- First version of a VTK vtkImageData to vtkPolyData filter: mesh an

iso-value in a 3D image.

.gitignore

@@ -293,6 +293,7 @@ Surface_mesher/demo/Surface_mesher/.*.deps
 Surface_mesher/demo/Surface_mesher/VTK/*.exe
 Surface_mesher/demo/Surface_mesher/VTK/Makefile
 Surface_mesher/demo/Surface_mesher/VTK/mesh_a_3D_image
+Surface_mesher/demo/Surface_mesher/VTK/mesh_a_VTK_3D_image
 Surface_mesher/demo/Surface_mesher/dump.ff
 Surface_mesher/demo/Surface_mesher/implicit_surface_mesher
 Surface_mesher/demo/Surface_mesher/my_makefile

Surface_mesher/demo/Surface_mesher/VTK/CMakeLists.txt

@@ -45,6 +45,10 @@ SET (SRCS
   mesh_a_3D_image.cpp
 )
 
+SET (SRCS_VTK
+  mesh_a_VTK_3D_image.cpp
+)
+
 # Use the include path and library for Qt that is used by VTK.
 INCLUDE_DIRECTORIES( ${QT_INCLUDE_DIR} ${QT_QTGUI_INCLUDE_DIR}
                      ${QT_QTCORE_INCLUDE_DIR})
@@ -62,4 +66,22 @@ TARGET_LINK_LIBRARIES( mesh_a_3D_image
   CGAL-ImageIO
 )
 
+SET (SRCS_VTK
+  mesh_a_VTK_3D_image.cpp
+)
+
+ADD_EXECUTABLE( mesh_a_VTK_3D_image MACOSX_BUNDLE ${SRCS_VTK})
+
+TARGET_LINK_LIBRARIES( mesh_a_VTK_3D_image
+  QVTK
+  ${QT_LIBRARIES}
+  vtkRendering
+  vtkGraphics
+  vtkIO
+  vtkCommon
+  CGAL
+  CGAL-ImageIO
+)
+
+
 

Surface_mesher/demo/Surface_mesher/VTK/mesh_a_VTK_3D_image.cpp

@@ -0,0 +1,142 @@
+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    $RCSfile: Medical1.cxx,v $
+
+  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.
+
+=========================================================================*/
+//
+// This example reads a volume dataset, extracts an isosurface that
+// represents the skin and displays it.
+//
+
+#include "vtkRenderer.h"
+#include "vtkRenderWindow.h"
+#include "vtkRenderWindowInteractor.h"
+#include "vtkVolume16Reader.h"
+#include "vtkPolyDataMapper.h"
+#include "vtkActor.h"
+#include "vtkOutlineFilter.h"
+#include "vtkCamera.h"
+#include "vtkProperty.h"
+#include "vtkPolyDataNormals.h"
+#include <CGAL/vtkSurfaceMesherContourFilter.h>
+
+int main (int argc, char **argv)
+{
+  if (argc < 2)
+    {
+      cout << "Usage: " << argv[0] << " DATADIR/headsq/quarter" << endl;
+    return 1;
+    }
+
+  // Create the renderer, the render window, and the interactor. The renderer
+  // draws into the render window, the interactor enables mouse- and 
+  // keyboard-based interaction with the data within the render window.
+  //
+  vtkRenderer *aRenderer = vtkRenderer::New();
+  vtkRenderWindow *renWin = vtkRenderWindow::New();
+    renWin->AddRenderer(aRenderer);
+  vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
+    iren->SetRenderWindow(renWin);
+
+  // The following reader is used to read a series of 2D slices (images)
+  // that compose the volume. The slice dimensions are set, and the
+  // pixel spacing. The data Endianness must also be specified. The reader
+  // usese the FilePrefix in combination with the slice number to construct
+  // filenames using the format FilePrefix.%d. (In this case the FilePrefix
+  // is the root name of the file: quarter.)
+  vtkVolume16Reader *v16 = vtkVolume16Reader::New();
+    v16->SetDataDimensions (64,64);
+    v16->SetImageRange (1,93);
+    v16->SetDataByteOrderToLittleEndian();
+    v16->SetFilePrefix (argv[1]);
+    v16->SetDataSpacing (3.2, 3.2, 1.5);
+
+  // An isosurface, or contour value of 500 is known to correspond to the
+  // skin of the patient. Once generated, a vtkPolyDataNormals filter is
+  // is used to create normals for smooth surface shading during rendering.
+  vtkCGALSurfaceMesherContourFilter *skinExtractor = vtkCGALSurfaceMesherContourFilter::New();
+    skinExtractor->SetInputConnection(v16->GetOutputPort());
+    skinExtractor->SetValue(500);
+  vtkPolyDataNormals *skinNormals = vtkPolyDataNormals::New();
+    skinNormals->SetInputConnection(skinExtractor->GetOutputPort());
+    skinNormals->SetFeatureAngle(60.0);
+  vtkPolyDataMapper *skinMapper = vtkPolyDataMapper::New();
+    skinMapper->SetInputConnection(skinNormals->GetOutputPort());
+    skinMapper->ScalarVisibilityOff();
+  vtkActor *skin = vtkActor::New();
+    skin->SetMapper(skinMapper);
+
+  // An outline provides context around the data.
+  //
+  vtkOutlineFilter *outlineData = vtkOutlineFilter::New();
+    outlineData->SetInputConnection(v16->GetOutputPort());
+  vtkPolyDataMapper *mapOutline = vtkPolyDataMapper::New();
+    mapOutline->SetInputConnection(outlineData->GetOutputPort());
+  vtkActor *outline = vtkActor::New();
+    outline->SetMapper(mapOutline);
+    outline->GetProperty()->SetColor(0,0,0);
+
+  // It is convenient to create an initial view of the data. The FocalPoint
+  // and Position form a vector direction. Later on (ResetCamera() method)
+  // this vector is used to position the camera to look at the data in
+  // this direction.
+  vtkCamera *aCamera = vtkCamera::New();
+    aCamera->SetViewUp (0, 0, -1);
+    aCamera->SetPosition (0, 1, 0);
+    aCamera->SetFocalPoint (0, 0, 0);
+    aCamera->ComputeViewPlaneNormal();
+
+  // Actors are added to the renderer. An initial camera view is created.
+  // The Dolly() method moves the camera towards the FocalPoint,
+  // thereby enlarging the image.
+  aRenderer->AddActor(outline);
+  aRenderer->AddActor(skin);
+  aRenderer->SetActiveCamera(aCamera);
+  aRenderer->ResetCamera ();
+  aCamera->Dolly(1.5);
+
+  // Set a background color for the renderer and set the size of the
+  // render window (expressed in pixels).
+  aRenderer->SetBackground(1,1,1);
+  renWin->SetSize(640, 480);
+
+  // Note that when camera movement occurs (as it does in the Dolly()
+  // method), the clipping planes often need adjusting. Clipping planes
+  // consist of two planes: near and far along the view direction. The 
+  // near plane clips out objects in front of the plane; the far plane
+  // clips out objects behind the plane. This way only what is drawn
+  // between the planes is actually rendered.
+  aRenderer->ResetCameraClippingRange ();
+
+  // Initialize the event loop and then start it.
+  iren->Initialize();
+  iren->Start(); 
+
+  // It is important to delete all objects created previously to prevent
+  // memory leaks. In this case, since the program is on its way to
+  // exiting, it is not so important. But in applications it is
+  // essential.
+  v16->Delete();
+  skinExtractor->Delete();
+  skinNormals->Delete();
+  skinMapper->Delete();
+  skin->Delete();
+  outlineData->Delete();
+  mapOutline->Delete();
+  outline->Delete();
+  aCamera->Delete();
+  iren->Delete();
+  renWin->Delete();
+  aRenderer->Delete();
+
+  return 0;
+}

