X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkDicomRT_ROI_ConvertToImageFilter.cxx;fp=tools%2FclitkDicomRT_ROI_ConvertToImageFilter.cxx;h=0000000000000000000000000000000000000000;hb=261a091dbabc5df821d4220a5a4a55f35e4d8eb0;hp=cedef817e23fcaa9beb8434765be2a99a91fd04d;hpb=82d0db04054ac02ddbd921427ddc2edf73d475a0;p=clitk.git

diff --git a/tools/clitkDicomRT_ROI_ConvertToImageFilter.cxx b/tools/clitkDicomRT_ROI_ConvertToImageFilter.cxx
deleted file mode 100644
index cedef81..0000000
--- a/tools/clitkDicomRT_ROI_ConvertToImageFilter.cxx
+++ /dev/null
@@ -1,191 +0,0 @@
-/*=========================================================================
-  Program:         vv http://www.creatis.insa-lyon.fr/rio/vv
-  Main authors :   XX XX XX
-
-  Authors belongs to: 
-  - University of LYON           http://www.universite-lyon.fr/
-  - Léon Bérard cancer center    http://oncora1.lyon.fnclcc.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       http://www.opensource.org/licenses/bsd-license.php
-  - CeCILL-B  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-
-  =========================================================================*/
-
-#include "clitkDicomRT_ROI_ConvertToImageFilter.h" 
-#include <vtkPolyDataToImageStencil.h>
-#include <vtkSmartPointer.h>
-#include <vtkImageStencil.h>
-#include <vtkLinearExtrusionFilter.h>
-#include <itkVTKImageToImageFilter.h>
-#include "clitkImageCommon.h"
-
-//--------------------------------------------------------------------
-clitk::DicomRT_ROI_ConvertToImageFilter::DicomRT_ROI_ConvertToImageFilter() {
-  mROI = NULL;
-  mImageInfoIsSet = false;
-  mWriteOutput = false;
-  mCropMask = true;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-clitk::DicomRT_ROI_ConvertToImageFilter::~DicomRT_ROI_ConvertToImageFilter() {
-  
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetROI(clitk::DicomRT_ROI * roi) {
-  mROI = roi;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetCropMaskEnabled(bool b) {
-  mCropMask = b;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputImageFilename(std::string s) {
-  mOutputFilename = s;
-  mWriteOutput = true;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetImageFilename(std::string f) {
-  itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
-  if (header->GetNumberOfDimensions() < 3) {
-    std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
-    exit(0);
-  }
-  if (header->GetNumberOfDimensions() > 3) {
-    std::cerr << "Warning dimension > 3 are ignored" << std::endl;
-  }
-  mSpacing.resize(3);
-  mOrigin.resize(3);
-  mSize.resize(3);
-  for(unsigned int i=0; i<3; i++) {
-    mSpacing[i] = header->GetSpacing(i);
-    mOrigin[i] = header->GetOrigin(i);
-    mSize[i] = header->GetDimensions(i);
-  }
-  mImageInfoIsSet = true;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::Update() {
-  if (!mROI) {
-    std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
-    exit(0);
-  }
-  if (!mImageInfoIsSet) {
-    std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
-    exit(0);
-  }
-  // DD("Update");
-  
-  // Get Mesh
-  vtkPolyData * mesh = mROI->GetMesh();
-  //  DD(mesh->GetNumberOfCells());
-  
-  // Get bounds
-  double *bounds=mesh->GetBounds(); 
-  // for(int i=0; i<6; i++){
-//     DD(bounds[i]);
-//   }
-
-  // Compute origin
-  std::vector<double> origin; 
-  origin.resize(3);
-  origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
-  origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
-  origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
-  
-  // Compute extend
-  std::vector<double> extend; 
-  extend.resize(3);
-  extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
-  extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
-  extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
-  
-  // If no crop, set initial image size/origin
-  if (!mCropMask) {
-    for(int i=0; i<3; i++) {
-      origin[i] = mOrigin[i];
-      extend[i] = mSize[i]-1;
-    }
-  }
-  
-  // Create new output image
-  mBinaryImage = vtkImageData::New();
-  mBinaryImage->SetScalarTypeToUnsignedChar();
-  mBinaryImage->SetOrigin(&origin[0]);
-  mBinaryImage->SetSpacing(&mSpacing[0]);
-  mBinaryImage->SetExtent(0, extend[0], 
-                          0, extend[1], 
-                          0, extend[2]);
-  mBinaryImage->AllocateScalars();
-
-  // for(int i=0; i<3; i++){
-  //     DD(origin[i]);
-  //     DD(extend[i]);
-  //     DD(mBinaryImage->GetDimensions()[i]);
-  //   }
-  memset(mBinaryImage->GetScalarPointer(), 0,
-         mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
-  
-  // Extrude
-  vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
-  extrude->SetInput(mesh);
-  ///We extrude in the -slice_spacing direction to respect the FOCAL convention // ?????????????
-  extrude->SetVector(0, 0, -mSpacing[2]);
-
-  // Binarization  
-  vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
-  //The following line is extremely important
-  //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
-  sts->SetTolerance(0);
-  sts->SetInformationInput(mBinaryImage);
-  sts->SetInput(extrude->GetOutput());
-  //sts->SetInput(mesh);
-
-  vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
-  stencil->SetStencil(sts->GetOutput());  
-  stencil->SetInput(mBinaryImage);
-  stencil->ReverseStencilOn();
-  stencil->Update();
-  mBinaryImage->ShallowCopy(stencil->GetOutput());
-  
-  if (mWriteOutput) {
-     typedef itk::Image<unsigned char, 3> ImageType;
-     typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
-     ConnectorType::Pointer connector = ConnectorType::New();
-     connector->SetInput(GetOutput());
-     connector->Update();
-     clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);  
-  }
-}
-//--------------------------------------------------------------------
-
-
-    
-//--------------------------------------------------------------------
-vtkImageData * clitk::DicomRT_ROI_ConvertToImageFilter::GetOutput() {
-  return mBinaryImage;
-}
-//--------------------------------------------------------------------