--- /dev/null
+/*=========================================================================
+ 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://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 http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+#include <iterator>
+#include <algorithm>
+
+// clitk
+#include "clitkDicomRTStruct2ImageFilter.h"
+#include "clitkImageCommon.h"
+
+// vtk
+#include <vtkPolyDataToImageStencil.h>
+#include <vtkSmartPointer.h>
+#include <vtkImageStencil.h>
+#include <vtkLinearExtrusionFilter.h>
+#include <vtkMetaImageWriter.h>
+
+
+//--------------------------------------------------------------------
+clitk::DicomRTStruct2ImageFilter::DicomRTStruct2ImageFilter()
+{
+ mROI = NULL;
+ mWriteOutput = false;
+ mCropMask = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+clitk::DicomRTStruct2ImageFilter::~DicomRTStruct2ImageFilter()
+{
+
+}
+//--------------------------------------------------------------------
+
+bool clitk::DicomRTStruct2ImageFilter::ImageInfoIsSet() const
+{
+ return mSize.size() && mSpacing.size() && mOrigin.size();
+}
+
+//--------------------------------------------------------------------
+void clitk::DicomRTStruct2ImageFilter::SetROI(clitk::DicomRT_ROI * roi)
+{
+ mROI = roi;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRTStruct2ImageFilter::SetCropMaskEnabled(bool b)
+{
+ mCropMask = b;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRTStruct2ImageFilter::SetOutputImageFilename(std::string s)
+{
+ mOutputFilename = s;
+ mWriteOutput = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRTStruct2ImageFilter::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);
+ }
+}
+//--------------------------------------------------------------------
+
+void clitk::DicomRTStruct2ImageFilter::SetOutputOrigin(const double* origin)
+{
+ std::copy(origin,origin+3,std::back_inserter(mOrigin));
+}
+//--------------------------------------------------------------------
+void clitk::DicomRTStruct2ImageFilter::SetOutputSpacing(const double* spacing)
+{
+ std::copy(spacing,spacing+3,std::back_inserter(mSpacing));
+}
+//--------------------------------------------------------------------
+void clitk::DicomRTStruct2ImageFilter::SetOutputSize(const unsigned long* size)
+{
+ std::copy(size,size+3,std::back_inserter(mSize));
+}
+
+//--------------------------------------------------------------------
+void clitk::DicomRTStruct2ImageFilter::Update()
+{
+ if (!mROI) {
+ std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
+ exit(0);
+ }
+ if (!ImageInfoIsSet()) {
+ std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
+ exit(0);
+ }
+
+ // Get Mesh
+ vtkPolyData * mesh = mROI->GetMesh();
+
+ // 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 = vtkSmartPointer<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 (NEEDED !)
+ 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();
+
+ /*
+ vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
+ w->SetInput(stencil->GetOutput());
+ w->SetFileName("binary2.mhd");
+ w->Write();
+ */
+
+ 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::DicomRTStruct2ImageFilter::GetOutput()
+{
+ assert(mBinaryImage);
+ return mBinaryImage;
+}
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff