def initialize(self, VTKWebApp, args):
dataid = args.id
treedata = getDBdata(dataid)
VTKWebApp.tree1 = treedata["tree1"]
VTKWebApp.tree2 = treedata["tree2"]
VTKWebApp.table = dataid+ ".csv"
# Create default pipeline (Only once for all the session)
if not VTKWebApp.view:
# read the trees
treeReader1 = vtk.vtkNewickTreeReader()
treeReader1.SetReadFromInputString(1)
treeReader1.SetInputString(VTKWebApp.tree1)
treeReader1.Update()
tree1 = treeReader1.GetOutput()
treeReader2 = vtk.vtkNewickTreeReader()
treeReader2.SetReadFromInputString(1)
treeReader2.SetInputString(VTKWebApp.tree2)
treeReader2.Update()
tree2 = treeReader2.GetOutput()
# read the table
tableReader = vtk.vtkDelimitedTextReader()
tableReader.SetFileName(VTKWebApp.table)
tableReader.SetHaveHeaders(True)
tableReader.DetectNumericColumnsOn()
tableReader.ForceDoubleOn()
tableReader.Update()
table = tableReader.GetOutput()
# setup the tanglegram
tanglegram = vtk.vtkTanglegramItem()
tanglegram.SetTree1(tree1);
tanglegram.SetTree2(tree2);
tanglegram.SetTable(table);
tanglegram.SetTree1Label("tree1");
tanglegram.SetTree2Label("tree2");
# setup the window
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1,1,1)
view.GetRenderWindow().SetSize(800,600)
iren = view.GetInteractor()
iren.SetRenderWindow(view.GetRenderWindow())
transformItem = vtk.vtkContextTransform()
transformItem.AddItem(tanglegram)
transformItem.SetInteractive(1)
view.GetScene().AddItem(transformItem)
view.GetRenderWindow().SetMultiSamples(0)
iren.Initialize()
view.GetRenderWindow().Render()
# VTK Web application specific
VTKWebApp.view = view.GetRenderWindow()
self.Application.GetObjectIdMap().SetActiveObject("VIEW", view.GetRenderWindow())
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_PhylogeneticTree.authKey)
# Create default pipeline (Only once for all the session)
if not _PhylogeneticTree.view:
# read in a tree
treeReader = vtk.vtkNewickTreeReader()
treeReader.SetFileName(_PhylogeneticTree.treeFilePath)
treeReader.Update()
reader = treeReader.GetOutput()
# read in a table
tableReader = vtk.vtkDelimitedTextReader()
tableReader.SetFileName(_PhylogeneticTree.csvFilePath)
tableReader.SetHaveHeaders(True)
tableReader.DetectNumericColumnsOn()
tableReader.Update()
table = tableReader.GetOutput()
# play with the heatmap vis
treeHeatmapItem = vtk.vtkTreeHeatmapItem()
treeHeatmapItem.SetTree(reader)
treeHeatmapItem.SetTable(table)
# setup the window
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1, 1, 1)
view.GetRenderWindow().SetSize(800, 600)
iren = view.GetInteractor()
iren.SetRenderWindow(view.GetRenderWindow())
transformItem = vtk.vtkContextTransform()
transformItem.AddItem(treeHeatmapItem)
transformItem.SetInteractive(1)
view.GetScene().AddItem(transformItem)
view.GetRenderWindow().SetMultiSamples(0)
iren.Initialize()
view.GetRenderWindow().Render()
# VTK Web application specific
_PhylogeneticTree.view = view.GetRenderWindow()
self.Application.GetObjectIdMap().SetActiveObject(
"VIEW", view.GetRenderWindow())
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_PhylogeneticTree.authKey)
# Create default pipeline (Only once for all the session)
if not _PhylogeneticTree.view:
# read in a tree
treeReader = vtk.vtkNewickTreeReader()
treeReader.SetFileName(_PhylogeneticTree.treeFilePath)
treeReader.Update()
reader = treeReader.GetOutput()
