def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkExtractSelectedPolyDataIds(), 'Processing.',
('vtkPolyData', 'vtkSelection'), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
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 LoadData(self):
# Remove all old actors from renderer
self.renderer.RemoveAllViewProps()
# Put back nav menu
menu_actor_list = self.menu.GetActorList()
for m_actor in menu_actor_list:
self.renderer.AddActor(m_actor)
tree = self.ds.GetTree()
# Parallel pipeline with no shrinkage to get TCoords
self.TreeLevels = vtk.vtkTreeLevelsFilter()
self.TreeLevels.SetInput(tree)
VertexDegree = vtk.vtkVertexDegree()
VertexDegree.SetInputConnection(self.TreeLevels.GetOutputPort(0))
TreeAggregation = vtk.vtkTreeFieldAggregator()
TreeAggregation.LeafVertexUnitSizeOff()
TreeAggregation.SetField('size')
TreeAggregation.SetInputConnection(VertexDegree.GetOutputPort(0))
# Layout without shrinkage for generating texture coordinates
strategy = vtk.vtkStackedTreeLayoutStrategy()
strategy.UseRectangularCoordinatesOn()
strategy.SetRootStartAngle(0.0)
strategy.SetRootEndAngle(15.0)
strategy.SetRingThickness(self.THICK) # layer thickness
strategy.ReverseOn()
strategy.SetShrinkPercentage(0.0)
layout = vtk.vtkAreaLayout()
layout.SetLayoutStrategy(strategy)
layout.SetInputConnection(TreeAggregation.GetOutputPort(0))
layout.SetAreaArrayName("area")
layout.SetSizeArrayName("num_in_vertex")
areapoly = vtk.vtkTreeMapToPolyData()
areapoly.SetInputConnection(layout.GetOutputPort(0))
areapoly.SetAddNormals(0)
areapoly.SetInputArrayToProcess( 0, 0, 0, 4, "area") # 4 = vtkDataObject::FIELD_ASSOCIATION_VERTICES
texPlane = vtk.vtkTextureMapToPlane()
texPlane.SetInputConnection(areapoly.GetOutputPort(0))
texPlane.AutomaticPlaneGenerationOn()
texPlane.Update()
# Layout with shrinkage for generating geometry
strategy0 = vtk.vtkStackedTreeLayoutStrategy()
strategy0.UseRectangularCoordinatesOn()
strategy0.SetRootStartAngle(0.0)
strategy0.SetRootEndAngle(15.0)
strategy0.SetRingThickness(self.THICK) # layer thickness
strategy0.ReverseOn()
strategy0.SetShrinkPercentage(self.SHRINK)
layout0 = vtk.vtkAreaLayout()
layout0.SetLayoutStrategy(strategy0)
layout0.SetInputConnection(TreeAggregation.GetOutputPort(0))
layout0.SetAreaArrayName("area")
layout0.SetSizeArrayName("num_in_vertex")
areapoly0 = vtk.vtkTreeMapToPolyData()
areapoly0.SetAddNormals(0)
areapoly0.SetInputConnection(layout0.GetOutputPort(0))
areapoly0.SetInputArrayToProcess( 0, 0, 0, 4, "area") # 4 = vtkDataObject::FIELD_ASSOCIATION_VERTICES
areapoly0.Update()
# Copy over texture coordinates
def transferTCoords():
input = paf.GetInputDataObject(0,0)
refin = paf.GetInputList().GetItem(0)
output = paf.GetPolyDataOutput()
TCorig = refin.GetPointData().GetTCoords()
