def main():
g = vtk.vtkMutableDirectedGraph()
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
g.AddEdge(v1, v2)
g.AddEdge(v2, v3)
g.AddEdge(v3, v1)
# Do layout manually before handing graph to the view.
# This allows us to know the positions of edge arrows.
graphLayoutView = vtk.vtkGraphLayoutView()
layout = vtk.vtkGraphLayout()
strategy = vtk.vtkSimple2DLayoutStrategy()
layout.SetInputData(g)
layout.SetLayoutStrategy(strategy)
# Tell the view to use the vertex layout we provide
graphLayoutView.SetLayoutStrategyToPassThrough()
# The arrows will be positioned on a straight line between two
# vertices so tell the view not to draw arcs for parallel edges
graphLayoutView.SetEdgeLayoutStrategyToPassThrough()
# Add the graph to the view. This will render vertices and edges,
# but not edge arrows.
graphLayoutView.AddRepresentationFromInputConnection(layout.GetOutputPort())
# Manually create an actor containing the glyphed arrows.
graphToPoly = vtk.vtkGraphToPolyData()
graphToPoly.SetInputConnection(layout.GetOutputPort())
graphToPoly.EdgeGlyphOutputOn()
# Set the position (0: edge start, 1: edge end) where
# the edge arrows should go.
graphToPoly.SetEdgeGlyphPosition(0.98)
# Make a simple edge arrow for glyphing.
arrowSource = vtk.vtkGlyphSource2D()
arrowSource.SetGlyphTypeToEdgeArrow()
arrowSource.SetScale(0.1)
arrowSource.Update()
# Use Glyph3D to repeat the glyph on all edges.
arrowGlyph = vtk.vtkGlyph3D()
arrowGlyph.SetInputConnection(0, graphToPoly.GetOutputPort(1))
arrowGlyph.SetInputConnection(1, arrowSource.GetOutputPort())
# Add the edge arrow actor to the view.
arrowMapper = vtk.vtkPolyDataMapper()
arrowMapper.SetInputConnection(arrowGlyph.GetOutputPort())
arrowActor = vtk.vtkActor()
arrowActor.SetMapper(arrowMapper)
graphLayoutView.GetRenderer().AddActor(arrowActor)
graphLayoutView.ResetCamera()
graphLayoutView.Render()
graphLayoutView.GetInteractor().Start()
def createGraph(points):
g = vtk.vtkMutableDirectedGraph()
vertexes = []
alreadyConnected = []
for i in range(0, points.GetNumberOfPoints()):
vertexes.append(g.AddVertex())
alreadyConnected.append(i)
for i in range(0, points.GetNumberOfPoints()):
index = -1
distance = float("inf")
distanceOrder = 0
record = float("inf")
for j in range(0, points.GetNumberOfPoints()):
distance = math.sqrt(
vtk.vtkMath.Distance2BetweenPoints(points.GetPoint(i),
points.GetPoint(j)))
if (distance > 0 and distance < record and alreadyConnected[j] != i
and alreadyConnected[alreadyConnected[j]] != i):
record = distance
index = j
elif (distance > 0 and distance < record):
distanceOrder += 1
if (index != -1 and distanceOrder < 2):
alreadyConnected[i] = index
g.AddGraphEdge(vertexes[i], vertexes[index])
for i in range(0, points.GetNumberOfPoints()):
index = -1
distance = float("inf")
distanceOrder = 0
record = float("inf")
for j in range(0, points.GetNumberOfPoints()):
distance = math.sqrt(
vtk.vtkMath.Distance2BetweenPoints(points.GetPoint(i),
points.GetPoint(j)))
if (distance > 0 and distance < record and alreadyConnected[j] != i
and alreadyConnected[i] != j
and alreadyConnected[alreadyConnected[j]] !=
alreadyConnected[alreadyConnected[i]]):
record = distance
index = j
elif (distance > 0 and distance < record):
distanceOrder += 1
if (index != -1 and distanceOrder < 2):
alreadyConnected[i] = index
g.AddGraphEdge(vertexes[i], vertexes[index])
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(g)
graphLayoutView.SetLayoutStrategy("Simple 2D")
graphLayoutView.ResetCamera()
graphLayoutView.Render()
graphLayoutView.GetLayoutStrategy().SetRandomSeed(0)
graphLayoutView.GetInteractor().Start()
def simpleVtkDiGraph():
g = vtk.vtkMutableDirectedGraph()
# Create 3 vertices
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
# Create a fully connected graph
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v2, v3)
g.AddGraphEdge(v1, v3)
# Create the edge weight array
weights = vtk.vtkDoubleArray()
weights.SetNumberOfComponents(1)
weights.SetName("Weights")
# Set the edge weights
weights.InsertNextValue(1.0)
weights.InsertNextValue(1.0)
weights.InsertNextValue(2.0)
# Add the edge weight array to the graph
g.GetEdgeData().AddArray(weights)
return g
def simpleVtkDiGraph():
g = vtk.vtkMutableDirectedGraph()
# Create 3 vertices
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
# Create a fully connected graph
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v2, v3)
g.AddGraphEdge(v1, v3)
