[ITK] [ITK-users] Symmetric Demons registration
stefano serviddio
s.serviddio at gmail.com
Sun Sep 27 18:56:00 EDT 2015
Hi Matt,
I have added this code:
"
Image2->SetOrigin(Image1->GetOrigin());
Image2->SetSpacing(Image1->GetSpacing());
Image2->SetDirection(Image1->GetDirection());"
but the problem remain the same.
2015-09-28 0:10 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
> Hi Stefano,
>
> The means that the images must occupy the same spatial domain. The
> domain is determined by the Origin, Spacing, Direction, and
> ImageRegion Size of the Image's. This is explained more in the ITK
> Software Guide:
>
>
> http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch4.html#x40-430004
>
> HTH,
> Matt
>
> On Sun, Sep 27, 2015 at 5:56 PM, stefano serviddio
> <s.serviddio at gmail.com> wrote:
> > HI,
> > I have always the same issue with my demons registration code, "Inputs do
> > not occupy the same physical space".
> > the fixed image is a Ct 512x512 dicom and the second one is a Pet
> 256x256
> > dicom.
> > May you help me to find out what is the problem?
> > Thank you very much.
> >
> >
> >
> > #include "itkImageFileReader.h"
> > #include "itkImageFileWriter.h"
> > #include <time.h>
> > #include <fstream>
> > #include "itkSymmetricForcesDemonsRegistrationFilter.h"
> > #include "itkHistogramMatchingImageFilter.h"
> > #include "itkCastImageFilter.h"
> > #include "itkWarpImageFilter.h"
> >
> > #include "itkGDCMImageIO.h"
> > #include "itkShrinkImageFilter.h"
> >
> >
> >
> > class CommandIterationUpdate : public itk::Command
> > {
> > public:
> > typedef CommandIterationUpdate Self;
> > typedef itk::Command Superclass;
> > typedef itk::SmartPointer<CommandIterationUpdate> Pointer;
> > itkNewMacro( CommandIterationUpdate );
> > protected:
> > CommandIterationUpdate() {};
> >
> > typedef itk::Image< double, 2 > InternalImageType;
> > typedef itk::Vector< double, 2 > VectorPixelType;
> > typedef itk::Image< VectorPixelType, 2 > DisplacementFieldType;
> >
> > typedef itk::SymmetricForcesDemonsRegistrationFilter<
> > InternalImageType,
> > InternalImageType,
> > DisplacementFieldType>
> > RegistrationFilterType;
> >
> > public:
> >
> > void Execute(itk::Object *caller, const itk::EventObject & event)
> > ITK_OVERRIDE
> > {
> > Execute( (const itk::Object *)caller, event);
> > }
> >
> > void Execute(const itk::Object * object, const itk::EventObject &
> event)
> > ITK_OVERRIDE
> > {
> > const RegistrationFilterType * filter = static_cast< const
> > RegistrationFilterType * >( object );
> > if( !(itk::IterationEvent().CheckEvent( &event )) )
> > {
> > return;
> > }
> > std::cout << filter->GetMetric() << std::endl;
> > }
> > };
> >
> >
> > int main( int argc, char *argv[] )
> > {
> > /*if( argc < 4 )
> > {
> > std::cerr << "Missing Parameters " << std::endl;
> > std::cerr << "Usage: " << argv[0];
> > std::cerr << " fixedImageFile movingImageFile ";
> > std::cerr << " outputImageFile " << std::endl;
> > std::cerr << " [outputDisplacementFieldFile] " << std::endl;
> > return EXIT_FAILURE;
> > }*/
> >
> >
> > time_t now = time(0);
> > struct tm tstruct;
> > char buf[80];
> > tstruct = *localtime(&now);
> > strftime(buf, sizeof(buf), "%Y-%m-%d %X", &tstruct);
> >
> > std::ofstream resultfile;
> > char Risultati[] = "D:/Images/MetricResultDeformaion.txt";
> >
> > resultfile.open(Risultati, std::ios::app);
> > if (resultfile.is_open())
> > {
> > std::cout << "File Open exists\n";
> >
> > }
> >
> > resultfile<<"Data :"<<buf<<std::endl;
> >
> >
> >
> >
> > const unsigned int Dimension = 2;
> > typedef unsigned int PixelType;
> >
> > typedef itk::Image< PixelType, Dimension > FixedImageType;
> > typedef itk::Image< PixelType, Dimension > MovingImageType;
> >
> >
> >
> >
> > typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
> > typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
> > typedef itk::GDCMImageIO GDCMType;
> > GDCMType::Pointer gdcm=GDCMType::New();
> > FixedImageReaderType::Pointer fixedImageReader =
> > FixedImageReaderType::New();
> > MovingImageReaderType::Pointer movingImageReader =
> > MovingImageReaderType::New();
> >
> > char* filename1="D:/Images/def00001.dcm";
> > char* filename2="D:/Images/def100001.dcm";
> > fixedImageReader->SetFileName( filename1 );
> > movingImageReader->SetFileName( filename2 );
> > fixedImageReader->SetImageIO(gdcm);
