# Background vertices
vertGlyph = vtk.vtkVertexGlyphFilter()
vertGlyph.SetInputConnection(0, edgeLayout.GetOutputPort(0))
vertexMapper = vtk.vtkPolyDataMapper()
vertexMapper.SetInputConnection(vertGlyph.GetOutputPort(0))
vertexActor = vtk.vtkActor()
vertexActor.SetMapper(vertexMapper)
vertexActor.GetProperty().SetPointSize(4)
vertexActor.GetProperty().SetOpacity(0.5)
vertexActor.GetProperty().SetColor(0.6, 0.6, 0.6)
vertexActor.SetPosition(0, 0, -0.004)
# ----------
# Vertex index labels
labelMapper = vtk.vtkDynamic2DLabelMapper()
# labelMapper.SetInputConnection(0, graphPoly.GetOutputPort(0)) # label background vertices
labelMapper.SetInputConnection(0, subgraph.GetOutputPort(0)) # label basis function vertices
labelMapper.SetLabelModeToLabelFieldData()
labelMapper.SetFieldDataName("label")
labelMapper.SetLabelFormat("%s")
labelMapper.GetLabelTextProperty().SetColor(0.0, 0.0, 0.0)
labelActor = vtk.vtkActor2D()
labelActor.SetMapper(labelMapper)
# ----------
# MultiScale Graph Edges
print 'Building all multi-scale graphs...'
msGraphList = range(minMSLevel) # will not be using 0 or 1 element for now
for ll in range(minMSLevel,levelMax+1):
def loadGraph():
# ----------
# Load and construct whole graph and multi-resolution data from Matlab structure
dataDir = '/Users/emonson/Programming/Matlab/EMonson/Fodava/DocumentAnalysis/Analysis/'
filename = dataDir + 'X20_042709b.mat'
# filename = '/Users/emonson/Programming/Python/VTK/X20_040609b.mat'
X = scipy.io.loadmat(filename)
# Get graph structure G out of matlab variables
G = X['G']
# ----------
# Set multi-resolution level bounds in GUI sliders
levelMax = G.Tree.shape[0]-1
ui_window.hSlider_level.setMinimum(1)
ui_window.hSlider_level.setMaximum(levelMax)
ui_window.spinBox_level.setMinimum(1)
ui_window.spinBox_level.setMaximum(levelMax)
# Start setting up basis function for display as subgraph
ExtBasis = GTree[level,0]['ExtBasis'][0][0][0]
basisMax = ExtBasis.shape[1]-1 # zero-based indices
# Set particular level basis function bounds in GUI sliders
ui_window.hSlider_basisIndex.setMinimum(0)
ui_window.hSlider_basisIndex.setMaximum(basisMax)
ui_window.spinBox_basisIndex.setMinimum(0)
ui_window.spinBox_basisIndex.setMaximum(basisMax)
# Build table which will become graph
table = vtk.vtkTable()
col0 = vtk.vtkIntArray()
col0.SetName('index1')
col1 = vtk.vtkIntArray()
col1.SetName('index2')
val = vtk.vtkDoubleArray()
val.SetName('weight')
Tmat = G.T
# Tmat = G.W
for ii in range(Tmat.nzmax):
col0.InsertNextValue(Tmat.rowcol(ii)[0])
col1.InsertNextValue(Tmat.rowcol(ii)[1])
val.InsertNextValue(abs(Tmat.getdata(ii)))
table.AddColumn(col0)
table.AddColumn(col1)
table.AddColumn(val)
# Vertex links need to be done with index2 first or indexing won't be right...
# TODO: Make this foolproof so that graph always ends up with correct ordering of indices...
tgraph = vtk.vtkTableToGraph()
tgraph.SetInput(table)
tgraph.AddLinkVertex('index2', 'stuff', False)
tgraph.AddLinkVertex('index1', 'stuff', False)
tgraph.AddLinkEdge('index2', 'index1')
rawGraph = tgraph.GetOutput()
rawGraph.Update()
# print graph
# Load and assign whole graph pre-layout coordinates
ptsFile = os.path.splitext(filename)[0] + '_pts.vtp'
if os.path.exists(ptsFile):
polyreader = vtk.vtkXMLPolyDataReader()
polyreader.SetFileName(ptsFile)
polyreader.Update()
pts = polyreader.GetOutput().GetPoints()
rawGraph.SetPoints(pts)
# print pts
strategy = vtk.vtkPassThroughLayoutStrategy()
layout = vtk.vtkGraphLayout()
layout.SetInput(rawGraph)
layout.SetLayoutStrategy(strategy)
edgeLayout = vtk.vtkEdgeLayout()
edgeStrategy = vtk.vtkArcParallelEdgeStrategy()
edgeStrategy.SetNumberOfSubdivisions(50)
edgeLayout.SetInputConnection(layout.GetOutputPort())
edgeLayout.SetLayoutStrategy(edgeStrategy)
graph = edgeLayout.GetOutput()
graph.Update()
# --------
# Add ExtBasis to graph data & Select particular basis function
# print 'ExtBasis shape: ' + str(ExtBasis[:,basisNum].data.shape) + ' (level,basis) (' + str(level) + ',' + str(basisNum) + ')'
# Indexing of ExtBasis is backwards from graph, so need to reverse with [::-1]
# and array not "contiguous" if don't do .copy()
Esub = ExtBasis[:,basisNum].data[::-1].copy()
EsubSq = Esub**2
# Esub = N.random.random(ExtBasis[:,basisNum].data.shape[0])
# SubIdxs = (Esub > 0.001).nonzero()
# SubIdxs = (Esub**2 > 0.8).nonzero()
# Set ExtBasis vertex data from numpy array
basisFunc = VN.numpy_to_vtk(Esub)
basisFunc.SetName('ExtBasis')
basisFuncSq = VN.numpy_to_vtk(EsubSq)
basisFuncSq.SetName('ExtBasisSq')
vertexData = graph.GetVertexData()
vertexData.AddArray(basisFunc)
vertexData.AddArray(basisFuncSq)
selection = vtk.vtkSelectionSource()
selection.SetContentType(7) # vtkSelection::THRESHOLDS
# selection.SetContentType(2) # vtkSelection::PEDIGREE_IDS
selection.SetFieldType(3) # vtkSelection::VERTEX
selection.SetArrayName("ExtBasisSq")
selection.AddThreshold(basisCutoff, 10)
# TODO: There was something wrong with the indexing in the PEDIGREE_IDS selection...
# for ii in SubIdxs[0]:
# selection.AddID(0,ii)
minmax = "(%3.2e, %3.2e)" % (EsubSq.min(), EsubSq.max())
ui_window.label_basisCutoff_minmax.setText(minmax)
selection.Update()
# ----------
# Back to pipeline
degree = vtk.vtkVertexDegree()
degree.SetInput(graph)
subgraph = vtk.vtkExtractSelectedGraph()
subgraph.SetRemoveIsolatedVertices(False)
subgraph.SetInputConnection(degree.GetOutputPort())
subgraph.SetSelectionConnection(selection.GetOutputPort())
# +++++++++++++
graphToPoly = vtk.vtkGraphToPolyData()
graphToPoly.SetInputConnection(subgraph.GetOutputPort())
edgeMapper = vtk.vtkPolyDataMapper()
edgeMapper.SetInputConnection(graphToPoly.GetOutputPort())
edgeMapper.SetScalarModeToUseCellData()
edgeMapper.SetScalarVisibility(False)
edgeMapper.SetImmediateModeRendering(True)
edgeActor = vtk.vtkActor()
edgeActor.SetMapper(edgeMapper)
edgeActor.SetPosition(0, 0, -0.003);
lut = vtk.vtkLookupTable()
lutNum = 256
lut.SetNumberOfTableValues(lutNum)
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)
vertGlyph = vtk.vtkVertexGlyphFilter()
vertGlyph.SetInputConnection(subgraph.GetOutputPort())
vertMapper = vtk.vtkPolyDataMapper()
vertMapper.SetInputConnection(vertGlyph.GetOutputPort())
vertMapper.SetImmediateModeRendering(True)
vertMapper.SetScalarModeToUsePointFieldData()
vertMapper.SetLookupTable(lut)
vertMapper.SelectColorArray('ExtBasis')
vertMapper.Update()
vertRange = vertMapper.GetInput().GetPointData().GetArray(vertMapper.GetArrayName()).GetRange()
vertMapper.SetScalarRange(-1.0*vertRange[1], vertRange[1])
vertActor = vtk.vtkActor()
vertActor.SetMapper(vertMapper)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetScalarVisibility(False)
outlineMapper.SetImmediateModeRendering(True)
