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toUInt16.cxx
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toUInt16.cxx
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////program to use itk to convert files to uint16 without any processing
//01: based on toUInt8.cxx
#include <complex>
#include "itkFilterWatcher.h"
#include <itkImageFileReader.h>
#include <itkCastImageFilter.h>
#include <itkImageFileWriter.h>
int dispatch_cT(itk::ImageIOBase::IOPixelType, itk::ImageIOBase::IOComponentType, size_t, int, char **);
template<typename InputComponentType>
int dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t, int, char **);
template<typename InputComponentType, typename InputPixelType>
int dispatch_D(size_t, int, char **);
template<typename InputComponentType, typename InputPixelType, size_t Dimension>
int DoIt(int, char *argv[]);
// void FilterEventHandlerITK(itk::Object *caller, const itk::EventObject &event, void*){
// const itk::ProcessObject* filter = static_cast<const itk::ProcessObject*>(caller);
// if(itk::ProgressEvent().CheckEvent(&event))
// fprintf(stderr, "\r%s progress: %5.1f%%", filter->GetNameOfClass(), 100.0 * filter->GetProgress());//stderr is flushed directly
// else if(strstr(filter->GetNameOfClass(), "ImageFileReader")){
// typedef itk::Image<unsigned char, 3> ImageType;
// const itk::ImageFileReader<ImageType>* reader = static_cast<const itk::ImageFileReader<ImageType>*>(caller);
// std::cerr << "Reading: " << reader->GetFileName() << std::endl;
// }
// else if(itk::EndEvent().CheckEvent(&event))
// std::cerr << std::endl;
// }
template<typename InputComponentType, typename InputPixelType, size_t Dimension>
int DoIt(int argc, char *argv[]){
typedef uint16_t OutputPixelType;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
// FilterWatcher watcherI(reader);
// watcherI.QuietOn();
// watcherI.ReportTimeOn();
// try{
// reader->Update();
// }
// catch(itk::ExceptionObject &ex){
// std::cerr << ex << std::endl;
// return EXIT_FAILURE;
// }
typedef itk::CastImageFilter<InputImageType, OutputImageType> CastFilterType;
typename CastFilterType::Pointer caster= CastFilterType::New();
caster->SetInput(reader->GetOutput());
caster->ReleaseDataFlagOn();
caster->InPlaceOn();
FilterWatcher watcherC(caster);
typedef itk::ImageFileWriter<OutputImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
FilterWatcher watcherO(writer);
writer->SetFileName(argv[2]);
writer->SetInput(caster->GetOutput());
writer->SetUseCompression(atoi(argv[3]));
try{
writer->Update();
}
catch(itk::ExceptionObject &ex){
std::cerr << ex << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
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;
}
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;
}
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;
}
////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<unsigned char, 3> ImageType;
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 != 4 ){
std::cerr << "Missing Parameters: "
<< argv[0]
<< " Input_Image"
<< " Output_Image"
<< " compress"
<< 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);
}