# Create the edge weight array
weights = vtk.vtkDoubleArray()
weights.SetNumberOfComponents(1)
weights.SetName("Weights")
# Set the edge weights
weights.InsertNextValue(1.0)
weights.InsertNextValue(1.0)
weights.InsertNextValue(2.0)
# Add the edge weight array to the graph
g.GetEdgeData().AddArray(weights)
return g
def __init__(self, filename, max_num_of_vertices=-1, edge_color_filename=None):
super(VTKVisualizer, self).__init__()
self.vertex_id_idx_map = {}
self.next_vertex_id = 0
self.edge_counter = 0
self.lookup_table = vtk.vtkLookupTable()
self.lookup_table.SetNumberOfColors(int(1e8))
self.edge_color_tuples = {}
self.edge_color_filename = edge_color_filename
self.label_vertex_id_map = {}
self.starting_vertex = None
self.starting_vertex_index = -1
self.filename = filename
self.max_num_of_vertices = max_num_of_vertices
self.g = vtk.vtkMutableDirectedGraph()
self.vertex_ids = vtk.vtkIntArray()
self.vertex_ids.SetNumberOfComponents(1)
self.vertex_ids.SetName(VERTEX_ID)
self.labels = vtk.vtkStringArray()
self.labels.SetNumberOfComponents(1)
self.labels.SetName(LABELS)
self.glyph_scales = vtk.vtkFloatArray()
self.glyph_scales.SetNumberOfComponents(1)
self.glyph_scales.SetName(SCALES)
self.edge_weights = vtk.vtkDoubleArray()
self.edge_weights.SetNumberOfComponents(1)
self.edge_weights.SetName(WEIGHTS)
self.edge_colors = vtk.vtkIntArray()
self.edge_colors.SetNumberOfComponents(1)
self.edge_colors.SetName(EDGE_COLORS)
def main():
# Create a graph
graph = vtk.vtkMutableDirectedGraph()
v1 = graph.AddVertex()
v2 = graph.AddVertex()
graph.AddEdge(v1, v2)
# Create an array for the vertex labels
vertexIDs = vtk.vtkIntArray()
vertexIDs.SetNumberOfComponents(1)
vertexIDs.SetName("VertexIDs")
# Set the vertex labels
vertexIDs.InsertNextValue(0)
vertexIDs.InsertNextValue(1)
# Add the array to the graph
graph.GetVertexData().AddArray(vertexIDs)
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(graph)
graphLayoutView.SetVertexLabelVisibility(1)
rGraph = vtk.vtkRenderedGraphRepresentation()
rGraph.SafeDownCast(graphLayoutView.GetRepresentation()
).GetVertexLabelTextProperty().SetColor(1, 0, 0)
graphLayoutView.SetLayoutStrategyToSimple2D()
graphLayoutView.SetVertexLabelArrayName("VertexIDs")
graphLayoutView.ResetCamera()
graphLayoutView.Render()
graphLayoutView.GetInteractor().Start()
def GenerateVTKGraph(graph):
'''
Take the vertices and edge list in the graph parameter
and return a VTK graph.
'''
g = vtk.vtkMutableDirectedGraph()
# Label the vertices
labels = vtk.vtkStringArray()
labels.SetNumberOfComponents(1)
labels.SetName("Labels")
index = dict()
l = list(graph[0])
# Make the vertex labels and create a dictionary with the
# keys as labels and the vertex ids as the values.
for i in range(0, len(l)):
# Set the vertex labels
labels.InsertNextValue(l[i])
index[l[i]] = g.AddVertex()
g.GetVertexData().AddArray(labels)
# Add edges
l = list(graph[1])
for i in range(0, len(l)):
ll = list(l[i])
g.AddGraphEdge(index[ll[0]], index[ll[1]])
# g.Dump()
return g
def main():
graph = vtk.vtkMutableDirectedGraph()
v1 = graph.AddVertex()
v2 = graph.AddChild(v1)
graph.AddChild(v1)
graph.AddChild(v2)
#equivalent to:
#V1 = g.AddVertex()
#V2 = g.AddVertex()
#V3 = g.AddVertex()
#V4 = g.AddVertex()
#g.AddEdge ( V1, V2 )
#g.AddEdge ( V1, V3 )
#g.AddEdge ( V2, V4 )
tree = vtk.vtkTree()
success = tree.CheckedShallowCopy(graph)
print('Success?', success)
#std::cout << "Success? " << success << std::endl
treeLayoutView = vtk.vtkGraphLayoutView()
treeLayoutView.AddRepresentationFromInput(tree)
treeLayoutView.SetLayoutStrategyToTree()
treeLayoutView.ResetCamera()
treeLayoutView.Render()
treeLayoutView.GetInteractor().Start()
def makegraph(table1, friends, clustering):
graph = vtk.vtkMutableDirectedGraph()
username = vtk.vtkStringArray()
username.SetName("username")
userid = vtk.vtkIntArray()
userid.SetName("uid")
classifier = vtk.vtkStringArray()
classifier.SetName(clustering)
v = []
## Add vertices to graph
for i in range(0, len(table1)):
v.append(graph.AddVertex())
username.InsertNextValue(table1.loc[i].username)
userid.InsertNextValue(table1.loc[i].userid)
if clustering == "city":
classifier.InsertNextValue(table1.loc[i].city)
else:
classifier.InsertNextValue(table1.loc[i].criminal)
graph.GetVertexData().AddArray(username)
graph.GetVertexData().AddArray(userid)
graph.GetVertexData().AddArray(classifier)
table1['vertex'] = v
## Add edges to graph, check to make sure the edge belongs in this graph
## (check that both vertices are in table1)
for i in range(0, len(table1)):
