ENH: Add a GML graph reader supplied by David Duke at University of Leeds

ENH: Add a new 3D graph layout strategy from David Duke at University of Leeds (vtkSpanTreeLayoutStrategy)
ENH: Add updated tests using the 3D layout in the graph layout view
ENH: Add python examples using the graph layout view for the new strategy

Examples/Infovis/Python/graph3d.py

+from vtk import *
+
+reader = vtkXGMLReader()
+reader.SetFileName("fsm.gml")
+reader.Update()
+
+strategy   = vtkSpanTreeLayoutStrategy()
+strategy.DepthFirstSpanningTreeOn()
+
+view = vtkGraphLayoutView()
+view.AddRepresentationFromInputConnection(reader.GetOutputPort())
+view.SetVertexLabelArrayName("vertex id")
+view.SetVertexLabelVisibility(True)
+view.SetVertexColorArrayName("vertex id")
+view.SetColorVertices(True)
+view.SetLayoutStrategy( strategy )
+view.SetInteractionModeTo3D() # Left mouse button causes 3D rotate instead of zoom
+view.SetLabelPlacementModeToLabelPlacer()
+
+theme = vtkViewTheme.CreateMellowTheme()
+theme.SetCellColor(.2,.2,.6)
+theme.SetLineWidth(2)
+theme.SetPointSize(10)
+view.ApplyViewTheme(theme)
+theme.FastDelete()
+
+window = vtkRenderWindow()
+window.SetSize(600, 600)
+view.SetupRenderWindow(window)
+view.GetRenderer().ResetCamera()
+window.Render()
+
+#Here's the window with David's original layout methodology
+#  Aside from the theme elements in the view above, the notable 
+#  difference between the two views is the angling on the edges.
+layout = vtkGraphLayout()
+layout.SetLayoutStrategy(strategy)
+layout.SetInputConnection(reader.GetOutputPort())
+
+edge_geom = vtkGraphToPolyData()
+edge_geom.SetInputConnection(layout.GetOutputPort())
+
+vertex_geom = vtkGraphToPoints()
+vertex_geom.SetInputConnection(layout.GetOutputPort())
+
+# Vertex pipeline - mark each vertex with a cube glyph
+cube = vtkCubeSource()
+cube.SetXLength(0.3)
+cube.SetYLength(0.3)
+cube.SetZLength(0.3)
+
+glyph = vtkGlyph3D()
+glyph.SetInputConnection(vertex_geom.GetOutputPort())
+glyph.SetSource(cube.GetOutput())
+
+gmap = vtkPolyDataMapper()
+gmap.SetInputConnection(glyph.GetOutputPort())
+
+gact = vtkActor()
+gact.SetMapper(gmap)
+gact.GetProperty().SetColor(0,0,1)
+
+# Edge pipeline - map edges to lines
+mapper = vtkPolyDataMapper()
+mapper.SetInputConnection(edge_geom.GetOutputPort())
+
+actor = vtkActor()
+actor.SetMapper(mapper)
+actor.GetProperty().SetColor(0.4,0.4,0.6)
+
+# Renderer, window, and interaction
+ren = vtkRenderer()
+ren.AddActor(actor)
+ren.AddActor(gact)
+ren.ResetCamera()
+
+renWin = vtkRenderWindow()
+renWin.AddRenderer(ren)
+renWin.SetSize(800,550)
+
+iren = vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+iren.Initialize()
+#iren.Start()
+
+window.GetInteractor().Start()

Examples/Infovis/Python/random3d.py

+from vtk import *
+
+source = vtkRandomGraphSource()
+source.SetNumberOfVertices(150)
+source.SetEdgeProbability(0.01)
+source.SetUseEdgeProbability(True)
+source.SetStartWithTree(True)
+
+view = vtkGraphLayoutView()
+view.AddRepresentationFromInputConnection(source.GetOutputPort())
+view.SetVertexLabelArrayName("vertex id")
+view.SetVertexLabelVisibility(True)
+view.SetVertexColorArrayName("vertex id")
+view.SetColorVertices(True)
+view.SetLayoutStrategyToSpanTree()
+view.SetInteractionModeTo3D() # Left mouse button causes 3D rotate instead of zoom
+view.SetLabelPlacementModeToLabelPlacer()
+
+theme = vtkViewTheme.CreateMellowTheme()
+theme.SetCellColor(.2,.2,.6)
+theme.SetLineWidth(2)
+theme.SetPointSize(10)
+view.ApplyViewTheme(theme)
+theme.FastDelete()
+
+window = vtkRenderWindow()
+window.SetSize(600, 600)
+view.SetupRenderWindow(window)
+view.GetRenderer().ResetCamera()
+window.Render()
+window.GetInteractor().Start()

