New class for extracting surfaces from label masks

The discrete flying edges classes extract isocontours from label masks.
Label masks are not continuous so special interpolation and treatment is
required. Each contour value generates a separate region.

Also, documentation in the form of cross referencing other contouring
classes was added. The discrete isocontouring classes are not well known
but very powerful and should be used more often.

Filters/Core/vtkContourFilter.h

@@ -40,8 +40,9 @@
  * normals.
  *
  * @sa
- * vtkMarchingContourFilter vtkMarchingCubes vtkSliceCubes
- * vtkMarchingSquares vtkImageMarchingCubes
+ * vtkFlyingEdges3D vtkFlyingEdges2D vtkDiscreteFlyingEdges3D
+ * vtkDiscreteFlyingEdges2D vtkMarchingContourFilter vtkMarchingCubes
+ * vtkSliceCubes vtkMarchingSquares vtkImageMarchingCubes
 */
 
 #ifndef vtkContourFilter_h
@@ -294,5 +295,3 @@ inline void vtkContourFilter::GenerateValues(int numContours, double
 
 
 #endif
-
-

Filters/Core/vtkFlyingEdges3D.h

@@ -55,7 +55,7 @@
  *
  * @sa
  * vtkContourFilter vtkFlyingEdges2D vtkSynchronizedTemplates3D
- * vtkMarchingCubes vtkSMPFlyingEdges3D
+ * vtkMarchingCubes vtkDiscreteFlyingEdges3D
 */
 
 #ifndef vtkFlyingEdges3D_h

Filters/Core/vtkMarchingCubes.h

@@ -26,8 +26,22 @@
  * This filter is specialized to volumes. If you are interested in
  * contouring other types of data, use the general vtkContourFilter. If you
  * want to contour an image (i.e., a volume slice), use vtkMarchingSquares.
+ *
+ * @sa
+ * Much faster implementations for isocontouring are available. In
+ * particular, vtkFlyingEdges3D and vtkFlyingEdges2D are much faster
+ * and if built with the right options, multithreaded, and scale well
+ * with additional processors.
+ *
+ * @sa
+ * If you are interested in extracting surfaces from label maps,
+ * consider using vtkDiscreteFlyingEdges3D, vtkDiscreteFlyingEdges2D, or
+ * vtkDiscreteMarchingCubes.
+ *
  * @sa
- * vtkContourFilter vtkSliceCubes vtkMarchingSquares vtkDividingCubes
+ * vtkFlyingEdges3D vtkFlyingEdges2D vtkSynchronizedTemplates3D
+ * vtkSynchronizedTemplates2D vtkContourFilter vtkSliceCubes
+ * vtkMarchingSquares vtkDividingCubes vtkDiscreteMarchingCubes
 */
 
 #ifndef vtkMarchingCubes_h

Filters/General/CMakeLists.txt

@@ -28,6 +28,8 @@ set(Module_SRCS
   vtkDeformPointSet.cxx
   vtkDensifyPolyData.cxx
   vtkDicer.cxx
+  vtkDiscreteFlyingEdges2D.cxx
+  vtkDiscreteFlyingEdges3D.cxx
   vtkDiscreteMarchingCubes.cxx
   vtkEdgePoints.cxx
   vtkExtractSelectedFrustum.cxx

Filters/General/Testing/Data/Baseline/TestDiscreteFlyingEdges2D.png.md5

@@ -0,0 +1 @@
+571c2c61232b41a961352e2fd036d984

Filters/General/Testing/Data/Baseline/TestDiscreteFlyingEdges2D_1.png.md5

@@ -0,0 +1 @@
+ebac6173f98ecd9d5eeb37a16ae17377

Filters/General/Testing/Data/Baseline/TestDiscreteFlyingEdges2D_2.png.md5

@@ -0,0 +1 @@
+20753aecfc1b8ff6ca4880d4ed8945dc

Filters/General/Testing/Data/Baseline/TestDiscreteFlyingEdges2D_3.png.md5

@@ -0,0 +1 @@
+20753aecfc1b8ff6ca4880d4ed8945dc

Filters/General/Testing/Data/Baseline/TestDiscreteFlyingEdges3D.png.md5

@@ -0,0 +1 @@
+7c4def60144af2d5fd57976222bd5d26

Filters/General/Testing/Python/CMakeLists.txt

@@ -7,6 +7,8 @@ vtk_add_test_python(
   TestClipOutline.py
   TestCurvatures.py
   TestDeformPointSet.py
+  TestDiscreteFlyingEdges2D.py
+  TestDiscreteFlyingEdges3D.py
   TestDiscreteMarchingCubes.py
   TestDiscreteMarchingCubesAdjacentScalars.py
   TestGraphLayoutFilter.py

