/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Program: vv
- Language: C++
- Author : Joel Schaerer (joel.schaerer@insa-lyon.fr)
+ 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
-Copyright (C) 2008
-Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
-CREATIS-LRMN 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.
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, version 3 of the License.
+ It is distributed under dual licence
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-=========================================================================*/
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
#include <QProgressDialog>
#include <QWidget>
#include <itkImage.h>
//====================================================================
vvImageWarp::vvImageWarp(vvImage::Pointer input,vvImage::Pointer vf,unsigned int ref_image,QWidget* parent):
- mRefImage(ref_image),
- parent_window(parent),
- mInputImage(input),
- mVF(vf)
+ mRefImage(ref_image),
+ parent_window(parent),
+ mInputImage(input),
+ mVF(vf)
{}
//====================================================================
template<unsigned int Dim>
-void vvImageWarp::Update_WithDim() {
+void vvImageWarp::Update_WithDim()
+{
#define TRY_TYPE(TYPE) \
- if (clitk::IsSameType<TYPE>(mInputImage->GetScalarTypeAsString())) { this->Update_WithDimAndPixelType<Dim, TYPE>(); return; }
+ if (clitk::IsSameType<TYPE>(mInputImage->GetScalarTypeAsITKString())) { this->Update_WithDimAndPixelType<Dim, TYPE>(); return; }
// TRY_TYPE(signed char);
// TRY_TYPE(uchar);
- TRY_TYPE(short);
+ TRY_TYPE(short);
// TRY_TYPE(ushort);
// TRY_TYPE(int); // no uint ...
// TRY_TYPE(float);
- //TRY_TYPE(double);
+ //TRY_TYPE(double);
#undef TRY_TYPE
- std::string list = clitk::CreateListOfTypes<char, clitk::uchar, short, ushort, int, float, double>();
- std::cerr << "Error, I don't know the type '" << mInputImage->GetScalarTypeAsString() << "' for the input image. "
- << std::endl << "Known types are " << list << std::endl;
- exit(0);
+ std::string list = clitk::CreateListOfTypes<char, clitk::uchar, short, ushort, int, float, double>();
+ std::cerr << "Error, I don't know the type '" << mInputImage->GetScalarTypeAsITKString() << "' for the input image. "
+ << std::endl << "Known types are " << list << std::endl;
+ exit(0);
}
//====================================================================
template<unsigned int Dim, class PixelType>
-void vvImageWarp::Update_WithDimAndPixelType() {
- QProgressDialog progress(parent_window);
- progress.setCancelButton(0);
- progress.setLabelText("Computing warped and ventilation images...");
- progress.show();
- typedef itk::Image<PixelType,Dim> ImageType;
- typedef itk::Image<float,Dim> JacobianImageType;
- typedef itk::Image<itk::Vector<float,Dim>,Dim> VectorImageType;
- typedef std::vector<typename ImageType::ConstPointer> ImageSeriesType;
- ImageSeriesType input = vvImageToITKImageVector<Dim,PixelType>(mInputImage);
- ImageSeriesType output;
-
- typename itk::VTKImageToImageFilter<VectorImageType>::Pointer vf_connector=
- itk::VTKImageToImageFilter<VectorImageType>::New();
-
- //Warp, then join, then convert to vv
- typedef itk::WarpImageFilter<ImageType,ImageType,VectorImageType> WarpFilterType;
- typedef itk::DisplacementFieldJacobianDeterminantFilter<VectorImageType> JacobianFilterType;
- vvImage::Pointer result=vvImage::New();
- typedef itk::JoinSeriesImageFilter< ImageType,itk::Image<PixelType,Dim+1> > JoinFilterType;
- typedef itk::JoinSeriesImageFilter< JacobianImageType,itk::Image<float,Dim+1> > JacobianJoinFilterType;
- typename JoinFilterType::Pointer join=JoinFilterType::New();
- typename JoinFilterType::Pointer diff_join=JoinFilterType::New();
- typename JacobianJoinFilterType::Pointer jacobian_join=JacobianJoinFilterType::New();
- join->SetSpacing(1);
- join->SetOrigin(0); //Set the temporal origin
- diff_join->SetSpacing(1);
- diff_join->SetOrigin(0);
- jacobian_join->SetSpacing(1);
- jacobian_join->SetOrigin(0);
- typedef itk::SubtractImageFilter<ImageType,ImageType,ImageType> DiffFilter;
- std::vector<typename ImageType::Pointer> warped_images;
-
- for (unsigned int num = 0; num < input.size(); num++)
- {
- typename WarpFilterType::Pointer warp_filter=WarpFilterType::New();
- typename JacobianFilterType::Pointer jacobian_filter=JacobianFilterType::New();
- jacobian_filter->SetUseImageSpacingOn();
- vf_connector->SetInput(mVF->GetVTKImages()[num]);
- warp_filter->SetInput(input[num]);
- warp_filter->SetDeformationField(vf_connector->GetOutput());
- jacobian_filter->SetInput(vf_connector->GetOutput());
- warp_filter->SetOutputSpacing(input[num]->GetSpacing());
- warp_filter->SetOutputOrigin(input[num]->GetOrigin());
- warp_filter->SetEdgePaddingValue(-1000);
- warp_filter->Update();
- jacobian_filter->Update();
- warped_images.push_back(warp_filter->GetOutput());
- jacobian_join->PushBackInput(jacobian_filter->GetOutput());
- join->PushBackInput(warp_filter->GetOutput());
- progress.setValue(progress.value()+1);
- }
- for (typename std::vector<typename ImageType::Pointer>::const_iterator i = warped_images.begin(); i!=warped_images.end();i++)
- {
- typename DiffFilter::Pointer diff_filter = DiffFilter::New();
- diff_filter->SetInput2(*i);
- diff_filter->SetInput1(*(warped_images.begin()+mRefImage));
- diff_filter->Update();
- diff_join->PushBackInput(diff_filter->GetOutput());
- progress.setValue(progress.value()+1);
- }
- join->Update();
- diff_join->Update();
- jacobian_join->Update();
- mWarpedImage = vvImageFromITK<Dim+1,PixelType>(join->GetOutput());
- mDiffImage = vvImageFromITK<Dim+1,PixelType>(diff_join->GetOutput());
- mJacobianImage = vvImageFromITK<Dim+1,float>(jacobian_join->GetOutput());
- //mJacobianImage = vvImageFromITK<Dim,float>(temporal_filter->GetOutput());
+void vvImageWarp::Update_WithDimAndPixelType()
+{
+ QProgressDialog progress(parent_window);
+ progress.setCancelButton(0);
+ progress.setLabelText("Computing warped and ventilation images...");
+ progress.show();
+ typedef itk::Image<PixelType,Dim> ImageType;
+ typedef itk::Image<float,Dim> JacobianImageType;
+ typedef itk::Image<itk::Vector<float,Dim>,Dim> VectorImageType;
+ typedef std::vector<typename ImageType::ConstPointer> ImageSeriesType;
+ ImageSeriesType input = vvImageToITKImageVector<Dim,PixelType>(mInputImage);
+ ImageSeriesType output;
+
+ typename itk::VTKImageToImageFilter<VectorImageType>::Pointer vf_connector=
+ itk::VTKImageToImageFilter<VectorImageType>::New();
+
+ //Warp, then join, then convert to vv
+ typedef itk::WarpImageFilter<ImageType,ImageType,VectorImageType> WarpFilterType;
+ typedef itk::DisplacementFieldJacobianDeterminantFilter<VectorImageType> JacobianFilterType;
+ vvImage::Pointer result=vvImage::New();