vertex1 = v[i]
for j in friends[friends.ID1 == table1.loc[i].userid].ID2.tolist():
if table1[table1.userid == j].userid.size == 1:
vertex2 = v[table1[table1.userid == j].vertex.tolist()[0]]
graph.AddEdge(vertex1, vertex2)
return graph
def main():
colors = vtk.vtkNamedColors()
# Create a graph
graph = vtk.vtkMutableDirectedGraph()
v1 = graph.AddVertex()
v2 = graph.AddVertex()
v3 = graph.AddVertex()
graph.AddEdge(v1, v2)
graph.AddEdge(v2, v3)
# Manually set the position of the vertices
points = vtk.vtkPoints()
points.InsertNextPoint(0, 0, 0)
points.InsertNextPoint(1, 0, 0)
points.InsertNextPoint(2, 0, 0)
graph.SetPoints(points)
# Create the color array
vertexColors = vtk.vtkIntArray()
vertexColors.SetNumberOfComponents(1)
vertexColors.SetName('Color')
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(3)
lookupTable.SetTableValue(0, colors.GetColor4d('Red'))
lookupTable.SetTableValue(1, colors.GetColor4d('White'))
lookupTable.SetTableValue(2, colors.GetColor4d('Lime'))
lookupTable.Build()
vertexColors.InsertNextValue(0)
vertexColors.InsertNextValue(1)
vertexColors.InsertNextValue(2)
# Add the color array to the graph
graph.GetVertexData().AddArray(vertexColors)
# Visualize
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(graph)
graphLayoutView.SetLayoutStrategyToPassThrough()
graphLayoutView.SetVertexColorArrayName('Color')
graphLayoutView.ColorVerticesOn()
theme = vtk.vtkViewTheme()
theme.SetPointLookupTable(lookupTable)
graphLayoutView.ApplyViewTheme(theme)
graphLayoutView.ResetCamera()
graphLayoutView.GetInteractor().Initialize()
graphLayoutView.GetRenderer().GetActiveCamera().Zoom(0.8)
graphLayoutView.GetInteractor().Start()
def main():
graph = vtk.vtkMutableDirectedGraph()
a = graph.AddVertex()
b = graph.AddChild(a)
c = graph.AddChild(a)
d = graph.AddChild(b)
e = graph.AddChild(c)
f = graph.AddChild(c)
vertex_labels = vtk.vtkStringArray()
vertex_labels.SetName('VertexLabel')
vertex_labels.InsertValue(a, 'a')
vertex_labels.InsertValue(b, 'b')
vertex_labels.InsertValue(c, 'c')
vertex_labels.InsertValue(d, 'd')
vertex_labels.InsertValue(e, 'e')
vertex_labels.InsertValue(f, 'f')
graph.GetVertexData().AddArray(vertex_labels)
edge_labels = vtk.vtkStringArray()
edge_labels.SetName('EdgeLabel')
edge_labels.InsertValue(graph.GetEdgeId(a, b), 'a -> b')
edge_labels.InsertValue(graph.GetEdgeId(a, c), 'a -> c')
edge_labels.InsertValue(graph.GetEdgeId(b, d), 'b -> d')
edge_labels.InsertValue(graph.GetEdgeId(c, e), 'c -> e')
edge_labels.InsertValue(graph.GetEdgeId(c, f), 'c -> f')
graph.GetEdgeData().AddArray(edge_labels)
tree = vtk.vtkTree()
valid_tree = tree.CheckedShallowCopy(graph)
if not valid_tree:
print('Invalid tree')
return
view = vtk.vtkGraphLayoutView()
view.SetRepresentationFromInput(tree)
# Apply a theme to the views
theme = vtk.vtkViewTheme()
view.ApplyViewTheme(theme.CreateMellowTheme())
view.SetVertexColorArrayName('VertexDegree')
view.SetColorVertices(True)
view.SetVertexLabelArrayName('VertexLabel')
view.SetVertexLabelVisibility(True)
view.SetEdgeLabelArrayName('EdgeLabel')
view.SetEdgeLabelVisibility(True)
view.SetLayoutStrategyToTree()
view.ResetCamera()
view.GetRenderWindow().SetSize(600, 600)
view.GetRenderWindow().SetWindowName('CreateTree')
view.GetRenderWindow().Render()
view.GetInteractor().Initialize()
view.GetInteractor().Start()
def generate_data():
g = vtk.vtkMutableDirectedGraph()
# add vertices
v = []
for i in range(6):
v.append(g.AddVertex())
g.AddEdge(v[0], v[1])
g.AddEdge(v[1], v[2])
g.AddEdge(v[1], v[3])
g.AddEdge(v[0], v[4])
g.AddEdge(v[0], v[5])
weights = vtk.vtkDoubleArray()
weights.SetNumberOfComponents(1)
weights.SetName("Weights")
X = vtk.vtkDoubleArray()
X.SetNumberOfComponents(1)
X.SetName("X")
Y = vtk.vtkDoubleArray()
Y.SetNumberOfComponents(1)
Y.SetName("Y")
X.InsertNextValue(0)
X.InsertNextValue(0)
X.InsertNextValue(1)
X.InsertNextValue(-1)
X.InsertNextValue(0.5)
X.InsertNextValue(-0.5)
Y.InsertNextValue(0)
Y.InsertNextValue(1)
Y.InsertNextValue(1.5)
Y.InsertNextValue(2)
Y.InsertNextValue(-.5)
Y.InsertNextValue(-.8)
weights.InsertNextValue(1.)
weights.InsertNextValue(2.)
weights.InsertNextValue(3.)
weights.InsertNextValue(4.)
weights.InsertNextValue(5.)
g.GetEdgeData().AddArray(weights)
g.GetVertexData().AddArray(X)
g.GetVertexData().AddArray(Y)
return g
def GetTree(self):
"""Returns a full vtkTree based on data loaded in LoadData()."""
if self.data_loaded:
vertex_id = vtk.vtkIdTypeArray()
vertex_id.SetName('vertex_ids')
for ii in range(len(self.cp)):
vertex_id.InsertNextValue(ii)
NINvtk = VN.numpy_to_vtk(self.NumberInNet, deep=True)
NINvtk.SetName('num_in_vertex')
SCALESvtk = VN.numpy_to_vtk(self.Scales, deep=True)
SCALESvtk.SetName('scale')
# This array will default to empty strings
BLANKvtk = vtk.vtkStringArray()
BLANKvtk.SetNumberOfComponents(1)
BLANKvtk.SetNumberOfTuples(self.NumberInNet.shape[0])
BLANKvtk.SetName('blank')
# Build tree out of CP list of "is a child of"
# remembering that Matlab indices are 1-based and numpy/VTK 0-based
print 'Building graph'
dg = vtk.vtkMutableDirectedGraph()
edge_id = vtk.vtkIdTypeArray()
edge_id.SetName('edge_ids')
for ii in range(self.cp.size):
dg.AddVertex()
for ii in range(self.cp.size):
if self.cp[ii] > 0: # CP already zero-based
dg.AddGraphEdge(self.cp[ii],ii) # Method for use with wrappers -- AddEdge() in C++
edge_id.InsertNextValue(ii)
dg.GetVertexData().AddArray(NINvtk)
dg.GetVertexData().AddArray(SCALESvtk)
dg.GetVertexData().AddArray(vertex_id)
dg.GetVertexData().SetActiveScalars('scale')
dg.GetVertexData().SetActivePedigreeIds('vertex_ids')
dg.GetEdgeData().AddArray(edge_id)
dg.GetEdgeData().SetActivePedigreeIds('edge_ids')
tree = vtk.vtkTree()
tree.CheckedShallowCopy(dg)
return tree
else:
raise IOError, "Can't get tree until data is loaded successfully"
def main():
colors = vtk.vtkNamedColors()
graph = vtk.vtkMutableDirectedGraph()
# Create a graph
v1 = graph.AddVertex()
v2 = graph.AddVertex()
v3 = graph.AddVertex()
graph.AddGraphEdge(v1, v2)
graph.AddGraphEdge(v2, v3)
# Create the color array
edgeColors = vtk.vtkIntArray()
edgeColors.SetNumberOfComponents(1)
edgeColors.SetName('Color')
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(2)
lookupTable.SetTableValue(0, colors.GetColor4d('Red'))
lookupTable.SetTableValue(1, colors.GetColor4d('Lime'))
lookupTable.Build()
edgeColors.InsertNextValue(0)
edgeColors.InsertNextValue(1)
# Add the color array to the graph
graph.GetEdgeData().AddArray(edgeColors)
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(graph)
graphLayoutView.SetLayoutStrategy('Simple 2D')
graphLayoutView.GetLayoutStrategy().SetEdgeWeightField('Graphs')
graphLayoutView.GetLayoutStrategy().SetWeightEdges(1)
graphLayoutView.SetEdgeColorArrayName('Color')
graphLayoutView.SetEdgeLabelVisibility(1)
graphLayoutView.ColorEdgesOn()
theme = vtk.vtkViewTheme()
theme.SetCellLookupTable(lookupTable)
graphLayoutView.ApplyViewTheme(theme)
graphLayoutView.ResetCamera()
graphLayoutView.GetRenderer().GetActiveCamera().Zoom(0.8)
graphLayoutView.Render()
graphLayoutView.GetLayoutStrategy().SetRandomSeed(0)
graphLayoutView.GetInteractor().Initialize()
graphLayoutView.GetInteractor().Start()
def _init(self):
g = vtk.vtkMutableDirectedGraph()
v1 = g.AddVertex()
v2 = g.AddVertex()
g.AddGraphEdge(v1,v2)
G_labels = vtk.vtkStringArray()
G_labels.SetName("VLabels")
G_labels.InsertNextValue("One")
G_labels.InsertNextValue("Two")
g.GetVertexData().AddArray(G_labels)
G_labels = vtk.vtkStringArray()
G_labels.SetName("VLabels")
G_labels.InsertNextValue("Three")
G_labels.InsertNextValue("Four")
g.GetVertexData().AddArray(G_labels)
return g
def _init(self):
g = vtk.vtkMutableDirectedGraph()
v1 = g.AddVertex()
v2 = g.AddVertex()
g.AddGraphEdge(v1, v2)
G_labels = vtk.vtkStringArray()
G_labels.SetName("VLabels")
G_labels.InsertNextValue("One")
G_labels.InsertNextValue("Two")
g.GetVertexData().AddArray(G_labels)
G_labels = vtk.vtkStringArray()
G_labels.SetName("VLabels")
G_labels.InsertNextValue("Three")
G_labels.InsertNextValue("Four")
g.GetVertexData().AddArray(G_labels)
return g
def main():
graph = vtk.vtkMutableDirectedGraph()
# Create a graph
v1 = graph.AddVertex()
v2 = graph.AddVertex()
v3 = graph.AddVertex()
graph.AddGraphEdge(v1, v2)
graph.AddGraphEdge(v2, v3)
# Create the color array
edgeColors = vtk.vtkIntArray()
edgeColors.SetNumberOfComponents(1)
edgeColors.SetName("Color")
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(2)
lookupTable.SetTableValue(0, 1.0, 0.0, 0.0) # red
lookupTable.SetTableValue(1, 0.0, 1.0, 0.0) # green
lookupTable.Build()
edgeColors.InsertNextValue(0)
edgeColors.InsertNextValue(1)
# Add the color array to the graph
graph.GetEdgeData().AddArray(edgeColors)
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(graph)
graphLayoutView.SetLayoutStrategy("Simple 2D")
graphLayoutView.GetLayoutStrategy().SetEdgeWeightField("Graphs")
graphLayoutView.GetLayoutStrategy().SetWeightEdges(1)
graphLayoutView.SetEdgeColorArrayName("Color")
graphLayoutView.SetEdgeLabelVisibility(1)
graphLayoutView.ColorEdgesOn()
theme = vtk.vtkViewTheme()
theme.SetCellLookupTable(lookupTable)
graphLayoutView.ApplyViewTheme(theme)
graphLayoutView.ResetCamera()
graphLayoutView.Render()
graphLayoutView.GetLayoutStrategy().SetRandomSeed(0)
graphLayoutView.GetInteractor().Initialize()
graphLayoutView.GetInteractor().Start()
def main():
g = vtk.vtkMutableDirectedGraph()
v1 = g.AddVertex()
v2 = g.AddVertex()
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v1, v2)
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(g)
graphLayoutView.SetLayoutStrategy('Simple 2D')
graphLayoutView.ResetCamera()
graphLayoutView.Render()
graphLayoutView.GetLayoutStrategy().SetRandomSeed(0)
graphLayoutView.GetInteractor().Start()
def main():
colors = vtk.vtkNamedColors()
g = vtk.vtkMutableDirectedGraph()
latitude = vtk.vtkDoubleArray()
latitude.SetName("latitude")
longitude = vtk.vtkDoubleArray()
longitude.SetName("longitude")
for i in range(-90, 90, 10):
for j in range(-180, 180, 20):
g.AddVertex()
latitude.InsertNextValue(i)
longitude.InsertNextValue(j)
g.GetVertexData().AddArray(latitude)
g.GetVertexData().AddArray(longitude)
assign = vtk.vtkGeoAssignCoordinates()
assign.SetInputData(g)
assign.SetLatitudeArrayName("latitude")
assign.SetLongitudeArrayName("longitude")
assign.SetGlobeRadius(1.0)
assign.Update()
mapper = vtk.vtkGraphMapper()
mapper.SetInputConnection(assign.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
iren = vtk.vtkRenderWindowInteractor()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetInteractor(iren)
ren.SetBackground(colors.GetColor3d('MidnightBlue'))
ren.ResetCamera()
ren.GetActiveCamera().SetPosition(-1.02, -4.6, 3.45)
ren.GetActiveCamera().SetViewUp(0.12, 0.78, 0.61)
ren.GetActiveCamera().SetDistance(4.53)
iren.Initialize()
renWin.Render()
iren.Start()
def main():
# colors = vtk.vtkNamedColors()
g = vtk.vtkMutableDirectedGraph()
# Create 3 vertices
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
# Create a fully connected graph
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v2, v3)
g.AddGraphEdge(v1, v3)
# Create the edge weight array
weights = vtk.vtkDoubleArray()
weights.SetNumberOfComponents(1)
weights.SetName("Weights")
# Set the edge weights
weights.InsertNextValue(1.0)
weights.InsertNextValue(1.0)
weights.InsertNextValue(2.0)
# Add the edge weight array to the graph
g.GetEdgeData().AddArray(weights)
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(g)
graphLayoutView.SetLayoutStrategy("Simple 2D")
graphLayoutView.GetLayoutStrategy().SetEdgeWeightField("Weights")
graphLayoutView.GetLayoutStrategy().SetWeightEdges(1)
graphLayoutView.SetEdgeLabelArrayName("Weights")
graphLayoutView.SetEdgeLabelVisibility(1)
graphLayoutView.ResetCamera()
graphLayoutView.Render()
graphLayoutView.GetLayoutStrategy().SetRandomSeed(0)
graphLayoutView.GetInteractor().Start()
def __init__(self, name=None):
"""Constructor
@type name: str
@param name: Graph name, defaults to None
"""
self._name = name
self._directed = False
self._vertex_dict = {}
self._edge_dict = {}
self._weights = vtk.vtkDoubleArray()
self._weights.SetName('Weights')
self._weights.SetNumberOfComponents(1)
self._labels = vtk.vtkStringArray()
self._labels.SetNumberOfComponents(1)
self._labels.SetName('labels')
self._graph = vtk.vtkMutableDirectedGraph()
self._color_picker = vtk.vtkColorSeries()
self._color_dict = {}
self._colors = []
self._vertex_types = 1
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()
g = vtk.vtkMutableDirectedGraph()
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
### g.AddEdge(v1, v2)
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v2, v3)
g.AddGraphEdge(v3, v1)
# Do layout manually before handing graph to the view.
# This allows us to know the positions of edge arrows.
graphLayoutView = vtk.vtkGraphLayoutView()
layout = vtk.vtkGraphLayout()
strategy = vtk.vtkSimple2DLayoutStrategy()
layout.SetInput(g)
layout.SetLayoutStrategy(strategy)
# Tell the view to use the vertex layout we provide
graphLayoutView.SetLayoutStrategyToPassThrough()
# The arrows will be positioned on a straight line between two
# vertices so tell the view not to draw arcs for parallel edges
graphLayoutView.SetEdgeLayoutStrategyToPassThrough()
# Add the graph to the view. This will render vertices and edges,
# but not edge arrows.
graphLayoutView.AddRepresentationFromInputConnection(
layout.GetOutputPort())
# Manually create an actor containing the glyphed arrows.
graphToPoly = vtk.vtkGraphToPolyData()
graphToPoly.SetInputConnection(layout.GetOutputPort())
graphToPoly.EdgeGlyphOutputOn()
# Set the position (0: edge start, 1:edge end) where
# the edge arrows should go.
graphToPoly.SetEdgeGlyphPosition(0.98)
# Make a simple edge arrow for glyphing.
arrowSource = vtk.vtkGlyphSource2D()
arrowSource.SetGlyphTypeToEdgeArrow()
arrowSource.SetScale(0.1)
arrowSource.Update()