Filters/General/Testing/Python/TestDiscreteFlyingEdges2D.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the RenderWindow, Renderer and both Actors
+#
+ren1 = vtk.vtkRenderer()
+ren1.SetBackground(1,1,1)
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren1)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+# Read the data. Note this creates a 3-component scalar.
+red = vtk.vtkPNGReader()
+red.SetFileName(VTK_DATA_ROOT + "/Data/RedCircle.png")
+red.Update()
+
+# Next filter can only handle RGB *(&&*@
+extract = vtk.vtkImageExtractComponents()
+extract.SetInputConnection(red.GetOutputPort())
+extract.SetComponents(0,1,2)
+
+# Quantize the image into an index
+quantize = vtk.vtkImageQuantizeRGBToIndex()
+quantize.SetInputConnection(extract.GetOutputPort())
+quantize.SetNumberOfColors(3)
+
+# Create the pipeline
+discrete = vtk.vtkDiscreteFlyingEdges2D()
+discrete.SetInputConnection(quantize.GetOutputPort())
+discrete.SetValue(0,0)
+
+# Create polgons
+polyLoops = vtk.vtkContourLoopExtraction()
+polyLoops.SetInputConnection(discrete.GetOutputPort())
+
+# Triangle filter because concave polygons are not rendered correctly
+triF = vtk.vtkTriangleFilter()
+triF.SetInputConnection(polyLoops.GetOutputPort())
+
+# Polylines are generated
+mapper = vtk.vtkPolyDataMapper()
+mapper.SetInputConnection(discrete.GetOutputPort())
+mapper.ScalarVisibilityOff()
+
+actor = vtk.vtkActor()
+actor.SetMapper(mapper)
+actor.GetProperty().SetColor(0,0,0)
+
+# Polygons are displayed
+polyMapper = vtk.vtkPolyDataMapper()
+polyMapper.SetInputConnection(triF.GetOutputPort())
+
+polyActor = vtk.vtkActor()
+polyActor.SetMapper(polyMapper)
+
+ren1.AddActor(actor)
+ren1.AddActor(polyActor)
+
+renWin.Render()
+iren.Start()

Filters/General/Testing/Python/TestDiscreteFlyingEdges3D.py

@@ -0,0 +1,90 @@
+#!/usr/bin/env python
+import vtk
+from vtk.util.misc import vtkGetDataRoot
+VTK_DATA_ROOT = vtkGetDataRoot()
+
+# Create the RenderWindow, Renderer and both Actors
+#
+ren1 = vtk.vtkRenderer()
+renWin = vtk.vtkRenderWindow()
+renWin.AddRenderer(ren1)
+iren = vtk.vtkRenderWindowInteractor()
+iren.SetRenderWindow(renWin)
+
+math = vtk.vtkMath()
+
+# Generate some random colors
+def MakeColors (lut, n):
+    lut.SetNumberOfColors(n)
+    lut.SetTableRange(0, n - 1)
+    lut.SetScaleToLinear()
+    lut.Build()
+    lut.SetTableValue(0, 0, 0, 0, 1)
+    math.RandomSeed(5071)
+    i = 1
+    while i < n:
+        lut.SetTableValue(i, math.Random(.2, 1),
+          math.Random(.2, 1), math.Random(.2, 1), 1)
+        i += 1
+
+lut = vtk.vtkLookupTable()
+MakeColors(lut, 256)
+n = 20
+radius = 10
+
+# This has been moved outside the loop so that the code can be correctly
+# translated to python
+blobImage = vtk.vtkImageData()
+
+i = 0
+while i < n:
+    sphere = vtk.vtkSphere()
+    sphere.SetRadius(radius)
+    max = 50 - radius
+    sphere.SetCenter(int(math.Random(-max, max)),
+      int(math.Random(-max, max)), int(math.Random(-max, max)))
+
+    sampler = vtk.vtkSampleFunction()
+    sampler.SetImplicitFunction(sphere)
+    sampler.SetOutputScalarTypeToFloat()
+    sampler.SetSampleDimensions(51, 51, 51)
+    sampler.SetModelBounds(-50, 50, -50, 50, -50, 50)
+
+    thres = vtk.vtkImageThreshold()
+    thres.SetInputConnection(sampler.GetOutputPort())
+    thres.ThresholdByLower(radius * radius)
+    thres.ReplaceInOn()
+    thres.ReplaceOutOn()
+    thres.SetInValue(i + 1)
+    thres.SetOutValue(0)
+    thres.Update()
+    if (i == 0):
+        blobImage.DeepCopy(thres.GetOutput())
+
+    maxValue = vtk.vtkImageMathematics()
+    maxValue.SetInputData(0, blobImage)
+    maxValue.SetInputData(1, thres.GetOutput())
+    maxValue.SetOperationToMax()
+    maxValue.Modified()
+    maxValue.Update()
+
+    blobImage.DeepCopy(maxValue.GetOutput())
+
+    i += 1
+
+discrete = vtk.vtkDiscreteFlyingEdges3D()
+discrete.SetInputData(blobImage)
+discrete.GenerateValues(n, 1, n)
+
+mapper = vtk.vtkPolyDataMapper()
+mapper.SetInputConnection(discrete.GetOutputPort())
+mapper.SetLookupTable(lut)
+mapper.SetScalarRange(0, lut.GetNumberOfColors())
+
+actor = vtk.vtkActor()
+actor.SetMapper(mapper)
+
+ren1.AddActor(actor)
+
+renWin.Render()
+iren.Start()

Filters/General/Testing/Python/TestDiscreteMarchingCubes.py

@@ -87,5 +87,4 @@ def MakeColors (lut, n):
 ren1.AddActor(actor)
 
 renWin.Render()
-
-#iren.Start()
+iren.Start()