> > movingImageReader->SetImageIO(gdcm);
> >
> > resultfile<<filename1<<std::endl;
> > resultfile<<filename2<<std::endl;
> >
> > fixedImageReader->Update();
> > movingImageReader->Update();
> >
> > typedef itk::ShrinkImageFilter<MovingImageType,MovingImageType>
> > ShrinkFilterType;
> > ShrinkFilterType::Pointer shrinkFilter = ShrinkFilterType::New();
> > shrinkFilter->SetShrinkFactors( 2 );
> > shrinkFilter->SetInput( fixedImageReader->GetOutput() );
> > shrinkFilter->Update();
> >
> > typedef double InternalPixelType;
> > typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
> > typedef itk::CastImageFilter< FixedImageType, InternalImageType >
> > FixedImageCasterType;
> > typedef itk::CastImageFilter< MovingImageType, InternalImageType >
> > MovingImageCasterType;
> >
> > FixedImageCasterType::Pointer fixedImageCaster =
> > FixedImageCasterType::New();
> > MovingImageCasterType::Pointer movingImageCaster=
> > MovingImageCasterType::New();
> >
> > fixedImageCaster->SetInput( shrinkFilter->GetOutput() );
> > movingImageCaster->SetInput( fixedImageReader->GetOutput() );
> >
> > fixedImageCaster->Update();
> > movingImageCaster->Update();
> >
> > typedef itk::HistogramMatchingImageFilter<
> > InternalImageType,InternalImageType > MatchingFilterType;
> > MatchingFilterType::Pointer matcher = MatchingFilterType::New();
> >
> > matcher->SetInput( movingImageCaster->GetOutput() );
> >
> > matcher->SetReferenceImage( fixedImageCaster->GetOutput() );
> >
> >
> > matcher->SetNumberOfHistogramLevels(1024);
> > matcher->SetNumberOfMatchPoints(7 );
> >
> >
> > matcher->ThresholdAtMeanIntensityOn();
> >
> > typedef itk::Vector< double, Dimension > VectorPixelType;
> > typedef itk::Image< VectorPixelType, Dimension >
> DisplacementFieldType;
> >
> >
> >
> > typedef
> >
> itk::SymmetricForcesDemonsRegistrationFilter<InternalImageType,InternalImageType,
> > DisplacementFieldType> RegistrationFilterType;
> > RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
> >
> >
> >
> > CommandIterationUpdate::Pointer observer =
> CommandIterationUpdate::New();
> > filter->AddObserver( itk::IterationEvent(), observer );
> >
> >
> >
> > filter->SetFixedImage( fixedImageCaster->GetOutput() );
> > filter->SetMovingImage( matcher->GetOutput());
> > filter->SetNumberOfIterations( 256 );
> > filter->SetStandardDeviations( 4.0 );
> >
> >
> >
> > try
> > {
> > filter->Update();
> > }
> > catch( itk::ExceptionObject & err )
> > {
> > std::cerr << "ExceptionObject caught !" << std::endl;
> > std::cerr << err << std::endl;
> > return EXIT_FAILURE;
> > }
> >
> >
> > typedef itk::WarpImageFilter< MovingImageType, MovingImageType,
> > DisplacementFieldType > WarperType;
> > typedef itk::LinearInterpolateImageFunction< MovingImageType, double
> >
> > InterpolatorType;
> > WarperType::Pointer warper = WarperType::New();
> > InterpolatorType::Pointer interpolator = InterpolatorType::New();
> > FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
> >
> > warper->SetInput( movingImageReader->GetOutput() );
> > warper->SetInterpolator( interpolator );
> > warper->SetOutputSpacing( fixedImage->GetSpacing() );
> > warper->SetOutputOrigin( fixedImage->GetOrigin() );
> > warper->SetOutputDirection( fixedImage->GetDirection() );
> >
> > warper->SetDisplacementField( filter->GetOutput() );
> >
> > warper->Update();
> >
> >
> >
> > typedef unsigned char OutputPixelType;
> > typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> > typedef itk::CastImageFilter<
> > MovingImageType,
> > OutputImageType > CastFilterType;
> > typedef itk::ImageFileWriter< OutputImageType > WriterType;
> >
> > WriterType::Pointer writer = WriterType::New();
> > CastFilterType::Pointer caster = CastFilterType::New();
> >
> >
> >
> >
> >
> >
> >
> > std::cout<<"last metric value "<<filter->GetMetric()<<std::endl;
> > resultfile<<"last metric value "<<filter->GetMetric()<<std::endl;
> > writer->SetFileName( "D:/Images/new.dcm" );
> >
> > caster->SetInput( warper->GetOutput() );
> > caster->Update();
> > writer->SetInput( caster->GetOutput() );
> > writer->SetImageIO(gdcm);
> > writer->Update();
> >
> >
> > return EXIT_SUCCESS;
> > }
> >
> >
> >
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
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> >
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>
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