int main(int argc,char ** argv){
typedef itk::Image<float,3> ImageType;
typedef itk::Image<float,2> SliceType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<SliceType> WriterType;
typedef itk::BoundedReciprocalImageFilter<ImageType,ImageType> BoundedReciprocalType;
BoundedReciprocalType::Pointer boundedReciprocal = BoundedReciprocalType::New();
typedef ttt::AdvectiveDiffusion2DIterationImageFilter<SliceType,SliceType> AdvectionDiffusion2DIterationType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
reader->UpdateOutputInformation();
typedef itk::ExtractImageFilter<ImageType,SliceType> ExtractorType;
ExtractorType::Pointer extractor = ExtractorType::New();
ImageType::RegionType extractionRegion = reader->GetOutput()->GetLargestPossibleRegion();
extractionRegion.SetSize(2,0);
boundedReciprocal->SetInput(reader->GetOutput());
extractor->SetInput(boundedReciprocal->GetOutput());
extractor->SetExtractionRegion(extractionRegion);
extractor->SetDirectionCollapseToIdentity();
AdvectionDiffusion2DIterationType::Pointer advectionDiffusionIteration =AdvectionDiffusion2DIterationType::New();
advectionDiffusionIteration->SetInput(extractor->GetOutput());
advectionDiffusionIteration->SetNumberOfThreads(1.0);
WriterType::Pointer sliceWriter = WriterType::New();
sliceWriter->SetInput(extractor->GetOutput());
sliceWriter->SetFileName(argv[2]);
sliceWriter->Update();
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(argv[3]);
writer->SetInput(advectionDiffusionIteration->GetOutput());
writer->Update();
}
int AffineTransformCentered2NotCentered( int argc , char* argv[] )
{
if( argc != 6 )
{
std::cout<< argv[ 0 ] << " " << argv[ 1 ] << " inputTransform Source Target outputTransform" << std::endl ;
return 1 ;
}
std::string inputTransform ;
inputTransform.assign( argv[ 2 ] ) ;
std::string source ;
source.assign( argv[ 3 ] ) ;
std::string target ;
target.assign( argv[ 4 ] ) ;
std::string outputTransform ;
outputTransform.assign( argv[ 5 ] ) ;
//Read transform files
itk::TransformFileReader::Pointer transformFile ;
transformFile = itk::TransformFileReader::New() ;
transformFile->SetFileName( inputTransform ) ;
transformFile->Update() ;
//Check that transform file contains only one transform
if( transformFile->GetTransformList()->size() != 1
)
{
std::cout<< "Transform file must contain only 1 transform" << std::endl ;
return 1 ;
}
typedef itk::AffineTransform< double , 3 > AffineTransformType ;
AffineTransformType::Pointer affineTransform
= dynamic_cast< AffineTransformType* > ( transformFile->GetTransformList()->front().GetPointer() ) ;
if( !affineTransform )
{
std::cout << "Transform must be of type AffineTransform_double_3_3" << std::endl ;
return 1 ;
}
typedef itk::Image< unsigned short , 3 > ImageType ;
typedef itk::ImageFileReader< ImageType > ReaderType ;
ReaderType::Pointer reader = ReaderType::New() ;
reader->SetFileName( source.c_str() ) ;
reader->UpdateOutputInformation() ;
itk::Vector< double , 3 > tSource ;
tSource = ComputeTranslationToCenter( reader->GetOutput() ) ;
reader->SetFileName( target.c_str() ) ;
reader->UpdateOutputInformation() ;
itk::Vector< double , 3 > tTarget ;
tTarget = - ComputeTranslationToCenter( reader->GetOutput() ) ;
// std::cout<<"Target: "<< tTarget<<std::endl;
// std::cout<<"Source: "<< tSource<<std::endl;
// itk::Vector< double , 3 > tSourceTransform ;
// tSourceTransform = affineTransform->TransformVector( tSource ) ;
itk::Vector< double , 3 > tTargetTransform ;
tTargetTransform = affineTransform->TransformVector( tTarget ) ;
itk::Vector< double , 3 > translation ;
translation = affineTransform->GetTranslation() ;
//std::cout<<translation<<std::endl;
// std::cout<<translation<<std::endl;
// translation += tSourceTransform ;
translation += tTargetTransform ;
// std::cout<<"Transformed Ttarget: "<<tTargetTransform<<std::endl;
// std::cout<<translation<<std::endl;
// translation += tTarget ;
translation += tSource ;
// std::cout<<translation<<std::endl;
affineTransform->SetTranslation( translation ) ;
//Compose transforms
//Save transform
itk::TransformFileWriter::Pointer outputTransformFile ;
outputTransformFile = itk::TransformFileWriter::New() ;
outputTransformFile->SetFileName( outputTransform.c_str() ) ;
outputTransformFile->SetInput( affineTransform ) ;
outputTransformFile->Update() ;
return 0 ;
}