# Use Glyph3D to repeat the glyph on all edges.
arrowGlyph = vtk.vtkGlyph3D()
arrowGlyph.SetInputConnection(0, graphToPoly.GetOutputPort(1))
arrowGlyph.SetInputConnection(1, arrowSource.GetOutputPort())
# Create a mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(arrowGlyph.GetOutputPort())
# Create an actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
self.ren.AddActor(actor)
self.ren.ResetCamera()
self._initialized = False
vertex_id.SetName('vertex_ids')
for ii in range(gW['PointsInNet'][0,0].shape[1]):
PIN.append(gW['PointsInNet'][0,0][0,ii][0]-1) # 0-based indices
NIN.append(gW['PointsInNet'][0,0][0,ii][0].size)
vertex_id.InsertNextValue(ii)
NINarray = N.array(NIN)
NINvtk = VN.numpy_to_vtk(NINarray)
NINvtk.SetName('num_in_vertex')
SCALESvtk = VN.numpy_to_vtk(gW['Scales'][0,0][0])
SCALESvtk.SetName('scale')
# Build tree out of CP list of "is a child of"
# remembering that Matlab indices are 1-based and numpy/VTK 0-based
print 'Building graph'
dg = vtk.vtkMutableDirectedGraph()
edge_id = vtk.vtkIdTypeArray()
edge_id.SetName('edge_ids')
for ii in range(CP.size):
dg.AddVertex()
for ii in range(CP.size):
tmp = CP[ii]-1 # 0-based indices
if tmp > 0:
dg.AddGraphEdge(tmp,ii) # Method for use with wrappers -- AddEdge() in C++
edge_id.InsertNextValue(ii)
dg.GetVertexData().AddArray(NINvtk)
dg.GetVertexData().AddArray(SCALESvtk)
dg.GetVertexData().AddArray(vertex_id)
dg.GetVertexData().SetActiveScalars('scale')
dg.GetVertexData().SetActivePedigreeIds('vertex_ids')
It creates nodes which lose their actual value since nodes in vtkGraph are referenced
strictly by their index. These nodes do retain metadata in the same way edges do
(see below).
It creates edges which maintain the proper association and any metadata, the caveat
is that all edges are given all metadata attributes with default values.
So if an edge has an integer 'distance' attribute, and another does not - the
non-distanced edge will have a distance of 0. This follows suit for all of pythons
defaults, bool(), str(), float(), etc.
As such it requires that all keys have the same type.
"""
if input.is_directed():
output = vtk.vtkMutableDirectedGraph()
else:
output = vtk.vtkMutableUndirectedGraph()
nodes = input.nodes(data=True)
edges = input.edges(data=True)
edge_field_types = {}
node_field_types = {}
# Find out fields and types
for (_, data) in nodes:
for key in data.keys():
data_type = type(data[key])
# Assert that every node which has key has the same type
if key in node_field_types and data_type != node_field_types[key]:
return vertexid
def parseClassTree(classtree, tree, names):
class_to_vertex_map = dict()
for (parent, child) in classtree:
parentid = addToTree(parent, class_to_vertex_map, tree, names)
childid = addToTree(child, class_to_vertex_map, tree, names)
tree.AddGraphEdge(parentid, childid)
# The tree that will hold vtk class hierarchy
builder = vtk.vtkMutableDirectedGraph()
names = vtk.vtkStringArray()
names.SetName("name")
# Allocate 100 tuples to start with. I picked this number
# out of air.
names.SetNumberOfTuples(100)
# load vtk class information
reader = csv.reader(open(VTK_DATA_ROOT + "/Data/Infovis/classes.csv", 'r'))
classes = []
for row in reader:
classes.append(row)
import vtk
g = vtk.vtkMutableDirectedGraph()
# Create 3 vertices
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
# Create a fully connected graph
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v2, v3)
g.AddGraphEdge(v1, v3)
# Create the edge weight array
weights = vtk.vtkDoubleArray()
weights.SetNumberOfComponents(1)
weights.SetName("Weights")
# Set the edge weights
weights.InsertNextValue(1.0)
weights.InsertNextValue(1.0)
weights.InsertNextValue(2.0)
# Add the edge weight array to the graph
g.GetEdgeData().AddArray(weights)
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(g)
graphLayoutView.SetLayoutStrategy("Simple 2D")
graphLayoutView.GetLayoutStrategy().SetEdgeWeightField("Weights")
return vertexid
def parseClassTree(classtree, tree, names):
class_to_vertex_map = dict()
for (parent, child) in classtree:
parentid = addToTree(parent, class_to_vertex_map, tree, names)
childid = addToTree(child, class_to_vertex_map, tree, names)
tree.AddGraphEdge(parentid, childid)
# The tree that will hold vtk class hierarchy
builder = vtk.vtkMutableDirectedGraph()
names = vtk.vtkStringArray()
names.SetName("name")
# Allocate 100 tuples to start with. I picked this number
# out of air.
names.SetNumberOfTuples(100)
# load vtk class information
reader = csv.reader(open(VTK_DATA_ROOT + "/Data/Infovis/classes.csv", 'r'))
classes = []
for row in reader:
classes.append(row)
def main():
user_file = "./data/M2/Flitter_Names.txt"
friend_file = "./data/M2/Links_Table.txt"
community_file = "./data/M2/People_Cities.txt"
## Read user_file and friend_file with numpy
names = pd.read_csv(user_file, delimiter='\t')
friends = pd.read_csv(friend_file, delimiter='\t')
communities = pd.read_csv(community_file, delimiter='\t')
## Add the size of each users network to the pandas dataframe
## and the city of each user to the pandas dataframe
size = []
for i in range(0, len(names)):
size.append(friends[friends.ID2 == i].ID2.size +
friends[friends.ID1 == i].ID1.size)
names.loc[:, 'followers'] = size
names.loc[:, 'city'] = communities.City.tolist()
