convert a DicomStruct into a binary image

[clitk.git] / tools / clitkDicomRT_ROI_ConvertToImageFilter.cxx

diff --git a/tools/clitkDicomRT_ROI_ConvertToImageFilter.cxx b/tools/clitkDicomRT_ROI_ConvertToImageFilter.cxx
new file mode 100644 (file)
index 0000000..cedef81
--- /dev/null
+++ b/tools/clitkDicomRT_ROI_ConvertToImageFilter.cxx
@@ -0,0 +1,191 @@
+/*=========================================================================
+  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;
+}
+//--------------------------------------------------------------------