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resample.cxx
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resample.cxx
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////program for itkResampleImageFilter
//01: based on template.cxx and http://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleSegmentedImage
#include "itkFilterWatcher.h"
#include <itkImageFileReader.h>
#include <itkIdentityTransform.h>
#include <itkNearestNeighborInterpolateImageFunction.h>
#include <itkLinearInterpolateImageFunction.h>
#include <itkGaussianInterpolateImageFunction.h>
#include <itkLabelImageGaussianInterpolateImageFunction.h>
#include <itkBSplineInterpolateImageFunction.h>
#include <itkWindowedSincInterpolateImageFunction.h>
#include <itkConstantBoundaryCondition.h>
#include <itkResampleImageFilter.h>
#include <itkImageFileWriter.h>
template<typename InputComponentType, typename InputPixelType, size_t Dimension, typename InputImageType, typename TCoordRep, typename InterpolatorType>
int DoIt2(int argc, char *argv[], InterpolatorType* interpolator){
if( argc != 4 + 1*Dimension + 1){
fprintf(stderr, "4 + 1*Dimension = %ld parameters are needed!\n", 4 + 1*Dimension);
return EXIT_FAILURE;
}
typedef InputPixelType OutputPixelType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
reader->ReleaseDataFlagOn();
FilterWatcher watcherI(reader);
watcherI.QuietOn();
watcherI.ReportTimeOn();
try{
reader->Update();
}
catch(itk::ExceptionObject &ex){
std::cerr << ex << std::endl;
return EXIT_FAILURE;
}
typename InputImageType::Pointer input= reader->GetOutput();
typedef itk::IdentityTransform<TCoordRep, Dimension> TransformType;
typename TransformType::Pointer transform= TransformType::New();
transform->SetIdentity();
const typename InputImageType::SpacingType& inputSpacing= input->GetSpacing();
typename InputImageType::SpacingType outputSpacing;
for (unsigned int i= 0; i < Dimension; i++)
outputSpacing[i]= atof(argv[5+i]);
const typename InputImageType::SizeType& inputSize= input->GetLargestPossibleRegion().GetSize();
typename OutputImageType::SizeType outputSize;
typedef typename InputImageType::SizeType::SizeValueType SizeValueType;
for (unsigned int i= 0; i < Dimension-1; i++)
outputSize[i]= static_cast<SizeValueType>((double) inputSize[i] * inputSpacing[i] / outputSpacing[i]);
const unsigned int i= Dimension-1;
outputSize[i]= static_cast<SizeValueType>((double) inputSize[i] * inputSpacing[i] / outputSpacing[i] - 1);; //do not resample last output slice
typedef itk::ResampleImageFilter<InputImageType, OutputImageType> FilterType;
typename FilterType::Pointer filter= FilterType::New();
filter->SetInput(input);
filter->SetTransform(transform);
filter->SetInterpolator(interpolator);
filter->SetOutputSpacing(outputSpacing);
filter->SetSize(outputSize);
filter->SetOutputOrigin(input->GetOrigin());//essential for images created with e.g. itkExtractImageFilter
filter->SetOutputDirection(input->GetDirection());
filter->SetDefaultPixelValue(itk::NumericTraits<InputPixelType>::Zero);
filter->ReleaseDataFlagOn();
FilterWatcher watcher1(filter);
try{
filter->Update();
}
catch(itk::ExceptionObject &ex){
std::cerr << ex << std::endl;
return EXIT_FAILURE;
}
typename OutputImageType::Pointer output= filter->GetOutput();
typedef itk::ImageFileWriter<OutputImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
FilterWatcher watcherO(writer);
writer->SetFileName(argv[2]);
writer->SetInput(output);
writer->SetUseCompression(atoi(argv[3]));
try{
writer->Update();
}
catch(itk::ExceptionObject &ex){
std::cerr << ex << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
template<typename InputComponentType, typename InputPixelType, size_t Dimension>
int DoIt(int argc, char *argv[]){
int res= 0;
typedef double TCoordRep;
typedef double TCoefficientType;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
switch(atoi(argv[4])){
case 0:{
typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, TCoordRep> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 1:{