+ typedef itk::JoinSeriesImageFilter< ImageType,itk::Image<PixelType,Dim+1> > JoinFilterType;
+ typedef itk::JoinSeriesImageFilter< JacobianImageType,itk::Image<float,Dim+1> > JacobianJoinFilterType;
+ typename JoinFilterType::Pointer join=JoinFilterType::New();
+ typename JoinFilterType::Pointer diff_join=JoinFilterType::New();
+ typename JacobianJoinFilterType::Pointer jacobian_join=JacobianJoinFilterType::New();
+ join->SetSpacing(1);
+ join->SetOrigin(0); //Set the temporal origin
+ diff_join->SetSpacing(1);
+ diff_join->SetOrigin(0);
+ jacobian_join->SetSpacing(1);
+ jacobian_join->SetOrigin(0);
+ typedef itk::SubtractImageFilter<ImageType,ImageType,ImageType> DiffFilter;
+ std::vector<typename ImageType::Pointer> warped_images;
+
+ for (unsigned int num = 0; num < input.size(); num++) {
+ typename WarpFilterType::Pointer warp_filter=WarpFilterType::New();
+ typename JacobianFilterType::Pointer jacobian_filter=JacobianFilterType::New();
+ jacobian_filter->SetUseImageSpacingOn();
+ vf_connector->SetInput(mVF->GetVTKImages()[num]);
+ warp_filter->SetInput(input[num]);
+#if ITK_VERSION_MAJOR >= 4
+ warp_filter->SetDisplacementField(vf_connector->GetOutput());
+#else
+ warp_filter->SetDeformationField(vf_connector->GetOutput());
+#endif
+ jacobian_filter->SetInput(vf_connector->GetOutput());
+ warp_filter->SetOutputSpacing(input[num]->GetSpacing());
+ warp_filter->SetOutputOrigin(input[num]->GetOrigin());
+ warp_filter->SetEdgePaddingValue(-1000);
+ warp_filter->Update();
+ jacobian_filter->Update();
+ warped_images.push_back(warp_filter->GetOutput());
+ jacobian_join->PushBackInput(jacobian_filter->GetOutput());
+ join->PushBackInput(warp_filter->GetOutput());
+ progress.setValue(progress.value()+1);
+ }
+ for (typename std::vector<typename ImageType::Pointer>::const_iterator i = warped_images.begin(); i!=warped_images.end(); i++) {
+ typename DiffFilter::Pointer diff_filter = DiffFilter::New();
+ diff_filter->SetInput2(*i);
+ diff_filter->SetInput1(*(warped_images.begin()+mRefImage));
+ diff_filter->Update();
+ diff_join->PushBackInput(diff_filter->GetOutput());
+ progress.setValue(progress.value()+1);
+ }
+ join->Update();
+ diff_join->Update();
+ jacobian_join->Update();
+ mWarpedImage = vvImageFromITK<Dim+1,PixelType>(join->GetOutput());
+ mDiffImage = vvImageFromITK<Dim+1,PixelType>(diff_join->GetOutput());
+ mJacobianImage = vvImageFromITK<Dim+1,float>(jacobian_join->GetOutput());
+ //mJacobianImage = vvImageFromITK<Dim,float>(temporal_filter->GetOutput());
}
//====================================================================
//
bool vvImageWarp::ComputeWarpedImage()
{
- for (int i=0;i<mInputImage->GetNumberOfDimensions();i++)
- {
- if (mInputImage->GetSpacing()[i] != mVF->GetSpacing()[i])
- return false;
- }
- switch (mInputImage->GetNumberOfDimensions())
- {
+ for (int i=0; i<mInputImage->GetNumberOfDimensions(); i++) {
+ if (mInputImage->GetSpacing()[i] != mVF->GetSpacing()[i])
+ return false;
+ }
+ switch (mInputImage->GetNumberOfDimensions()) {
// case 2: this->Update_WithDim<2>(); break;;
// case 3: this->Update_WithDim<3>(); break;;
- case 4:
- this->Update_WithDim<3>();
- break;;
- default:
- DD("Error: dimension not handled.");
- }
- return true;
+ case 4:
+ this->Update_WithDim<3>();
+ break;;
+ default:
+ DD("Error: dimension not handled.");
+ }
+ return true;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff