def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkTreeFieldAggregator(), 'Processing.',
('vtkTree',), ('vtkTree',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkTreeFieldAggregator(),
'Processing.', ('vtkTree', ),
('vtkTree', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
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 __init__(self, data_source):
"""Icicle view constructor needs a valid DataSource and will pull data
from it immediately."""
self.ds = data_source
SHRINK = 0.1
THICK = 1.0
tree = self.ds.GetTree()
# Build view
self.view = vtk.vtkIcicleView()
self.view.SetRepresentationFromInput(tree)
self.view.SetAreaSizeArrayName("num_in_vertex")
self.view.SetAreaColorArrayName("scale")
self.view.SetAreaLabelArrayName("blank")
self.view.SetLabelPriorityArrayName("VertexDegree")
self.view.SetAreaLabelVisibility(True)
self.view.SetAreaHoverArrayName("vertex_ids")
self.view.SetDisplayHoverText(True)
self.view.SetShrinkPercentage(SHRINK)
self.view.SetLayerThickness(THICK)
self.view.UseGradientColoringOff()
self.style = vtk.vtkInteractorStyleImage()
self.view.SetInteractorStyle(self.style)
# Parallel pipeline with no shrinkage to get TCoords
TreeLevels = vtk.vtkTreeLevelsFilter()
TreeLevels.SetInput(tree)
VertexDegree = vtk.vtkVertexDegree()
VertexDegree.SetInputConnection(TreeLevels.GetOutputPort(0))
TreeAggregation = vtk.vtkTreeFieldAggregator()
TreeAggregation.LeafVertexUnitSizeOff()
TreeAggregation.SetField('size')
TreeAggregation.SetInputConnection(VertexDegree.GetOutputPort(0))
# Layout with shrinkage for generating geometry
strategy = vtk.vtkStackedTreeLayoutStrategy()
strategy.UseRectangularCoordinatesOn()
strategy.SetRootStartAngle(0.0)
strategy.SetRootEndAngle(15.0)
strategy.SetRingThickness(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 without shrinkage for generating texture coordinates
strategy0 = vtk.vtkStackedTreeLayoutStrategy()
strategy0.UseRectangularCoordinatesOn()
strategy0.SetRootStartAngle(0.0)
strategy0.SetRootEndAngle(15.0)
strategy0.SetRingThickness(THICK) # layer thickness
strategy0.ReverseOn()
strategy0.SetShrinkPercentage(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'))
LeafIds = vertex_ids[isleaf>0]
LeafXmins = poly_bounds[isleaf>0,0]
XOrderedLeafIds = LeafIds[LeafXmins.argsort()]
# And then grab the Wavelet Coefficients matrix sorted according to this
WCimageData = self.ds.GetWaveletCoeffImage(XOrderedLeafIds)
WCrange = N.array(WCimageData.GetPointData().GetScalars().GetRange())
WCext = abs(WCrange.min()) if (abs(WCrange.min()) > abs(WCrange.max())) else abs(WCrange.max())
# print WCext
# Create blue to white to red lookup table
lut = vtk.vtkLookupTable()
lutNum = 256
lut.SetNumberOfTableValues(lutNum)
lut.Build()
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
ctf.AddRGBPoint(0.0, 0, 0, 1.0)
ctf.AddRGBPoint(1.0, 1.0, 0, 0)
for ii,ss in enumerate([float(xx)/float(lutNum) for xx in range(lutNum)]):
cc = ctf.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
lut.SetRange(-WCext,WCext)
# Set up texture with lookup table for matrix polys
tex = vtk.vtkTexture()
tex.SetInput(WCimageData)
tex.SetLookupTable(lut)
# Separate mapper and actor for textured polys
map2 = vtk.vtkPolyDataMapper()
map2.SetInputConnection(paf.GetOutputPort(0))
map2.ScalarVisibilityOff()
act2 = vtk.vtkActor()
act2.SetMapper(map2)
act2.SetTexture(tex)
act2.GetProperty().SetColor(1,1,1)
act2.SetPickable(0)
act2.SetPosition(0,0,0.1)
# Add textured polys to the view
ren = self.view.GetRenderer()
ren.AddActor(act2)
# NOTE: This is the one place I'm still hacking into the view -- to set the
# normal icicle view to wireframe and set the color...
# Ren has an actor2d which is a scalar bar (edge)
acts = ren.GetActors()
# Acts has two actors -- graph blocks (0) and labels (1)
act0 = acts.GetItemAsObject(0)
act0.GetProperty().SetRepresentationToWireframe()
act0.GetProperty().SetLineWidth(3.0)
# Apply a theme to the views
theme = vtk.vtkViewTheme.CreateMellowTheme()
theme.SetPointHueRange(0,0)
theme.SetPointSaturationRange(0.2,0.5)
theme.SetPointValueRange(0.0,0.0)
theme.SetPointAlphaRange(0.0,0.0)
c = N.array([255,204,0])/255.0
theme.SetSelectedPointColor(c[0],c[1],c[2])
theme.SetBackgroundColor(0.1, 0.1, 0.06)
theme.SetBackgroundColor2(0.25, 0.25, 0.2)
self.view.ApplyViewTheme(theme)
theme.FastDelete()
# Connect the annotation link to the icicle representation
rep = self.view.GetRepresentation(0)
# Grab annotation link to monitor selection changes
self.link = rep.GetAnnotationLink()
# If you don't set the FieldType explicitly it ends up as UNKNOWN (as of 21 Feb 2010)
# See vtkSelectionNode doc for field and content type enum values
# enum SelectionContent {
# SELECTIONS, GLOBALIDS, PEDIGREEIDS, VALUES,
# INDICES, FRUSTUM, LOCATIONS, THRESHOLDS,
# BLOCKS
# }
# enum SelectionField {
# CELL, POINT, FIELD, VERTEX,
# EDGE, ROW
# }
# Note: This may be the defaults, anyway, for the IcicleView annotation link
self.link.GetCurrentSelection().GetNode(0).SetFieldType(3) # Vertex
self.link.GetCurrentSelection().GetNode(0).SetContentType(2) # Pedigree Ids
# TEST: Set up callback to test icicle view selection IDs
self.link.AddObserver("AnnotationChangedEvent", self.IcicleSelectionCallback)
self.view.GetRenderer().GetActiveCamera().ParallelProjectionOn()
self.view.ResetCamera()
self.view.Render()