typedef itk::LinearInterpolateImageFunction<InputImageType, TCoordRep> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 2:{
typedef itk::BSplineInterpolateImageFunction<InputImageType, TCoordRep, TCoefficientType> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
interpolator->SetSplineOrder(2);
std::cerr << "Spline order: " << interpolator->GetSplineOrder() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 3:{
typedef itk::BSplineInterpolateImageFunction<InputImageType, TCoordRep, TCoefficientType> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
interpolator->SetSplineOrder(3);
std::cerr << "Spline order: " << interpolator->GetSplineOrder() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 4:{
typedef itk::BSplineInterpolateImageFunction<InputImageType, TCoordRep, TCoefficientType> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
interpolator->SetSplineOrder(4);
std::cerr << "Spline order: " << interpolator->GetSplineOrder() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 5:{
typedef itk::BSplineInterpolateImageFunction<InputImageType, TCoordRep, TCoefficientType> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
interpolator->SetSplineOrder(5);
std::cerr << "Spline order: " << interpolator->GetSplineOrder() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 10:{
typedef itk::GaussianInterpolateImageFunction<InputImageType, TCoordRep> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
typename InterpolatorType::ArrayType sigma;
for (unsigned int i= 0; i < Dimension; i++)
sigma[i]= 0.8; //as suggested in pub: http://www.insight-journal.org/browse/publication/705
interpolator->SetSigma(sigma);
interpolator->SetAlpha(3.0);
std::cerr << "Sigma: " << interpolator->GetSigma() << " Alpha: " << interpolator->GetAlpha() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 11:{
typedef itk::LabelImageGaussianInterpolateImageFunction<InputImageType, TCoordRep> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
typename InterpolatorType::ArrayType sigma;
for (unsigned int i= 0; i < Dimension; i++)
sigma[i]= 0.8; //as suggested in pub: http://www.insight-journal.org/browse/publication/705
interpolator->SetSigma(sigma);
interpolator->SetAlpha(3.0);
std::cerr << "Sigma: " << interpolator->GetSigma() << " Alpha: " << interpolator->GetAlpha() << std::endl;
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
case 20:{//from: http://www.itk.org/Doxygen/html/Examples_2Filtering_2ResampleImageFilter8_8cxx-example.html#_a7
typedef itk::ConstantBoundaryCondition<InputImageType> BoundaryConditionType;
const unsigned int WindowRadius = 5;
typedef itk::Function::HammingWindowFunction<WindowRadius> WindowFunctionType;
typedef itk::WindowedSincInterpolateImageFunction<InputImageType, WindowRadius, WindowFunctionType, BoundaryConditionType, TCoordRep> InterpolatorType;
typename InterpolatorType::Pointer interpolator= InterpolatorType::New();
std::cerr << "Using interpolator: " << interpolator->GetNameOfClass() << std::endl;
fprintf(stderr, "With a %s and a window size of: %d\n", "HammingWindowFunction", WindowRadius);//no GetNameOfClass() for itkWindowFunction: http://public.kitware.com/pipermail/insight-users/2004-July/009440.html
res= DoIt2<InputComponentType, InputPixelType, Dimension, InputImageType, TCoordRep, InterpolatorType>(argc, argv, interpolator);
}break;
default:
std::cerr << "unknown interpolation type." << std::endl;
res= EXIT_FAILURE;
break;
}//switch
return res;
}
template<typename InputComponentType, typename InputPixelType>
int dispatch_D(size_t dimensionType, int argc, char *argv[]){
int res= 0;
switch (dimensionType){
case 1:
res= DoIt<InputComponentType, InputPixelType, 1>(argc, argv);
break;
case 2:
res= DoIt<InputComponentType, InputPixelType, 2>(argc, argv);
break;
case 3:
res= DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
break;
default:
std::cerr << "Error: Images of dimension " << dimensionType << " are not handled!" << std::endl;
break;
}//switch
return res;
}
template<typename InputComponentType>
int dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc, char *argv[]){
