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/**
* Use ITK library to deal with image IO.
*/
#ifndef IMAGEIO_H
#define IMAGEIO_H
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionIterator.h"
#include "data.h"
typedef std::vector<std::string> StringVector;
template<typename TImageType>
void ImageSizeReader(const std::string& filename, typename TImageType::SizeType& size, typename TImageType::Pointer& image)
{
typedef itk::ImageFileReader<TImageType> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
typename TImageType::RegionType region;
try
{
reader->SetFileName(filename);
reader->Update();
image = reader->GetOutput();
region = image->GetLargestPossibleRegion();
size = region.GetSize();
}
catch( itk::ExceptionObject &err )
{
std::cerr << "ImageSizeReader Exception Caught !" << std::endl;
std::cerr << err << std::endl;
exit(1);
}
}
template<typename TImageType, typename dataT, typename labelT>
MLData<dataT, labelT>* ImageSeriesReader(StringVector& filenames,
size_t& dataNum,
size_t& dataDim,
typename TImageType::SizeType& size)
{
typedef itk::ImageRegionConstIterator<TImageType> ConstIteratorType;
typename TImageType::Pointer image;
typename TImageType::SizeType curSize;
int imageDim = size.GetSizeDimension();
dataDim = filenames.size() - 1;
dataNum = 1;
MLData<dataT, labelT>* data;
int dimIdx = -1;
for (StringVector::const_iterator filename = filenames.begin();
filename != filenames.end(); ++filename, ++dimIdx)
{
ImageSizeReader<TImageType>(*filename, curSize, image);
if (filename == filenames.begin())
{
size = curSize;
for (int i = 0; i < imageDim; i++)
{
dataNum *= size[i];
}
data = new MLData<dataT, labelT>(dataNum, dataDim);
// data = new double*[dataNum];
// double *block = new double[dataNum*dataDim];
// for (int i = 0; i < dataNum; i++)
// {
// data[i] = &block[i*dataDim];
// }
}
else if (curSize != size)
{
std::cerr << "ImageSeriesReader size different !" << std::endl;
exit(1);
}
ConstIteratorType iter(image, image->GetLargestPossibleRegion());
size_t dataIdx = 0;
if (filename == filenames.begin())
{
for (iter.GoToBegin(); !iter.IsAtEnd(); ++iter, ++dataIdx)
{
data->label[dataIdx] = iter.Get();
}
}
else
{
for (iter.GoToBegin(); !iter.IsAtEnd(); ++iter, ++dataIdx)
{
data->data[dataIdx][dimIdx] = iter.Get();
}
}
}
return data;
}
template<typename TImageType>
void ImageWriter(const std::string& filename, typename TImageType::Pointer image)
{
typedef itk::ImageFileWriter<TImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
try
{
writer->SetFileName(filename);
writer->SetInput(image);
writer->Update();
}
catch( itk::ExceptionObject &err )
{
std::cerr << "ImageWriter Exception Caught !" << std::endl;
std::cerr << err << std::endl;
exit(1);
}
}
template<typename TImageType>
void ImageSeriesWriter(StringVector& filenames,
Matrix<double>& data,
typename TImageType::SizeType size)
{
typename TImageType::IndexType index;
index.Fill(0);
typename TImageType::RegionType region(index, size);
typename TImageType::Pointer image = TImageType::New();
image->SetRegions(region);
image->Allocate();
typedef itk::ImageRegionIterator<TImageType> IteratorType;
int dimIdx = 0;
for (StringVector::const_iterator filename = filenames.begin();
filename != filenames.end(); ++filename, ++dimIdx)
{
IteratorType iter(image, image->GetLargestPossibleRegion());
long dataIdx = 0;
for (iter.GoToBegin(); !iter.IsAtEnd(); ++iter, ++dataIdx)
{
iter.Set(data[dataIdx][dimIdx]);
}
ImageWriter<TImageType>(*filename, image);
}
}
#endif // IMAGEIO_H
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