## First round of checks, do the sizes of their networks make sense?
employees = names[(names['followers'] >= 37) & (names['followers'] <= 43)]
handlers = names[(names['followers'] >= 28) & (names['followers'] <= 42)]
middlemen = names[(names['followers'] >= 4) & (names['followers'] <= 5)]
leaders = names[(names['followers'] >= 125)]
middlemen = check(middlemen, leaders, friends, 1, "ge")
potentials = leaders
potentials = update_suspects(potentials, handlers, employees, middlemen,
leaders)
allgraph = vtk.vtkMutableDirectedGraph()
allgraph = makegraph(potentials, friends, "city")
## Second round of check, do they havethe appropriate links?
handlers = check(handlers, handlers, friends, 2, "le")
employees = check(employees, handlers, friends, 3, "eq")
middlemen = check(middlemen, handlers, friends, 2, "ge")
## Finally we remove all extras based on our employees
handlers = check(handlers, employees, friends, 1, "eq")
middlemen = check(middlemen, handlers, friends, 1, "ge")
leaders = check(leaders, middlemen, friends, 1, "ge")
potentials = update_suspects(potentials, handlers, employees, middlemen,
leaders)
potentialgraph = vtk.vtkMutableDirectedGraph()
potentialgraph = makesolution(potentials, friends, "criminal")
### VTK pipeline stuff
strategy = vtk.vtkAttributeClustering2DLayoutStrategy()
strategy.SetVertexAttribute("city")
strategy.SetGraph(allgraph)
graphLayoutView = vtk.vtkGraphLayoutView()
graphLayoutView.AddRepresentationFromInput(allgraph)
graphLayoutView.GetRenderWindow().SetSize(1024, 1024)
graphLayoutView.SetLayoutStrategy(strategy)
graphLayoutView.SetVertexLabelArrayName("city")
graphLayoutView.SetVertexLabelVisibility(1)
graphLayoutView.ResetCamera()
## Render Just potential employees, handlers, middlemen, and leaders
strategy2 = vtk.vtkAttributeClustering2DLayoutStrategy()
strategy2.SetVertexAttribute("criminal")
strategy2.SetGraph(potentialgraph)
graphLayoutView2 = vtk.vtkGraphLayoutView()
graphLayoutView2.AddRepresentationFromInput(potentialgraph)
graphLayoutView2.GetRenderWindow().SetSize(1024, 1024)
graphLayoutView2.SetLayoutStrategy(strategy2)
graphLayoutView2.SetVertexLabelArrayName("username")
graphLayoutView2.SetVertexLabelVisibility(1)
graphLayoutView2.ResetCamera()
### implementing kayleigh's fancy linking code
annotationlink = vtk.vtkAnnotationLink()
graphLayoutView.GetRepresentation(0).SetAnnotationLink(annotationlink)
graphLayoutView2.GetRepresentation(0).SetAnnotationLink(annotationlink)
updater = vtk.vtkViewUpdater()
updater.AddAnnotationLink(annotationlink)
updater.AddView(graphLayoutView)
updater.AddView(graphLayoutView2)
graphLayoutView.Render()
graphLayoutView.GetInteractor().Start()
graphLayoutView2.Render()
graphLayoutView2.GetInteractor().Start()
def displayTree(self):
print ("displayTree")
tree = self.segmentor.getContourTree()
self.graphWidget.viewer.updateCornerAnnotation("featureAnnotation", "Features: {}".format(len(tree)/2))
graph = vtk.vtkMutableDirectedGraph()
X = vtk.vtkDoubleArray()
X.SetNumberOfComponents(1)
X.SetName("X")
Y = vtk.vtkDoubleArray()
Y.SetNumberOfComponents(1)
Y.SetName("Y")
weights = vtk.vtkDoubleArray()
weights.SetNumberOfComponents(1)
weights.SetName("Weights")
vertex_id = vtk.vtkDoubleArray()
vertex_id.SetNumberOfComponents(1)
vertex_id.SetName("VertexID")
print("creating graph")
# Adding to graph now
N = int(len(tree) / 2)
# normalise the values in Y
# transpose tree
treeT = list(zip(*tree))
maxY = max(treeT[1])
minY = min(treeT[1])
deltaY = maxY - minY
print(minY, maxY, deltaY)
maxX = max(treeT[0])
minX = min(treeT[0])
deltaX = maxX - minX
print(minX, maxX, deltaX)
for i in range(N):
even = 2 * i
odd = even + 1
if odd >= len(tree):
raise ValueError('out of bounds')
v = [tree[2 * i], tree[2 * i + 1]]
# print(i, even, odd, "Adding",v[0],v[1])
v1 = graph.AddVertex()
v2 = graph.AddVertex()
graph.AddEdge(v1, v2)
# Insert XY as a % of max range
X.InsertNextValue((v[0][0] - minX)/deltaX )
X.InsertNextValue((v[1][0] - minX) / deltaX )
Y.InsertNextValue((v[0][1] - minY)/ deltaY)
Y.InsertNextValue((v[1][1] - minY)/ deltaY )
weights.InsertNextValue(1.)
vertex_id.InsertNextValue(2*i)
vertex_id.InsertNextValue(2*i+1)
print("Finished") # Execution reaches here, error seems to be in cleanup upon closing
graph.GetVertexData().AddArray(X)
graph.GetVertexData().AddArray(Y)
graph.GetEdgeData().AddArray(weights)
graph.GetVertexData().AddArray(vertex_id)
print("Added Data")
layoutStrategy = vtk.vtkAssignCoordinatesLayoutStrategy()
layoutStrategy.SetYCoordArrayName('Y')
layoutStrategy.SetXCoordArrayName('X')
self.graphWidget.viewer.update(graph)
def openFile(self, progress_callback=None, **kwargs):
"""
Open file(s) based on results from QFileDialog
:param (function) progress_callback:
Callback funtion to emit progress percentage.