int res= 0;
//http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#abd189f096c2a1b3ea559bc3e4849f658
//http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00099
//IOPixelType:: UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX
switch (pixelType){
case itk::ImageIOBase::SCALAR:{
typedef InputComponentType InputPixelType;
res= dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc, argv);
} break;
case itk::ImageIOBase::UNKNOWNPIXELTYPE:
default:
std::cerr << std::endl << "Error: Pixel type not handled!" << std::endl;
break;
}//switch
return res;
}
int dispatch_cT(itk::ImageIOBase::IOComponentType componentType, itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc, char *argv[]){
int res= 0;
//http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#a8dc783055a0af6f0a5a26cb080feb178
//http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00107
//IOComponentType: UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT, INT, ULONG, LONG, FLOAT, DOUBLE
switch (componentType){
case itk::ImageIOBase::UCHAR:{ // uint8_t
typedef unsigned char InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::CHAR:{ // int8_t
typedef char InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::USHORT:{ // uint16_t
typedef unsigned short InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::SHORT:{ // int16_t
typedef short InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::UINT:{ // uint32_t
typedef unsigned int InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::INT:{ // int32_t
typedef int InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::ULONG:{ // uint64_t
typedef unsigned long InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::LONG:{ // int64_t
typedef long InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::FLOAT:{ // float32
typedef float InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::DOUBLE:{ // float64
typedef double InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
default:
std::cerr << "unknown component type" << std::endl;
break;
}//switch
return res;
}
////from http://itk-users.7.n7.nabble.com/Pad-image-with-0-but-keep-its-type-what-ever-it-is-td27442.html
//namespace itk{
// Description:
// Get the PixelType and ComponentType from fileName
void GetImageType (std::string fileName,
itk::ImageIOBase::IOPixelType &pixelType,
itk::ImageIOBase::IOComponentType &componentType,
size_t &dimensionType
){
typedef itk::Image<char, 1> ImageType; //template initialization parameters need to be given but can be arbitrary here
itk::ImageFileReader<ImageType>::Pointer imageReader= itk::ImageFileReader<ImageType>::New();
imageReader->SetFileName(fileName.c_str());
imageReader->UpdateOutputInformation();
pixelType = imageReader->GetImageIO()->GetPixelType();
componentType = imageReader->GetImageIO()->GetComponentType();
dimensionType= imageReader->GetImageIO()->GetNumberOfDimensions();
std::cerr << std::endl << "dimensions: " << dimensionType << std::endl;
std::cerr << "component type: " << imageReader->GetImageIO()->GetComponentTypeAsString(componentType) << std::endl;
std::cerr << "component size: " << imageReader->GetImageIO()->GetComponentSize() << std::endl;
std::cerr << "pixel type (string): " << imageReader->GetImageIO()->GetPixelTypeAsString(imageReader->GetImageIO()->GetPixelType()) << std::endl;
std::cerr << "pixel type: " << pixelType << std::endl << std::endl;
}
int main(int argc, char *argv[]){
if ( argc < 6 ){
std::cerr << "Missing Parameters: "
<< argv[0]
<< " Input_Image"
<< " Output_Image"
<< " compress"
<< " Interpolator_Type"
<< " spacing..."
<< std::endl;
return EXIT_FAILURE;
}
itk::ImageIOBase::IOPixelType pixelType;
typename itk::ImageIOBase::IOComponentType componentType;
size_t dimensionType;
try {
GetImageType(argv[1], pixelType, componentType, dimensionType);
}//try
catch( itk::ExceptionObject &excep){
std::cerr << argv[0] << ": exception caught !" << std::endl;
std::cerr << excep << std::endl;
return EXIT_FAILURE;
}
return dispatch_cT(componentType, pixelType, dimensionType, argc, argv);
}