# read in a table
tableReader = vtk.vtkDelimitedTextReader()
tableReader.SetFileName(_PhylogeneticTree.csvFilePath)
tableReader.SetHaveHeaders(True)
tableReader.DetectNumericColumnsOn()
tableReader.Update()
table = tableReader.GetOutput()
# play with the heatmap vis
treeHeatmapItem = vtk.vtkTreeHeatmapItem()
treeHeatmapItem.SetTree(reader);
treeHeatmapItem.SetTable(table);
# setup the window
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1,1,1)
view.GetRenderWindow().SetSize(800,600)
iren = view.GetInteractor()
iren.SetRenderWindow(view.GetRenderWindow())
transformItem = vtk.vtkContextTransform()
transformItem.AddItem(treeHeatmapItem)
transformItem.SetInteractive(1)
view.GetScene().AddItem(transformItem)
view.GetRenderWindow().SetMultiSamples(0)
iren.Initialize()
view.GetRenderWindow().Render()
# VTK Web application specific
_PhylogeneticTree.view = view.GetRenderWindow()
self.Application.GetObjectIdMap().SetActiveObject("VIEW", view.GetRenderWindow())
def testReadWrite(self):
t = '(A:1,B:2,(C:3,D:4)E:5)F;'
reader = vtk.vtkNewickTreeReader()
reader.SetReadFromInputString(True)
reader.SetInputString(t)
reader.Update()
writer = vtk.vtkNewickTreeWriter()
writer.WriteToOutputStringOn()
writer.SetInputData(reader.GetOutput())
writer.Update()
t_return = writer.GetOutputStdString()
self.assertEqual(t,t_return)
def testReadWrite(self):
t = '(A:1,B:2,(C:3,D:4)E:5)F;'
reader = vtk.vtkNewickTreeReader()
reader.SetReadFromInputString(True)
reader.SetInputString(t)
reader.Update()
writer = vtk.vtkNewickTreeWriter()
writer.WriteToOutputStringOn()
writer.SetInputData(reader.GetOutput())
writer.Update()
t_return = writer.GetOutputStdString()
self.assertEqual(t, t_return)
def testTreeOutput(self):
tree_reader = vtk.vtkNewickTreeReader()
tree_reader.ReadFromInputStringOn()
tree_reader.SetInputString(tree_data)
rcal = vtk.vtkRCalculatorFilter()
rcal.SetInputConnection(tree_reader.GetOutputPort())
rcal.SetRscript("library(ape)\n\
output = read.tree(text=\"" + tree_data + "\")\n")
rcal.GetTree('output')
rcal.Update()
expected_tree = tree_reader.GetOutput()
self.assertTrue(treeEquals(expected_tree, rcal.GetOutput()))
def initialize(self, VTKWebApp, args):
VTKWebApp.treeFilePath = args.tree
VTKWebApp.csvFilePath = args.table
# Create default pipeline (Only once for all the session)
if not VTKWebApp.view:
# read in a tree
treeReader = vtk.vtkNewickTreeReader()
treeReader.SetFileName(VTKWebApp.treeFilePath)
treeReader.Update()
reader = treeReader.GetOutput()
# read in a table
tableReader = vtk.vtkDelimitedTextReader()
tableReader.SetFileName(VTKWebApp.csvFilePath)
tableReader.SetHaveHeaders(1)
tableReader.DetectNumericColumnsOn()
tableReader.Update()
table = tableReader.GetOutput()
# play with the heatmap vis
treeHeatmapItem = vtk.vtkTreeHeatmapItem()
treeHeatmapItem.SetTree(reader)
treeHeatmapItem.SetTable(table)
# setup the window
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1, 1, 1)
view.GetRenderWindow().SetSize(800, 600)
iren = view.GetInteractor()
iren.SetRenderWindow(view.GetRenderWindow())
transformItem = vtk.vtkContextTransform()
transformItem.AddItem(treeHeatmapItem)
transformItem.SetInteractive(1)
view.GetScene().AddItem(transformItem)
view.GetRenderWindow().SetMultiSamples(0)
iren.Initialize()
view.GetRenderWindow().Render()
# VTK Web application specific
VTKWebApp.view = view.GetRenderWindow()