TC = vtk.vtkFloatArray()
TC.SetNumberOfComponents(TCorig.GetNumberOfComponents())
TC.SetNumberOfTuples(TCorig.GetNumberOfTuples())
TC.SetName('Texture Coordinates')
for ii in range(TCorig.GetNumberOfTuples()):
ff = TCorig.GetTuple2(ii)
TC.SetTuple2(ii,ff[0],ff[1])
output.GetPointData().AddArray(TC)
output.GetPointData().SetActiveTCoords('Texture Coordinates')
paf = vtk.vtkProgrammableAttributeDataFilter()
paf.SetInput(areapoly0.GetOutput())
paf.AddInput(texPlane.GetOutput())
paf.SetExecuteMethod(transferTCoords)
# Need to find proper ordering of wavelet coeffs based on icicle layout
# tree.GetVertexData().GetArray('area') is 4-component (Xmin,Xmax,Ymin,Ymax)
print 'Reordering wavelet coeffs'
out_polys = areapoly.GetOutputDataObject(0)
isleaf = VN.vtk_to_numpy(out_polys.GetCellData().GetArray('leaf'))
poly_bounds = VN.vtk_to_numpy(out_polys.GetCellData().GetArray('area'))
vertex_ids = VN.vtk_to_numpy(out_polys.GetCellData().GetArray('vertex_ids'))
self.LeafIds = vertex_ids[isleaf>0]
self.LeafXmins = poly_bounds[isleaf>0,0]
self.XOrderedLeafIds = self.LeafIds[self.LeafXmins.argsort()]
# Grab texture images and color map
self.GrabTextureImagesAndLUT()
# For each node and corresponding image data in self.WCimageDataList, need to create a texture,
# then pull out the correct rectangle from areapoly0 (using vtkExtractSelectedPolyDataIds
# and create a mapper and actor and apply the texture.
self.texture_list = []
self.tex_mapper_list = []
self.tex_actor_list = []
for ii in range(len(self.WCimageDataList)):
# Set up texture with lookup table for matrix polys
tex = vtk.vtkTexture()
tex.SetInput(self.WCimageDataList[ii])
tex.SetLookupTable(self.lut)
self.texture_list.append(tex)
# Grab correct poly out of areapoly0
sel = vtk.vtkSelection()
node = vtk.vtkSelectionNode()
node.SetContentType(4) # 4 = indices
node.SetFieldType(0) # 0 = cell
id_array = N.array([ii],dtype='int64')
id_list = VN.numpy_to_vtkIdTypeArray(id_array)
node.SetSelectionList(id_list)
sel.AddNode(node)
ext_id_poly = vtk.vtkExtractSelectedPolyDataIds()
ext_id_poly.SetInput(1, sel)
ext_id_poly.SetInputConnection(0, areapoly0.GetOutputPort(0))
# ext_id_poly.Update()
# print ext_id_poly.GetOutput()
poly_tm = vtk.vtkTextureMapToPlane()
poly_tm.SetInputConnection(ext_id_poly.GetOutputPort(0))
poly_tm.AutomaticPlaneGenerationOn()
poly_tm.Update()
# Separate mapper and actor for textured polys
map2 = vtk.vtkPolyDataMapper()
map2.SetInputConnection(poly_tm.GetOutputPort(0))
map2.ScalarVisibilityOff()
self.tex_mapper_list.append(map2)
act2 = vtk.vtkActor()
act2.SetMapper(self.tex_mapper_list[ii])
act2.SetTexture(self.texture_list[ii])
act2.GetProperty().SetColor(1,1,1)
act2.SetPickable(0)
act2.SetPosition(0,0,0.1) # ???
self.tex_actor_list.append(act2)
# Add textured polys to the view
self.renderer.AddActor(self.tex_actor_list[ii])
# Layout with shrinkage for generating outline geometry for showing selections
self.applycolors1 = vtk.vtkApplyColors()
self.applycolors1.SetInputConnection(0,layout0.GetOutputPort(0))
self.applycolors1.AddInputConnection(1,self.output_link.GetOutputPort(0))
self.applycolors1.SetDefaultPointColor(self.theme.GetPointColor())
self.applycolors1.SetDefaultPointOpacity(self.theme.GetPointOpacity())
self.applycolors1.SetSelectedPointColor(self.theme.GetSelectedPointColor())
self.applycolors1.SetSelectedPointOpacity(self.theme.GetSelectedPointOpacity())
self.areapoly1 = vtk.vtkTreeMapToPolyData()
self.areapoly1.SetInputConnection(self.applycolors1.GetOutputPort(0))
self.areapoly1.SetAddNormals(0)
self.areapoly1.SetInputArrayToProcess( 0, 0, 0, 4, "area") # 4 = vtkDataObject::FIELD_ASSOCIATION_VERTICES
# Separate mapper and actor for icicle polys outlines (pickable)
map = vtk.vtkPolyDataMapper()
map.SetInputConnection(self.areapoly1.GetOutputPort(0))
map.SetScalarModeToUseCellFieldData()
map.SelectColorArray("vtkApplyColors color")
map.SetScalarVisibility(True)
act = vtk.vtkActor()
act.SetMapper(map)
act.GetProperty().SetColor(1,1,1)
act.SetPickable(True)
act.SetPosition(0,0,0)
act.GetProperty().SetRepresentationToWireframe()
act.GetProperty().SetLineWidth(4.0)
self.icicle_actor = act
# Add actor for selection highlight outlines
self.renderer.AddActor(act)
# Now need to set up data for generating "selection lines" which come from
# xy or pcoords chart. Basic method is to create a new scalar array out of x-coord
# of the texture coordinates, then do a Delaunay2D on the shrunken polys and contour
# that at values obtained by finding what normalized distance along data set are
# selected pedigree ids.
self.calc = vtk.vtkArrayCalculator()
self.calc.SetInputConnection(paf.GetOutputPort())
self.calc.SetAttributeModeToUsePointData()
self.calc.AddScalarVariable("tcoords_X", "Texture Coordinates", 0)
self.calc.SetFunction("tcoords_X")
self.calc.SetResultArrayName("tcx")
# self.calc.Update()
# print VN.vtk_to_numpy(self.calc.GetOutput().GetPointData().GetArray('tcx'))
self.group_contour = vtk.vtkContourFilter()
self.group_contour.SetInputConnection(self.calc.GetOutputPort(0))
self.group_contour.SetInputArrayToProcess(0,0,0,0,'tcx')
self.highlight_contour = vtk.vtkContourFilter()
self.highlight_contour.SetInputConnection(self.calc.GetOutputPort(0))
self.highlight_contour.SetInputArrayToProcess(0,0,0,0,'tcx')
# Separate mapper and actor group selection (pcoords or xy) lines
map3 = vtk.vtkPolyDataMapper()
map3.SetInputConnection(self.group_contour.GetOutputPort(0))
map3.SetScalarVisibility(0)
act3 = vtk.vtkActor()
act3.SetMapper(map3)
act3.SetPickable(False)
act3.SetPosition(0,0,0.2)
act3.GetProperty().SetRepresentationToWireframe()
act3.GetProperty().SetLineWidth(2.0)
act3.GetProperty().SetColor(1,0,0)
act3.GetProperty().SetOpacity(0.6)
self.group_actor = act3
# Add actor for selection highlight outlines
self.renderer.AddActor(act3)
# Separate mapper and actor for individual (image_flow) selection highlight
map4 = vtk.vtkPolyDataMapper()
map4.SetInputConnection(self.highlight_contour.GetOutputPort(0))
map4.SetScalarVisibility(0)
act4 = vtk.vtkActor()
act4.SetMapper(map4)
act4.SetPickable(False)
act4.SetPosition(0,0,0.25)
act4.GetProperty().SetRepresentationToWireframe()
act4.GetProperty().SetLineWidth(3.0)
act4.GetProperty().SetColor(0,0.5,1)
act4.GetProperty().SetOpacity(0.6)
self.highlight_actor = act4
# Add actor for selection highlight outlines
self.renderer.AddActor(act4)
# Get Ordered fractional positions for pedigree ids (for setting contour values)
self.ped_id_fracs = self.ds.GetIdsFractionalPosition(self.XOrderedLeafIds)
# Clear out selections on data change
self.output_link.GetCurrentSelection().RemoveAllNodes()
self.output_link.InvokeEvent("AnnotationChangedEvent")
self.renderer.ResetCamera(self.icicle_actor.GetBounds())
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')