Surface_mesher/include/CGAL/vtkSurfaceMesherContourFilter.h

@@ -0,0 +1,156 @@
+// Copyright (c) 2008  GeometryFactory, Sophia-Antipolis (France).
+// All rights reserved.
+//
+// This file is part of CGAL (www.cgal.org); you may redistribute it under
+// the terms of the Q Public License version 1.0.
+// See the file LICENSE.QPL distributed with CGAL.
+//
+// Licensees holding a valid commercial license may use this file in
+// accordance with the commercial license agreement provided with the software.
+//
+// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+//
+// $URL$
+// $Id$
+//
+//
+// Author(s)     : Laurent Rineau
+
+#ifndef CGAL_VTK_SURFACE_MESHER_CONTOUR_FILTER_H
+#define CGAL_VTK_SURFACE_MESHER_CONTOUR_FILTER_H
+
+#include <vtkPolyDataAlgorithm.h>
+
+class vtkCGALSurfaceMesherContourFilter : public vtkPolyDataAlgorithm
+{
+public:
+  static vtkCGALSurfaceMesherContourFilter *New();
+  vtkTypeMacro(vtkCGALSurfaceMesherContourFilter,vtkPolyDataAlgorithm);
+  void PrintSelf(ostream& os, vtkIndent indent);
+
+  // Methods to set contour values
+  vtkSetMacro(Value,double);
+  vtkGetMacro(Value,double);
+
+protected:
+  vtkCGALSurfaceMesherContourFilter();
+  ~vtkCGALSurfaceMesherContourFilter();
+
+  virtual int FillInputPortInformation(int port, vtkInformation *info);
+
+  virtual int RequestData(vtkInformation *, vtkInformationVector **, vtkInformationVector *);
+
+  double Value;
+
+private:
+  vtkCGALSurfaceMesherContourFilter(const vtkCGALSurfaceMesherContourFilter&);  // Not implemented.
+  void operator=(const vtkCGALSurfaceMesherContourFilter&);  // Not implemented.
+};
+  
+// IMPLEMENTATION
+
+#include "vtkCellArray.h"
+#include "vtkImageData.h"
+#include "vtkInformation.h"
+#include "vtkInformationVector.h"
+#include "vtkObjectFactory.h"
+#include "vtkPointData.h"
+#include "vtkPolyData.h"
+
+#ifndef CGAL_USE_VTK
+#  define CGAL_USE_VTK
+#endif
+
+#include <CGAL/Image_3.h>
+#include <CGAL/Surface_mesh_default_triangulation_3.h>
+#include <CGAL/Surface_mesh_default_criteria_3.h>
+#include <CGAL/Complex_2_in_triangulation_3.h>
+#include <CGAL/IO/Complex_2_in_triangulation_3_file_writer.h>
+#include <CGAL/IO/Complex_2_in_triangulation_3_to_vtk.h>
+#include <CGAL/make_surface_mesh.h>
+#include <CGAL/Gray_level_image_3.h>
+#include <CGAL/Implicit_surface_3.h>
+
+vtkStandardNewMacro(vtkCGALSurfaceMesherContourFilter);
+
+vtkCGALSurfaceMesherContourFilter::vtkCGALSurfaceMesherContourFilter()
+{
+  Value = 0.;
+}
+  
+vtkCGALSurfaceMesherContourFilter::~vtkCGALSurfaceMesherContourFilter()
+{
+}
+
+int 
+vtkCGALSurfaceMesherContourFilter::
+FillInputPortInformation(int, vtkInformation *info)
+{
+  info->Set(vtkAlgorithm::INPUT_REQUIRED_DATA_TYPE(), "vtkImageData");
+  return 1;
+}
+
+void vtkCGALSurfaceMesherContourFilter::PrintSelf(ostream& os,
+                                                  vtkIndent indent)
+{
+  this->Superclass::PrintSelf(os,indent);
+
+  os << indent << "Value: " << this->Value << "\n";
+}
+
+int vtkCGALSurfaceMesherContourFilter::RequestData(
+  vtkInformation *vtkNotUsed(request),
+  vtkInformationVector **inputVector,
+  vtkInformationVector *outputVector)
+{
+  // get the info objects
+  vtkInformation *inInfo = inputVector[0]->GetInformationObject(0);
+  vtkInformation *outInfo = outputVector->GetInformationObject(0);
+
+  // get the input and ouptut
+  vtkImageData *inData = vtkImageData::SafeDownCast(
+    inInfo->Get(vtkDataObject::DATA_OBJECT()));
+  vtkPolyData *output = vtkPolyData::SafeDownCast(
+    outInfo->Get(vtkDataObject::DATA_OBJECT()));
+
+  typedef CGAL::Surface_mesh_default_triangulation_3 Tr;
+
+  // c2t3
+  typedef CGAL::Complex_2_in_triangulation_3<Tr> C2t3;
+
+  typedef Tr::Geom_traits GT;
+  typedef CGAL::Gray_level_image_3<GT::FT, GT::Point_3> Gray_level_image;
+  typedef CGAL::Implicit_surface_3<GT, Gray_level_image> Surface_3;
+
+  Tr tr;            // 3D-Delaunay triangulation
+  C2t3 c2t3 (tr);   // 2D-complex in 3D-Delaunay triangulation
+
+  CGAL::Image_3 image;
+  if(!image.read_vtk_image_data(inData))
+    return 0;
+  Gray_level_image gray_level_image(image, Value);
+
+  GT::FT radius = std::max(image.xdim() * image.vx(),
+                           std::max(image.ydim() * image.vy(),
+                                    image.zdim() * image.vz())
+                           );
+  GT::Sphere_3 bounding_sphere(GT::Point_3(image.xdim() * image.vx()/2.,
+                                           image.ydim() * image.vy()/2.,
+                                           image.zdim() * image.vz()/2.),
+                               radius*radius);
+  // definition of the surface, with 10^-2 as relative precision
+  Surface_3 surface(gray_level_image, bounding_sphere, 1e-5);
+  CGAL::Surface_mesh_default_criteria_3<Tr> criteria(30.,
+                                                     radius/100.,
+                                                     radius/500.);
+  // meshing surface, with the "manifold without boundary" algorithm
+  CGAL::make_surface_mesh(c2t3, surface, criteria, CGAL::Manifold_tag());
+
+  CGAL::output_c2t3_to_vtk_polydata(c2t3, output);
+  output->Squeeze();
+
+  return 1;
+}
+
+#endif // CGAL_VTK_SURFACE_MESHER_CONTOUR_FILTER_H