Merge branch 'master' of /home/dsarrut/clitk3.server

diff --git a/itk/clitkMeshToBinaryImageFilter.h b/itk/clitkMeshToBinaryImageFilter.h
index 67607b8c05846446ceaf193649054ed6eaaac471..acecc385558081696b5b5db039770c2edccbf313 100644 (file)
--- a/itk/clitkMeshToBinaryImageFilter.h
+++ b/itk/clitkMeshToBinaryImageFilter.h
@@ -22,6 +22,13 @@
 // clitk
 #include "clitkCommon.h"
 
+// itk
+#include <itkImageSource.h>
+
+// vtk
+#include <vtkSmartPointer.h>
+#include <vtkPolyData.h>
+
 namespace clitk {
     
   /* --------------------------------------------------------------------     
@@ -67,6 +74,9 @@ namespace clitk {
     itkSetMacro(LikeImage, ImagePointer);
     itkGetConstMacro(LikeImage, ImagePointer);
 
+    itkSetMacro(Extrude, bool);
+    itkGetMacro(Extrude, bool);
+
   protected:
     MeshToBinaryImageFilter();
     virtual ~MeshToBinaryImageFilter() {}
@@ -74,6 +84,7 @@ namespace clitk {
     virtual void GenerateOutputInformation();
     virtual void GenerateData();
 
+    bool m_Extrude;
     ImagePointer m_LikeImage;
     vtkSmartPointer<vtkPolyData> m_Mesh;
 

diff --git a/itk/clitkMeshToBinaryImageFilter.txx b/itk/clitkMeshToBinaryImageFilter.txx
index be482f5232dc0320c61022943e4b2bc72e5d628e..94424b8631ca4e9fa7d7e1f3c4af3fbf90bf1d70 100644 (file)
--- a/itk/clitkMeshToBinaryImageFilter.txx
+++ b/itk/clitkMeshToBinaryImageFilter.txx
@@ -30,7 +30,7 @@
 //--------------------------------------------------------------------
 template <class ImageType>
 clitk::MeshToBinaryImageFilter<ImageType>::
-MeshToBinaryImageFilter():itk::ImageSource<ImageType>()
+MeshToBinaryImageFilter() : itk::ImageSource<ImageType>(), m_Extrude(true)
 {
 }
 //--------------------------------------------------------------------
@@ -102,11 +102,16 @@ GenerateData()
   sts->SetInformationInput(binary_image);
     
   // Extrusion
-  vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
-  extrude->SetInput(m_Mesh);
-  // We extrude in the -slice_spacing direction to respect the FOCAL convention 
-  extrude->SetVector(0, 0, -m_LikeImage->GetSpacing()[2]);
-  sts->SetInput(extrude->GetOutput());
+  if (m_Extrude)
+  {
+    vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
+    extrude->SetInput(m_Mesh);
+    // We extrude in the -slice_spacing direction to respect the FOCAL convention 
+    extrude->SetVector(0, 0, -m_LikeImage->GetSpacing()[2]);
+    sts->SetInput(extrude->GetOutput());
+  }
+  else
+    sts->SetInput(m_Mesh);
 
   // Stencil
   vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 4ce6ac79a09b122a0649786ad601f51222870f2f..4bd6e1511c38e961a5b53ee8501d77aac805bcd8 100644 (file)
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -351,6 +351,11 @@ IF (CLITK_BUILD_TOOLS)
     TARGET_LINK_LIBRARIES(clitkBinaryImageToMesh ${ITK_LIBRARIES} vtkCommon vtkRendering)
     SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBinaryImageToMesh)
 
