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Write image as a sequence #2

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Write image as a sequence #2

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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ endif()

message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")

set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD 20)

set(DEBUG_CXX_FLAGS "-ggdb;-O1;-Wall;-Wextra;-march=native;-fPIC")
set(RELEASE_CXX_FLAGS "-O3;-Wall;-march=native;-fPIC;-ffast-math")
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65 changes: 65 additions & 0 deletions include/util.hxx
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Expand Up @@ -25,6 +25,71 @@
#include <itkLogger.h>
#include <itkImageFileWriter.h>
#include <itkImageFileReader.h>
#include <itkExtractImageFilter.h>
#include <type_traits>
#include <concepts>

#include "config.h"


template<typename T> requires std::integral<T>
std::string int_to_string(T n, int width = 5){
std::ostringstream ss;
ss.width(width);
ss.fill('0');
ss << n;
return ss.str();
}

template<typename TImage>
void writeImageSequence(const std::string & filePath, const typename TImage::Pointer &image,
const itk::Logger::Pointer &logger) {
using ImagePixelType = typename TImage::PixelType;
constexpr unsigned Dimension = TImage::ImageDimension;
using ImagePlaneType = itk::Image<ImagePixelType, Dimension-1>;

using FileSequenceWriterType = itk::ImageFileWriter<ImagePlaneType>;
auto writer = FileSequenceWriterType::New();

auto totalRegion = image->GetLargestPossibleRegion();
auto index = totalRegion.GetIndex();
auto fullSize = totalRegion.GetSize();
int planeCount = fullSize[Dimension-1];

using ExtractFilterType = itk::ExtractImageFilter<TImage, ImagePlaneType>;
auto extractFilter = ExtractFilterType::New();
extractFilter->SetDirectionCollapseToSubmatrix();
extractFilter->SetInput(image);

typename TImage::RegionType desiredPlane;

fullSize[Dimension-1] = 0;
desiredPlane.SetSize(fullSize);

auto stem = fs::path(filePath).stem();
auto extension = fs::path(filePath).extension();

for(int plane = 0;plane < planeCount; ++plane){
auto fname = (stem.string() +"-" + int_to_string(plane) + extension.string() );
fs::path planePath = fs::path(filePath).parent_path()/ fname;
auto currentIndex = index;
currentIndex[Dimension-1] += plane;
desiredPlane.SetIndex(currentIndex);

extractFilter->SetExtractionRegion(desiredPlane);
//extractFilter->Update();
writer->SetFileName(planePath );
writer->SetInput( extractFilter->GetOutput() );
try {
writer->Update();
logger->Debug( "Wrote file " + std::string(writer->GetFileName()) + "\n");
}catch (itk::ExceptionObject &e){
logger->Critical( "Failed writing " + std::string(writer->GetFileName()) + "\n");
logger->Critical( std::string(e.what()) + "\n");
}
}
}


template<typename TImage>
void writeImage(const std::string & filePath, const typename TImage::Pointer &image,
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