"""
if 'filename' not in kwargs.keys():
fn = self.fn
else:
fn = ([kwargs['filename']],)
# If the user has pressed cancel, the first element of the tuple will be empty.
# Quit the method cleanly
if not fn[0]:
return
# Single file selection
if len(fn[0]) == 1:
file = fn[0][0]
if progress_callback:
progress_callback.emit(30)
reader = vtk.vtkMetaImageReader()
reader.AddObserver("ErrorEvent", self.e)
reader.SetFileName(file)
reader.Update()
if progress_callback:
progress_callback.emit(90)
self.mainwindow.setStatusTip('File Read: {}'.format(reader.GetOutput().GetExtent()))
# Multiple TIFF files selected
else:
# Make sure that the files are sorted 0 - end
filenames = natsorted(fn[0])
increment = 30.0 / len(filenames)
# Basic test for tiff images
for n,file in enumerate(filenames,1):
ftype = imghdr.what(file)
if ftype != 'tiff':
# A non-TIFF file has been loaded, present error message and exit method
self.e('','','Problem reading file: {}'.format(file))
raise ReadError("File read error!")
if progress_callback:
progress_callback.emit(int(n * increment))
# Have passed basic test, can attempt to load
numpy_image = Converter.pureTiff2Numpy(filenames=filenames, bounds=(256,256,256), progress_callback=progress_callback)
reader = Converter.numpy2vtkImporter(numpy_image)
reader.Update()
if self.e.ErrorOccurred():
raise ReadError()
else:
self.viewerWidget.viewer.setInput3DData(reader.GetOutput())
if progress_callback:
progress_callback.emit(91)
self.mainwindow.setStatusTip('display 2D')
if progress_callback:
progress_callback.emit(92)
self.viewer3DWidget.viewer.setInput3DData(reader.GetOutput())
if progress_callback:
progress_callback.emit(93)
self.graph_numpy_input_data = Converter.vtk2numpy(reader.GetOutput(), transpose=[2,1,0])
if progress_callback:
progress_callback.emit(94)
self.mainwindow.setStatusTip('convert to numpy')
self.mainwindow.setStatusTip('Ready')
if progress_callback:
progress_callback.emit(95)
self.spacing = reader.GetOutput().GetSpacing()
if progress_callback:
progress_callback.emit(96)
self.origin = reader.GetOutput().GetOrigin()
if progress_callback:
progress_callback.emit(97)
### After successfully opening file, reset the interface ###
# Reset linked state
self.linkViewers(force_linked=True)
# Reset graph if drawn
self.graphWidget.viewer.update(vtk.vtkMutableDirectedGraph())
# Reset graph parameter panel
if self.hasDockableWindow:
for element in self.treeWidgetInitialElements:
element.setEnabled(True)
for element in self.treeWidgetUpdateElements:
element.setEnabled(False)
print ("finished openFile")
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()
g = vtk.vtkMutableDirectedGraph()
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
### g.AddEdge(v1, v2)
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v2, v3)
g.AddGraphEdge(v3, v1)
# Do layout manually before handing graph to the view.
# This allows us to know the positions of edge arrows.
graphLayoutView = vtk.vtkGraphLayoutView()
layout = vtk.vtkGraphLayout()
strategy = vtk.vtkSimple2DLayoutStrategy()
layout.SetInput(g)
layout.SetLayoutStrategy(strategy)
# Tell the view to use the vertex layout we provide
graphLayoutView.SetLayoutStrategyToPassThrough()
# The arrows will be positioned on a straight line between two
# vertices so tell the view not to draw arcs for parallel edges
graphLayoutView.SetEdgeLayoutStrategyToPassThrough()
# Add the graph to the view. This will render vertices and edges,
# but not edge arrows.
graphLayoutView.AddRepresentationFromInputConnection(layout.GetOutputPort())
# Manually create an actor containing the glyphed arrows.
graphToPoly = vtk.vtkGraphToPolyData()
graphToPoly.SetInputConnection(layout.GetOutputPort())
graphToPoly.EdgeGlyphOutputOn()
# Set the position (0: edge start, 1:edge end) where
# the edge arrows should go.
graphToPoly.SetEdgeGlyphPosition(0.98)
# Make a simple edge arrow for glyphing.
arrowSource = vtk.vtkGlyphSource2D()
arrowSource.SetGlyphTypeToEdgeArrow()
arrowSource.SetScale(0.1)
arrowSource.Update()
# Use Glyph3D to repeat the glyph on all edges.
arrowGlyph = vtk.vtkGlyph3D()
arrowGlyph.SetInputConnection(0, graphToPoly.GetOutputPort(1))
arrowGlyph.SetInputConnection(1, arrowSource.GetOutputPort())
# Create a mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(arrowGlyph.GetOutputPort())
# Create an actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
self.ren.AddActor(actor)
self.ren.ResetCamera()
self._initialized = False
#!/usr/bin/env python
'''
Online example from :
http://www.vtk.org/Wiki/VTK/Examples/Python/Graphs/EdgeWeights
Going to heavly comment out the steps to understand how to edit
this into what we need to make other graphs
'''
import vtk # Manditory on all python VTK
g = vtk.vtkMutableDirectedGraph() # Sets up empty data structure
# Create 3 vertices # Adding nodes to your graph
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
# Create a fully connected graph # Adding in the edges between them
g.AddGraphEdge(v1, v2)
g.AddGraphEdge(v2, v3)
g.AddGraphEdge(v1, v3)
# Create the edge weight array
weights = vtk.vtkDoubleArray() # This is VTK version of an array of data,
# in this case weights
weights.SetNumberOfComponents(1) # Since we are just doing weights it 1 dimensional
weights.SetName("Weights") # Creates an name to recover later with