Program: vv http://www.creatis.insa-lyon.fr/rio/vv
Main authors : XX XX XX
- Authors belongs to:
+ Authors belongs to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.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
=========================================================================*/
-#include "clitkDicomRT_ROI_ConvertToImageFilter.h"
+#include <iterator>
+#include <algorithm>
+#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() {
+clitk::DicomRT_ROI_ConvertToImageFilter::DicomRT_ROI_ConvertToImageFilter()
+{
mROI = NULL;
- mImageInfoIsSet = false;
mWriteOutput = false;
mCropMask = true;
}
//--------------------------------------------------------------------
-clitk::DicomRT_ROI_ConvertToImageFilter::~DicomRT_ROI_ConvertToImageFilter() {
-
+clitk::DicomRT_ROI_ConvertToImageFilter::~DicomRT_ROI_ConvertToImageFilter()
+{
+
}
//--------------------------------------------------------------------
+bool clitk::DicomRT_ROI_ConvertToImageFilter::ImageInfoIsSet() const
+{
+ return mSize.size() && mSpacing.size() && mOrigin.size();
+}
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetROI(clitk::DicomRT_ROI * roi) {
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetROI(clitk::DicomRT_ROI * roi)
+{
mROI = roi;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetCropMaskEnabled(bool b) {
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetCropMaskEnabled(bool b)
+{
mCropMask = b;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputImageFilename(std::string s) {
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputImageFilename(std::string s)
+{
mOutputFilename = s;
mWriteOutput = true;
}
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::SetImageFilename(std::string f) {
+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;
mOrigin[i] = header->GetOrigin(i);
mSize[i] = header->GetDimensions(i);
}
- mImageInfoIsSet = true;
}
//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputOrigin(const double* origin)
+{
+ std::copy(origin,origin+3,std::back_inserter(mOrigin));
+}
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputSpacing(const double* spacing)
+{
+ std::copy(spacing,spacing+3,std::back_inserter(mSpacing));
+}
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputSize(const unsigned long* size)
+{
+ std::copy(size,size+3,std::back_inserter(mSize));
+}
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI_ConvertToImageFilter::Update() {
+void clitk::DicomRT_ROI_ConvertToImageFilter::Update()
+{
if (!mROI) {
std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
exit(0);
}
- if (!mImageInfoIsSet) {
+ if (!ImageInfoIsSet()) {
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();
+ double *bounds=mesh->GetBounds();
// for(int i=0; i<6; i++){
// DD(bounds[i]);
// }
// Compute origin
- std::vector<double> 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;
+ 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++) {
extend[i] = mSize[i]-1;
}
}
-
+
// Create new output image
- mBinaryImage = vtkImageData::New();
+ mBinaryImage = vtkSmartPointer<vtkImageData>::New();
mBinaryImage->SetScalarTypeToUnsignedChar();
mBinaryImage->SetOrigin(&origin[0]);
mBinaryImage->SetSpacing(&mSpacing[0]);
- mBinaryImage->SetExtent(0, extend[0],
- 0, extend[1],
+ mBinaryImage->SetExtent(0, extend[0],
+ 0, extend[1],
0, extend[2]);
mBinaryImage->AllocateScalars();
// }
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]);
+ extrude->SetVector(0, 0, mROI->GetContourSpacing());
- // Binarization
+ // Binarization
vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
//The following line is extremely important
//http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
//sts->SetInput(mesh);
vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
- stencil->SetStencil(sts->GetOutput());
+ 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);
+ 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() {
+vtkImageData * clitk::DicomRT_ROI_ConvertToImageFilter::GetOutput()
+{
+ assert(mBinaryImage);
return mBinaryImage;
}
//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff