volume_size
# Create a sphere implicit function sphere = vtk.vtkSphereSource() sphere.SetCenter(2,0,0) sphere.SetRadius(0.8) sphere.SetThetaResolution(96) sphere.SetPhiResolution(48) # Boolean (union) these together append = vtk.vtkAppendPolyData() append.AddInputConnection(cyl.GetOutputPort()) append.AddInputConnection(plane.GetOutputPort()) append.AddInputConnection(sphere.GetOutputPort()) # Extract points along sphere surface pts = vtk.vtkPolyDataPointSampler() pts.SetInputConnection(append.GetOutputPort()) pts.SetDistance(0.025) pts.Update() # Now see if we can extract the three objects as separate clusters. extr = vtk.vtkEuclideanClusterExtraction() extr.SetInputConnection(pts.GetOutputPort()) extr.SetRadius(0.1) extr.ColorClustersOn() extr.SetExtractionModeToAllClusters() # Time execution timer = vtk.vtkTimerLog() timer.StartTimer() extr.Update()
def process(self):
if not self.inputCurve:
msg = "No curve."
slicer.util.showStatusMessage(msg, 4000)
slicer.app.processEvents()
logging.info(msg)
return
# Don't do anything if there are 2 points only, already a line.
if (self.inputCurve.GetNumberOfControlPoints() == 2):
# Just signal widget to fill the table with results.
if self.widgetCallback:
self.widgetCallback()
return
# Generate a linear polydata from first and last control point.
numberOfControlPoints = self.inputCurve.GetNumberOfControlPoints()
lineSource = vtk.vtkLineSource()
curveControlPoints = vtk.vtkPoints()
self.inputCurve.GetControlPointPositionsWorld(curveControlPoints)
firstControlPointPosition = curveControlPoints.GetPoint(0)
lastControlPointPosition = curveControlPoints.GetPoint(
numberOfControlPoints - 1)
lineSource.SetPoint1(firstControlPointPosition)
lineSource.SetPoint2(lastControlPointPosition)
lineSource.Update()
linePolyData = lineSource.GetOutput()
# The polydata contains 2 points. Generate more points.
polydataSampler = vtk.vtkPolyDataPointSampler()
polydataSampler.SetInputData(linePolyData)
polydataSampler.Update()
# This is the reference line polydata.
straightLinePolyData = polydataSampler.GetOutput()
startPoint = curveControlPoints.GetPoint(0)
cumulativeDistanceArray = [[0.0, startPoint]]
# Iterate over all curve points, ignoring first and last.
for pointIndex in range(1, numberOfControlPoints - 1):
point = curveControlPoints.GetPoint(pointIndex)
closestIdOnStraightLine = straightLinePolyData.FindPoint(point)
closestPointOnStraightLine = straightLinePolyData.GetPoint(
closestIdOnStraightLine)
cumulativeDistanceOfClosestPoint = vtk.vtkMath.Distance2BetweenPoints(
startPoint, closestPointOnStraightLine)
cumulativeDistanceArray.append(
[cumulativeDistanceOfClosestPoint, closestPointOnStraightLine])
"""
Move each control point to the closest point on the virtual line.
If we have n control points ABCD..., C can be pushed
between A and B on the virtual line. The curve is still valid, though
the points are in zig-zag order. Distances will be less or not meaningful.
Sort the points by distance from start to avoid this.
"""
sortedCumulativeDistanceArray = sorted(
cumulativeDistanceArray, key=lambda distance: distance[0])
for pointIndex in range(1, numberOfControlPoints - 1):
self.inputCurve.SetNthControlPointPosition(
pointIndex, sortedCumulativeDistanceArray[pointIndex][1])
# Signal widget to fill the table with results.
if self.widgetCallback:
self.widgetCallback()
def rasterizeFibers(self,fiberNode,labelNode,labelValue=1,samplingDistance=0.1):
"""Trace through the given fiber bundles and
set the corresponding pixels in the given labelNode volume"""
print('rasterizing...')
rasToIJK = vtk.vtkMatrix4x4()
labelNode.GetRASToIJKMatrix(rasToIJK)
labelArray = slicer.util.array(labelNode.GetID())
polyData = fiberNode.GetPolyData()
cellCount = polyData.GetNumberOfCells()
selection = vtk.vtkSelection()
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
extractor = vtk.vtkExtractSelectedPolyDataIds()
extractor.SetInputData(0, polyData)
resampler = vtk.vtkPolyDataPointSampler()
resampler.GenerateEdgePointsOn()
resampler.GenerateVertexPointsOff()
resampler.GenerateInteriorPointsOff()
resampler.GenerateVerticesOff()
resampler.SetDistance(samplingDistance)
cellIds = vtk.vtkIdTypeArray()