Infovis/CMakeLists.txt

@@ -77,6 +77,7 @@ vtkSimple2DLayoutStrategy.cxx
 vtkSliceAndDiceLayoutStrategy.cxx
 vtkSplineGraphEdges.cxx
 vtkSquarifyLayoutStrategy.cxx
+vtkSpanTreeLayoutStrategy.cxx
 vtkStackedTreeLayoutStrategy.cxx
 vtkStatisticsAlgorithm.cxx
 vtkStringToCategory.cxx
@@ -96,6 +97,7 @@ vtkTreeRingToPolyData.cxx
 vtkTulipReader.cxx
 vtkUnivariateStatisticsAlgorithm.cxx
 vtkVertexDegree.cxx
+vtkXGMLReader.cxx
 vtkXMLTreeReader.cxx
 )
 

Infovis/vtkSpanTreeLayoutStrategy.h

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    vtkSpanTreeLayoutStrategy.h
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+//-------------------------------------------------------------------------
+//Copyright 2008 Sandia Corporation.
+//Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+//the U.S. Government retains certain rights in this software.
+//-------------------------------------------------------------------------
+
+// .NAME vtkSpanTreeLayoutStrategy
+// .SECTION Description
+// vtkSpanTreeLayout is a strategy for drawing directed graphs that
+// works by first extracting a spanning tree (more accurately, a 
+// spanning forest), and using this both to position graph vertices
+// and to plan the placement of non-tree edges.  The latter are drawn
+// with the aid of edge points to produce a tidy drawing.
+//
+// The approach is best suited to "quasi-trees", graphs where the number
+// of edges is of the same order as the number of nodes; it is less well
+// suited to denser graphs.  The boolean flag DepthFirstSpanningTree
+// determines whether a depth-first or breadth-first strategy is used to
+// construct the underlying forest, and the choice of strategy affects
+// the output layout significantly.  Informal experiments suggest that
+// the breadth-first strategy is better for denser graphs.
+//
+// Different layouts could also be produced by plugging in alternative
+// tree layout strategies.  To work with the method of routing non-tree
+// edges, any strategy should draw a tree so that levels are equally
+// spaced along the z-axis, precluding for example the use of a radial
+// or balloon layout.
+//
+// vtkSpanTreeLayout is based on an approach to 3D graph layout first 
+// developed as part of the "tulip" tool by Dr. David Auber at LaBRI, 
+// U.Bordeaux: see www.tulip-software.org   
+//
+// This implementation departs from the original version in that:
+// (a) it is reconstructed to use Titan/VTK data structures;
+// (b) it uses a faster method for dealing with non-tree edges,
+//     requiring at most two edge points per edge
+// (c) allows for plugging in different tree layout methods
+// (d) allows selection of two different strategies for building
+//     the underlying layout tree, which can yield significantly
+//     different results depending on the data.
+//
+// .SECTION Thanks
+// Thanks to David Duke from the University of Leeds for providing this 
+// implementation.
+
+
+#ifndef __vtkSpanTreeLayoutStrategy_h
+#define __vtkSpanTreeLayoutStrategy_h
+
+#include "vtkGraphLayoutStrategy.h"
+#include "vtkPoints.h"
+
+
+class VTK_INFOVIS_EXPORT vtkSpanTreeLayoutStrategy : public vtkGraphLayoutStrategy 
+{
+public:
+  static vtkSpanTreeLayoutStrategy *New();
+
+  vtkTypeRevisionMacro(vtkSpanTreeLayoutStrategy, vtkGraphLayoutStrategy);
+  void PrintSelf(ostream& os, vtkIndent indent);
+
+  // Description:
+  // Set the strategy that is to be used in laying out the
+  // underlying spanning tree.  For sensible results, any
+  // tree layout used should place each layer of the tree
+  // in a single X-Y plane.
+  // By default, vtkConeTreeLayoutStrategy is used.
+  vtkSetObjectMacro(TreeLayout,vtkGraphLayoutStrategy);
+  vtkGetObjectMacro(TreeLayout,vtkGraphLayoutStrategy);
+ 
+  // Description:
+  // If set, base the layout on a depth-first spanning tree,
+  // rather than the default breadth-first spanning tree.
+  // Switching between DFT and BFT may significantly change
+  // the layout, and choice must be made on a per-graph basis.
+  // Default value is off.
+  vtkSetMacro(DepthFirstSpanningTree, bool);
+  vtkGetMacro(DepthFirstSpanningTree, bool);
+  vtkBooleanMacro(DepthFirstSpanningTree, bool);
+
+  // Description:
+  // Perform the layout.
+  void Layout();
+  
+protected:
+  vtkSpanTreeLayoutStrategy();
+  ~vtkSpanTreeLayoutStrategy();
+
+  vtkGraphLayoutStrategy *TreeLayout;
+  bool DepthFirstSpanningTree;
+  
+private:
+  vtkSpanTreeLayoutStrategy(const vtkSpanTreeLayoutStrategy&);  // Not implemented.
+  void operator=(const vtkSpanTreeLayoutStrategy&);  // Not implemented.
+};
+
+#endif
+

Infovis/vtkXGMLReader.h

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    vtkXGMLReader.h
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+//-------------------------------------------------------------------------
+//Copyright 2008 Sandia Corporation.
+//Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+//the U.S. Government retains certain rights in this software.
+//-------------------------------------------------------------------------
+
+// .NAME vtkXGMLReader - Reads XGML graph files.
+// This reader is developed for a simple graph file format based
+// loosely on the "GML" notation.  This implementation is based
+// heavily on the vtkTulipReader class that forms part of the 
+// Titan toolkit.
+
+// .SECTION Thanks
+// Thanks to David Duke from the University of Leeds for providing this 
+// implementation.
+
+#ifndef _vtkXGMLReader_h
+#define _vtkXGMLReader_h
+
+#include "vtkUndirectedGraphAlgorithm.h"
+
+class VTK_INFOVIS_EXPORT vtkXGMLReader : public vtkUndirectedGraphAlgorithm
+{
+public:
+  static vtkXGMLReader *New();
+  vtkTypeRevisionMacro(vtkXGMLReader, vtkUndirectedGraphAlgorithm);
+  void PrintSelf(ostream& os, vtkIndent indent);
+
+  // Description:
+  // The XGML file name.
+  vtkGetStringMacro(FileName);
+  vtkSetStringMacro(FileName);
+
+protected:
+  vtkXGMLReader();
+  ~vtkXGMLReader();
+
+  virtual int RequestData(
+    vtkInformation *, 
+    vtkInformationVector **, 
+    vtkInformationVector *);
+
+private:
+  char* FileName;
+
+  vtkXGMLReader(const vtkXGMLReader&);  // Not implemented.
+  void operator=(const vtkXGMLReader&);  // Not implemented.
+};
+
+#endif // _vtkXGMLReader_h
+

Views/Testing/Cxx/CMakeLists.txt

@@ -18,6 +18,7 @@ IF (VTK_USE_RENDERING AND VTK_USE_DISPLAY)
       TestTreeRingView.cxx
       TestIcicleView.cxx
       TestConeLayoutStrategy.cxx
+      TestSpanTreeLayoutStrategy.cxx
       )
     IF (VTK_USE_QT)
       # add tests that require Qt

Views/Testing/Cxx/TestSpanTreeLayoutStrategy.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    TestSpanTreeLayoutStrategy.cxx
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+/*-------------------------------------------------------------------------
+  Copyright 2008 Sandia Corporation.
+  Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+  the U.S. Government retains certain rights in this software.
+-------------------------------------------------------------------------*/
+
+#include "vtkSpanTreeLayoutStrategy.h"
+#include "vtkGraphLayoutView.h"
+#include "vtkInteractorEventRecorder.h"
+#include "vtkRegressionTestImage.h"
+#include "vtkRenderer.h"
+#include "vtkRenderWindow.h"
+#include "vtkRenderWindowInteractor.h"
+#include "vtkTestUtilities.h"
+#include "vtkXGMLReader.h"
+
+using vtkstd::string;
+
+#include "vtkSmartPointer.h"
+#define VTK_CREATE(type, name) \
+  vtkSmartPointer<type> name = vtkSmartPointer<type>::New()
+
+int TestSpanTreeLayoutStrategy(int argc, char* argv[])
+{
+  VTK_CREATE(vtkTesting, testHelper);
+  testHelper->AddArguments(argc,const_cast<const char **>(argv));
+  string dataRoot = testHelper->GetDataRoot();
+  string file = dataRoot + "/Data/Infovis/fsm.gml";
+
+  VTK_CREATE(vtkXGMLReader, reader);
+  reader->SetFileName(file.c_str());
+  reader->Update();
+
+  // Graph layout view
+  VTK_CREATE(vtkGraphLayoutView, view);
+//  VTK_CREATE(vtkSpanTreeLayoutStrategy, strategy);
+//  strategy->DepthFirstSpanningTreeOn();
+//  view->SetLayoutStrategy(strategy);
+  view->SetLayoutStrategyToSpanTree();
+  view->SetVertexLabelArrayName("vertex id");
+  view->VertexLabelVisibilityOn();
+  view->SetVertexColorArrayName("vertex id");
+  view->SetColorVertices(true);
+//  view->SetEdgeColorArrayName("distance");
+//  view->ColorEdgesOn();
+//  view->SetEdgeLabelArrayName("edge label");
+//  view->EdgeLabelVisibilityOn();
+  view->SetRepresentationFromInputConnection(reader->GetOutputPort());
+
+  view->GetRenderer()->ResetCamera();
+
+  VTK_CREATE(vtkRenderWindow, win);
+  win->SetSize( 600, 600 );
+  win->SetMultiSamples(0); // ensure to have the same test image everywhere
+  view->SetupRenderWindow(win);
+  view->SetInteractionModeTo3D();
+  view->SetLabelPlacementModeToLabelPlacer();
+  view->Update();
+
+  int retVal = vtkRegressionTestImage(win);
+  if( retVal == vtkRegressionTester::DO_INTERACTOR )
+    {
+    win->GetInteractor()->Initialize();
+    win->GetInteractor()->Start();
+
+    retVal = vtkRegressionTester::PASSED;
+    }
+
+ return !retVal;
+}