outlineMapper.SetInputConnection(vertGlyph.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.PickableOff()
outlineActor.SetPosition(0, 0, -0.001)
outlineActor.GetProperty().SetRepresentationToWireframe()
outlineActor.SetMapper(outlineMapper)
# Create an Actor Collection for applying visibility to group
basisActorCollection = vtk.vtkActorCollection()
basisActorCollection.AddItem(vertActor)
# basisActorCollection.AddItem(edgeActor)
basisActorCollection.AddItem(outlineActor)
# Apply a theme to the views
theme = vtk.vtkViewTheme.CreateMellowTheme()
theme.SetLineWidth(3)
theme.SetPointSize(5)
theme.SetSelectedCellColor(1,1,1)
theme.SetSelectedPointColor(1,1,1)
theme.SetOutlineColor(0.8, 0.8, 0.8)
# theme.SetPointColor(0.9, 0.7, 0.3)
theme.SetCellColor(0.9, 0.7, 0.3)
# theme.SetPointOpacity(0.5)
# theme.SetPointHueRange(0.0, 0.15)
# theme.SetPointSaturationRange(0.6, 0.8)
# theme.SetPointValueRange(0.4,0.8)
# theme.SetPointAlphaRange(0.2,0.8)
# theme.SetPointAlphaRange(1.0,1.0)
# Apply theme
# vertActor.GetProperty().SetColor(theme.GetPointColor())
# vertActor.GetProperty().SetOpacity(theme.GetPointOpacity())
vertActor.GetProperty().SetPointSize(theme.GetPointSize())
outlineActor.GetProperty().SetPointSize(vertActor.GetProperty().GetPointSize()+2)
outlineActor.GetProperty().SetColor(theme.GetOutlineColor())
outlineActor.GetProperty().SetOpacity(theme.GetPointOpacity())
edgeActor.GetProperty().SetColor(theme.GetCellColor())
edgeActor.GetProperty().SetOpacity(theme.GetCellOpacity())
edgeActor.GetProperty().SetLineWidth(theme.GetLineWidth())
# ----------
# Background graph skeleton
graphMapper = vtk.vtkGraphMapper()
graphMapper.SetInputConnection(0, degree.GetOutputPort(0))
# Apply a theme to the background graph
gtheme = vtk.vtkViewTheme()
gtheme.SetLineWidth(1)
gtheme.SetPointSize(0)
gtheme.SetCellColor(0.8, 0.8, 0.8)
gtheme.SetCellOpacity(0.2)
gtheme.SetOutlineColor(0.8, 0.8, 0.8)
gtheme.SetPointColor(0.8, 0.8, 0.8)
gtheme.SetPointOpacity(0.0)
graphMapper.ApplyViewTheme(gtheme)
graphActor = vtk.vtkActor()
graphActor.SetMapper(graphMapper)
graphActor.SetPosition(0,0,-0.005)
# ----------
# Background vertices
graphPoly = vtk.vtkGraphToPolyData()
graphPoly.SetInputConnection(0, tgraph.GetOutputPort(0))
vertGlyph = vtk.vtkGlyph3D()
vertGlyph.SetInputConnection(0, graphPoly.GetOutputPort())
glyphSource = vtk.vtkGlyphSource2D()
glyphSource.SetGlyphTypeToVertex()
# glyphSource.SetGlyphTypeToCircle()
# glyphSource.SetScale(0.025)
vertGlyph.SetInputConnection(1, glyphSource.GetOutputPort())
vertexMapper = vtk.vtkPolyDataMapper()
vertexMapper.SetInputConnection(vertGlyph.GetOutputPort())
vertexActor = vtk.vtkActor()
vertexActor.SetMapper(vertexMapper)
vertexActor.GetProperty().SetPointSize(4)
vertexActor.GetProperty().SetOpacity(0.5)
vertexActor.GetProperty().SetColor(0.6, 0.6, 0.6)
vertexActor.SetPosition(0, 0, -0.004)
# ----------
# Vertex index labels
labelMapper = vtk.vtkDynamic2DLabelMapper()
labelMapper.SetInputConnection(0, graphPoly.GetOutputPort(0))
labelMapper.SetLabelModeToLabelFieldData()
labelMapper.SetFieldDataName("label")
labelMapper.SetLabelFormat("%s")
labelMapper.GetLabelTextProperty().SetColor(0.0, 0.0, 0.0)
labelActor = vtk.vtkActor2D()
labelActor.SetMapper(labelMapper)
# ----------
# MultiScale Graph
msGraph = buildSubGraph(level)
msMapper = vtk.vtkGraphMapper()
msMapper.SetInput(msGraph)
msMapper.SetColorEdges(True)
msMapper.SetEdgeColorArrayName('weight')
# Apply a theme to the background graph
mtheme = vtk.vtkViewTheme()
mtheme.SetLineWidth(3)
mtheme.SetPointSize(11)
# mtheme.SetCellColor(0.5, 0.5, 0.7)
# mtheme.SetCellOpacity(0.5)
mtheme.SetOutlineColor(0.8, 0.8, 0.8)
mtheme.SetPointColor(0.3, 0.3, 0.6)
mtheme.SetPointOpacity(1.0)
mtheme.SetCellHueRange(0.67, 0.67)
mtheme.SetCellSaturationRange(0.6, 0.1)
mtheme.SetCellValueRange(0.5,1.0)
mtheme.SetCellAlphaRange(0.2,0.8)
msMapper.ApplyViewTheme(mtheme)
msActor = vtk.vtkActor()
msActor.SetMapper(msMapper)
msActor.SetPosition(0,0,-0.002)
# ----------
# Set up window and add actors
view.SetLayoutStrategyToPassThrough()
# view.ApplyViewTheme(theme)
# view.SetupRenderWindow(win)
view.GetRenderer().SetBackground(theme.GetBackgroundColor())
view.GetRenderer().SetBackground2(theme.GetBackgroundColor2())
view.GetRenderer().SetGradientBackground(True)
view.GetRenderer().AddActor(vertActor)
view.GetRenderer().AddActor(outlineActor)
view.GetRenderer().AddActor(edgeActor)
view.GetRenderer().AddActor(graphActor)
view.GetRenderer().AddActor(vertexActor)
view.GetRenderer().AddActor(labelActor)
view.GetRenderer().AddActor(msActor)
# ----------
# General interactor
isty = vtk.vtkInteractorStyleRubberBand2D()
# RubberBand2D assumes/needs parallel projection ON
view.GetRenderer().GetActiveCamera().ParallelProjectionOn()
iren = view.GetRenderWindow().GetInteractor()
iren.SetInteractorStyle(isty)
# Interactor style must be set before scalar bar can be shown
# view.SetVertexScalarBarVisibility(True)
sbActor = vtk.vtkScalarBarActor()
sbActor.SetLookupTable(vertMapper.GetLookupTable())
sbActor.SetTitle(vertMapper.GetArrayName())
sbActor.SetNumberOfLabels(3)
vertexScalarBar = vtk.vtkScalarBarWidget()
vertexScalarBar.SetScalarBarActor(sbActor)
vertexScalarBar.SetInteractor(iren)
vertexScalarBar.SetDefaultRenderer(view.GetRenderer())
vertexScalarBar.SetCurrentRenderer(view.GetRenderer())
vertexScalarBar.SetEnabled(True)
scalarBarRep = vertexScalarBar.GetRepresentation()
scalarBarRep.SetOrientation(1) # 0 = Horizontal, 1 = Vertical
scalarBarRep.GetPositionCoordinate().SetValue(0.05,0.05)
scalarBarRep.GetPosition2Coordinate().SetValue(0.15,0.25)
# Adding it this way gets it to show up, but it's not interactive
view.GetRenderer().AddActor(sbActor)
view.ResetCamera()
view.Render()
# ----------
# Add Actors to QListWidget to allow check and uncheck for visibility
listItem0 = QtGui.QListWidgetItem()
listItem0.setText('Index Labels')
listItem0.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
labelActor.SetVisibility(0)
listItem0.setCheckState(QtCore.Qt.Unchecked)
# Put actor it in as data in the list widget item
listItem0.setData(QtCore.Qt.UserRole, QtCore.QVariant(labelActor))
ui_window.listWidget.insertItem(0,listItem0)
# Test retrieval of actor from list widget item
# tmpItem = ui_window.listWidget.item(0)
# tmpQtActor = tmpItem.data(QtCore.Qt.UserRole)
# tmpActor = tmpQtActor.toPyObject()
# tmpActor.SetVisibility(0)
# Shorter way to add item to list widget
listItem1 = QtGui.QListWidgetItem('Vertices (background)', ui_window.listWidget)
listItem1.setData(QtCore.Qt.UserRole, QtCore.QVariant(vertexActor))
listItem1.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem1.setCheckState(QtCore.Qt.Checked)
listItem2 = QtGui.QListWidgetItem('Graph (background)', ui_window.listWidget)
listItem2.setData(QtCore.Qt.UserRole, QtCore.QVariant(graphActor))
listItem2.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem2.setCheckState(QtCore.Qt.Checked)
listItem3 = QtGui.QListWidgetItem()
listItem3.setText('Basis Function Vertices')
listItem3.setData(QtCore.Qt.UserRole, QtCore.QVariant(basisActorCollection))
listItem3.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem3.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(1,listItem3)
listItem6 = QtGui.QListWidgetItem()
listItem6.setText('Basis Function Edges')
listItem6.setData(QtCore.Qt.UserRole, QtCore.QVariant(edgeActor))
listItem6.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem6.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(2,listItem6)
listItem4 = QtGui.QListWidgetItem()
listItem4.setText('MultiScale Graph')
listItem4.setData(QtCore.Qt.UserRole, QtCore.QVariant(msActor))
listItem4.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem4.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(3,listItem4)
listItem5 = QtGui.QListWidgetItem()
listItem5.setText('Basis Function Scale Bar')
listItem5.setData(QtCore.Qt.UserRole, QtCore.QVariant(sbActor))
listItem5.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem5.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(3,listItem5)
iren.Initialize()
iren.Start()