+    WRAP_GGO(clitkMeshToBinaryImage_GGO_C clitkMeshToBinaryImage.ggo)
+    ADD_EXECUTABLE(clitkMeshToBinaryImage clitkMeshToBinaryImage.cxx ${clitkMeshToBinaryImage_GGO_C})
+    TARGET_LINK_LIBRARIES(clitkMeshToBinaryImage clitkCommon ${ITK_LIBRARIES} ${VTK_LIBRARIES})
+    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshToBinaryImage)
+
     WRAP_GGO(clitkMeshViewer_GGO_C clitkMeshViewer.ggo)
     ADD_EXECUTABLE(clitkMeshViewer clitkMeshViewer.cxx ${clitkMeshViewer_GGO_C})
     TARGET_LINK_LIBRARIES(clitkMeshViewer vtkCommon vtkRendering)

diff --git a/tools/clitkMeshToBinaryImage.cxx b/tools/clitkMeshToBinaryImage.cxx
new file mode 100644 (file)
index 0000000..2c3d8cc
--- /dev/null
+++ b/tools/clitkMeshToBinaryImage.cxx
@@ -0,0 +1,94 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to:
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================*/
+#include "clitkMeshToBinaryImage_ggo.h"
+#include "clitkMeshToBinaryImageFilter.h"
+#include "clitkCommon.h"
+#include "clitkImageCommon.h"
+
+#include <itkImageIOBase.h>
+#include <itkInvertIntensityImageFilter.h>
+
+#include <vtkOBJReader.h>
+
+#include <string>
+
+template <unsigned dim>
+void run(const args_info_clitkMeshToBinaryImage& argsInfo,
+         const itk::ImageIOBase * header)
+{
+  typedef itk::Image<unsigned char, dim> ImageType;
+  typename ImageType::Pointer like = ImageType::New();
+
+  typename ImageType::SizeType size;
+  for (unsigned i = 0; i < dim; ++i)
+    size[i] = header->GetDimensions(i);
+  typename ImageType::RegionType region;
+  region.SetSize(size);
+  like->SetRegions(region);
+
+  typename ImageType::SpacingType spacing;
+  for (unsigned i = 0; i < dim; ++i)
+    spacing[i] = header->GetSpacing(i);
+  like->SetSpacing(spacing);
+
+
+  typename ImageType::PointType origin;
+  for (unsigned i = 0; i < dim; ++i)
+    origin[i] = header->GetOrigin(i);
+  like->SetOrigin(origin);
+
+  vtkSmartPointer<vtkOBJReader> reader = vtkOBJReader::New();
+  reader->SetFileName(argsInfo.input_arg);
+  reader->Update();
+
+  typename clitk::MeshToBinaryImageFilter<ImageType>::Pointer filter =
+    clitk::MeshToBinaryImageFilter<ImageType>::New();
+  filter->SetExtrude(false);
+  filter->SetMesh(reader->GetOutput());
+  filter->SetLikeImage(like);
+  filter->Update();
+
+  typedef itk::InvertIntensityImageFilter<ImageType> InvertFilterType;
+  typename InvertFilterType::Pointer ifilter = InvertFilterType::New();
+  ifilter->SetInput(filter->GetOutput());
+  ifilter->SetMaximum(1);
+
+  clitk::writeImage(ifilter->GetOutput(), argsInfo.output_arg);
+}
+
+int main(int argc, char** argv)
+{
+  GGO(clitkMeshToBinaryImage, args_info);
+
+  itk::ImageIOBase::Pointer header =
+    clitk::readImageHeader(args_info.like_arg);
+  switch (header->GetNumberOfDimensions())
+  {
+    case 2:
+      run<2>(args_info, header);
+      break;
+    case 3:
+      run<3>(args_info, header);
+      break;
+    case 4:
+      run<4>(args_info, header);
+      break;
+  }
+
+  return EXIT_SUCCESS;
+}

diff --git a/tools/clitkMeshToBinaryImage.ggo b/tools/clitkMeshToBinaryImage.ggo
new file mode 100644 (file)
index 0000000..64577b3
--- /dev/null
+++ b/tools/clitkMeshToBinaryImage.ggo
@@ -0,0 +1,11 @@
+#File clitkBinaryImageToMesh.ggo
+package "clitkMeshToBinaryImage"
+version "1.0"
+purpose "Transform a vtk obj file into a binary mask"
+
+option "config"   - "Config file"   string  no
+option "verbose"  v     "Verbose"   flag  off
+
+option "input"      i "Input obj file"   string  yes
+option "output"     o "Output binary image"  string yes 
+option "like"       l "Output image will be like this one (size, spacing)"  string yes