self.Application.GetObjectIdMap().SetActiveObject("VIEW", view.GetRenderWindow())
def testTreeOutput(self):
tree_reader = vtk.vtkNewickTreeReader()
tree_reader.ReadFromInputStringOn()
tree_reader.SetInputString(tree_data)
rcal = vtk.vtkRCalculatorFilter()
rcal.SetInputConnection(tree_reader.GetOutputPort())
rcal.SetRscript("library(ape)\n\
output = read.tree(text=\"" + tree_data + "\")\n");
rcal.GetTree('output')
rcal.Update()
expected_tree = tree_reader.GetOutput()
self.assertTrue(treeEquals(expected_tree, rcal.GetOutput()))
def NewickToVTKTree(newick): reader = vtk.vtkNewickTreeReader() reader.SetReadFromInputString(1) reader.SetInputString(newick, len(newick)) reader.Update() return reader.GetOutput()
def initialize(self, VTKWebApp, args):
dataid = args.id
treedata = getDBdata(dataid)
VTKWebApp.tree = treedata["tree"]
VTKWebApp.table = dataid+ ".csv"
# Create default pipeline (Only once for all the session)
if not VTKWebApp.view:
treeHeatmapItem = vtk.vtkTreeHeatmapItem()
# read in a tree
treeReader = vtk.vtkNewickTreeReader()
treeReader.SetReadFromInputString(1)
treeReader.SetInputString(VTKWebApp.tree)
treeReader.Update()
tree = treeReader.GetOutput()
treeHeatmapItem.SetTree(tree)
if (VTKWebApp.table != "none" and os.path.isfile(VTKWebApp.table)):
# read in a table
print("read table"+ VTKWebApp.table)
tableReader = vtk.vtkDelimitedTextReader()
tableReader.SetFileName(VTKWebApp.table)
tableReader.SetHaveHeaders(1)
tableReader.DetectNumericColumnsOn()
tableReader.Update()
table = tableReader.GetOutput()
if (table):
treeHeatmapItem.SetTable(table)
# setup the window
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1,1,1)
view.GetRenderWindow().SetSize(800,600)
iren = view.GetInteractor()
iren.SetRenderWindow(view.GetRenderWindow())
transformItem = vtk.vtkContextTransform()
transformItem.AddItem(treeHeatmapItem)
transformItem.SetInteractive(1)
view.GetScene().AddItem(transformItem)
view.GetRenderWindow().SetMultiSamples(0)
iren.Initialize()
view.GetRenderWindow().Render()
# adjust zoom so the item nicely fills the screen
itemSize = [0, 0]
treeHeatmapItem.GetSize(itemSize)
itemSize.append(0)
transformItem.GetTransform().MultiplyPoint(itemSize, itemSize)
newWidth = view.GetScene().GetSceneWidth()
newHeight = view.GetScene().GetSceneHeight()
pageWidth = newWidth
pageHeight = newHeight
sx = pageWidth / itemSize[0]
sy = pageHeight / itemSize[1]
if sy < sx:
scale = sy;
else:
scale = sx;
if scale > 1:
scale = scale * 0.5
else:
scale = scale * 0.9
transformItem.Scale(scale, scale)
# center the item within the screen
itemCenter = [0, 0]
treeHeatmapItem.GetCenter(itemCenter)
itemCenter.append(0)
centerPt = vtk.vtkPoints2D()
centerPt.InsertNextPoint(newWidth / 2.0, newHeight / 2.0)
transformItem.GetTransform().InverseTransformPoints(centerPt, centerPt)
sceneCenter = [0, 0]
centerPt.GetPoint(0, sceneCenter)
dx = -1 * (itemCenter[0] - sceneCenter[0])
dy = -1 * (itemCenter[1] - sceneCenter[1])
transformItem.Translate(dx, dy)
# VTK Web application specific
VTKWebApp.view = view.GetRenderWindow()
self.Application.GetObjectIdMap().SetActiveObject("VIEW", view.GetRenderWindow())
import vtk reader = vtk.vtkNewickTreeReader() reader.SetReadFromInputString(True) reader.SetInputString(input, len(input)) reader.Update() output = reader.GetOutput()