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/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkTestingMacros.h"
#include "itkGDCMImageIO.h"
int
itkGDCMImageReadSeriesWriteTest(int argc, char * argv[])
{
if (argc < 4)
{
std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv);
std::cerr << " InputImage OutputDicomDirectory SingleOutputImage" << std::endl;
return EXIT_FAILURE;
}
const char * inputImage = argv[1];
const char * outputDirectory = argv[2];
const char * singleOutputImage = argv[3];
using PixelType = short;
constexpr unsigned int Dimension = 3;
using ImageType = itk::Image<PixelType, Dimension>;
using ReaderType = itk::ImageFileReader<ImageType>;
auto reader = ReaderType::New();
reader->SetFileName(inputImage);
ITK_TRY_EXPECT_NO_EXCEPTION(reader->Update());
using ImageIOType = itk::GDCMImageIO;
using NamesGeneratorType = itk::NumericSeriesFileNames;
auto gdcmIO = ImageIOType::New();
itksys::SystemTools::MakeDirectory(outputDirectory);
using OutputPixelType = short;
constexpr unsigned int OutputDimension = 2;
using Image2DType = itk::Image<OutputPixelType, OutputDimension>;
using SeriesWriterType = itk::ImageSeriesWriter<ImageType, Image2DType>;
auto namesGenerator = NamesGeneratorType::New();
itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
std::string tagkey, value;
tagkey = "0008|0060"; // Modality
value = "MR";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
tagkey = "0008|0008"; // Image Type
value = "DERIVED\\SECONDARY";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
tagkey = "0008|0064"; // Conversion Type
value = "DV";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
auto seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput(reader->GetOutput());
seriesWriter->SetImageIO(gdcmIO);
ITK_TEST_SET_GET_VALUE(gdcmIO, seriesWriter->GetImageIO());
ImageType::RegionType region = reader->GetOutput()->GetLargestPossibleRegion();
ImageType::IndexType start = region.GetIndex();
ImageType::SizeType size = region.GetSize();
std::string format = outputDirectory;
format += "/image%03d.dcm";
namesGenerator->SetSeriesFormat(format.c_str());
namesGenerator->SetStartIndex(start[2]);
namesGenerator->SetEndIndex(start[2] + size[2] - 1);
namesGenerator->SetIncrementIndex(1);
seriesWriter->SetFileNames(namesGenerator->GetFileNames());
ITK_TRY_EXPECT_NO_EXCEPTION(seriesWriter->Update());
// Now read back in and write out as 3D image for comparison with the input.
using SeriesReaderType = itk::ImageSeriesReader<ImageType>;
auto seriesReader = SeriesReaderType::New();
seriesReader->SetFileNames(namesGenerator->GetFileNames());
using SingleWriterType = itk::ImageFileWriter<ImageType>;
auto singleWriter = SingleWriterType::New();
singleWriter->SetInput(seriesReader->GetOutput());
singleWriter->SetFileName(singleOutputImage);
ITK_TRY_EXPECT_NO_EXCEPTION(singleWriter->Update());
return EXIT_SUCCESS;
}
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