Views/vtkGraphLayoutView.h

@@ -149,6 +149,7 @@ public:
   //  - "Pass Through"  Use locations assigned to the input.
   //  - "Circular"      Places vertices uniformly on a circle.
   //  - "Cone"          Cone tree layout.
+  //  - "Span Tree"     Span Tree Layout.
   // Default is "Simple 2D".
   void SetLayoutStrategy(const char* name);
   void SetLayoutStrategyToRandom()
@@ -173,6 +174,8 @@ public:
     { this->SetLayoutStrategy("Cosmic Tree"); }
   void SetLayoutStrategyToCone()
     { this->SetLayoutStrategy("Cone"); }
+  void SetLayoutStrategyToSpanTree()
+    { this->SetLayoutStrategy("Span Tree"); }
   const char* GetLayoutStrategyName();
 
   // Description:

Views/vtkRenderedGraphRepresentation.cxx

@@ -65,6 +65,7 @@
 #include "vtkSelectionNode.h"
 #include "vtkSimple2DLayoutStrategy.h"
 #include "vtkSmartPointer.h"
+#include "vtkSpanTreeLayoutStrategy.h"
 #include "vtkSphereSource.h"
 #include "vtkTable.h"
 #include "vtkTextProperty.h"
@@ -74,7 +75,7 @@
 
 #include <vtkstd/algorithm>
 
-vtkCxxRevisionMacro(vtkRenderedGraphRepresentation, "1.5");
+vtkCxxRevisionMacro(vtkRenderedGraphRepresentation, "1.6");
 vtkStandardNewMacro(vtkRenderedGraphRepresentation);
 
 vtkRenderedGraphRepresentation::vtkRenderedGraphRepresentation()
@@ -748,6 +749,10 @@ void vtkRenderedGraphRepresentation::SetLayoutStrategy(vtkGraphLayoutStrategy* s
     {
     this->SetLayoutStrategyName("Cone");
     }
+  else if (vtkSpanTreeLayoutStrategy::SafeDownCast(s))
+    {
+    this->SetLayoutStrategyName("Span Tree");
+    }
   else
     {
     this->SetLayoutStrategyName("Unknown");
@@ -807,6 +812,10 @@ void vtkRenderedGraphRepresentation::SetLayoutStrategy(const char* name)
     {
     strategy = vtkSmartPointer<vtkConeLayoutStrategy>::New();
     }
+  else if (str == "spantree")
+    {
+    strategy = vtkSmartPointer<vtkSpanTreeLayoutStrategy>::New();
+    }
   else if (str != "passthrough")
     {
     vtkErrorMacro("Unknown layout strategy: \"" << name << "\"");

Views/vtkRenderedGraphRepresentation.h

@@ -173,6 +173,8 @@ public:
     { this->SetLayoutStrategy("Cosmic Tree"); }
   void SetLayoutStrategyToCone()
     { this->SetLayoutStrategy("Cone"); }
+  void SetLayoutStrategyToSpanTree()
+    { this->SetLayoutStrategy("Span Tree"); }
 
   // Description:
   // Set the layout strategy to use coordinates from arrays.