# as a compromise between memory blowup (for large fiberbundles) and not
# eating time in the python loop, resample CELLS_TO_PROCESS at once.
CELLS_TO_PROCESS = 100
for startCellId in xrange(0, cellCount, CELLS_TO_PROCESS):
# generate list of cell Ids to sample
cellIdsAr = numpy.arange(startCellId,
min(cellCount, startCellId + CELLS_TO_PROCESS))
cellIds.SetVoidArray(cellIdsAr, cellIdsAr.size, 1)
# update the selection node to extract those cells
selectionNode.SetSelectionList(cellIds)
selection.AddNode(selectionNode)
selection.Modified()
extractor.SetInputData(1, selection)
extractor.Update()
resampler.SetInputConnection(extractor.GetOutputPort())
resampler.Update()
# get the resampler output
# note: to test without resampling, just use
# `pdSubset = extractor.GetOutput()` instead
pdSubset = resampler.GetOutput()
pointCount = pdSubset.GetNumberOfPoints()
points = pdSubset.GetPoints()
for pointIndex in xrange(pointCount):
point = points.GetPoint(pointIndex)
ijkFloat = rasToIJK.MultiplyPoint(point+(1,))[:3]
# skip any negative indices to avoid wrap-around
# to the other side of the image.
if (any(coord < 0 for coord in ijkFloat)):
continue
ijk = [int(round(element)) for element in ijkFloat]
ijk.reverse()
try:
# paint the voxels
labelArray[tuple(ijk)] = labelValue
except IndexError:
pass
# reset the selection node
selection.RemoveAllNodes()
labelNode.GetImageData().Modified()
labelNode.Modified()
print('finished')
def rasterizeFibers(self,
fiberNode,
labelNode,
labelValue=1,
samplingDistance=0.1):
"""Trace through the given fiber bundles and
set the corresponding pixels in the given labelNode volume"""
print('rasterizing...')
rasToIJK = vtk.vtkMatrix4x4()
labelNode.GetRASToIJKMatrix(rasToIJK)
labelArray = slicer.util.array(labelNode.GetID())
polyData = fiberNode.GetPolyData()
cellCount = polyData.GetNumberOfCells()
selection = vtk.vtkSelection()
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
extractor = vtk.vtkExtractSelectedPolyDataIds()
extractor.SetInputData(0, polyData)
resampler = vtk.vtkPolyDataPointSampler()
resampler.GenerateEdgePointsOn()
resampler.GenerateVertexPointsOff()
resampler.GenerateInteriorPointsOff()
resampler.GenerateVerticesOff()
resampler.SetDistance(samplingDistance)
cellIds = vtk.vtkIdTypeArray()
# as a compromise between memory blowup (for large fiberbundles) and not
# eating time in the python loop, resample CELLS_TO_PROCESS at once.
CELLS_TO_PROCESS = 100
for startCellId in xrange(0, cellCount, CELLS_TO_PROCESS):
# generate list of cell Ids to sample
cellIdsAr = numpy.arange(startCellId,
min(cellCount,
startCellId + CELLS_TO_PROCESS),
dtype=vtk.util.numpy_support.ID_TYPE_CODE)
cellIds.SetVoidArray(cellIdsAr, cellIdsAr.size, 1)
# update the selection node to extract those cells
selectionNode.SetSelectionList(cellIds)
selection.AddNode(selectionNode)
selection.Modified()
extractor.SetInputData(1, selection)
extractor.Update()
resampler.SetInputConnection(extractor.GetOutputPort())
resampler.Update()
# get the resampler output
# note: to test without resampling, just use
# `pdSubset = extractor.GetOutput()` instead
pdSubset = resampler.GetOutput()
pointCount = pdSubset.GetNumberOfPoints()
points = pdSubset.GetPoints()
for pointIndex in xrange(pointCount):
point = points.GetPoint(pointIndex)
ijkFloat = rasToIJK.MultiplyPoint(point + (1, ))[:3]
# skip any negative indices to avoid wrap-around
# to the other side of the image.
if (any(coord < 0 for coord in ijkFloat)):
continue
ijk = [int(round(element)) for element in ijkFloat]
ijk.reverse()
try:
# paint the voxels
labelArray[tuple(ijk)] = labelValue
except IndexError:
pass
# reset the selection node
selection.RemoveAllNodes()
labelNode.GetImageData().Modified()
labelNode.Modified()
print('finished')
ellipFunc.SetXRadius(a)
ellipFunc.SetYRadius(b)
ellipFunc.SetZRadius(c)
ellipFunc.SetN1(N1)
ellipFunc.SetN2(N2)
ellip = vtk.vtkParametricFunctionSource()
ellip.SetParametricFunction(ellipFunc)
ellip.SetUResolution(50)
ellip.SetVResolution(30)
ellip.SetWResolution(30)
ellip.SetScalarModeToNone()
ellip.Update()
d = np.pi / 15 * lam1 * a
resample = vtk.vtkPolyDataPointSampler()
resample.SetInputData(ellip.GetOutput())
resample.SetDistance(d)
resample.Update()
delaunay = vtk.vtkDelaunay3D()
delaunay.SetInputData(resample.GetOutput())
delaunay.Update()
geo = vtk.vtkGeometryFilter()
geo.SetInputData(delaunay.GetOutput())
geo.Update()
decim = vtk.vtkDecimatePro()
decim.SetInputData(geo.GetOutput())
decim.SetTargetReduction(.2)
