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DicomSeriesReadGaussianImageWrite.cxx
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DicomSeriesReadGaussianImageWrite.cxx
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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 "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkSmoothingRecursiveGaussianImageFilter.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
int
main(int argc, char * argv[])
{
if (argc < 4)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0]
<< " DicomDirectory outputFileName sigma [seriesName] "
<< std::endl;
return EXIT_FAILURE;
}
using PixelType = short;
constexpr unsigned int Dimension = 3;
using ImageType = itk::Image<PixelType, Dimension>;
using ReaderType = itk::ImageSeriesReader<ImageType>;
auto reader = ReaderType::New();
using ImageIOType = itk::GDCMImageIO;
auto dicomIO = ImageIOType::New();
reader->SetImageIO(dicomIO);
using NamesGeneratorType = itk::GDCMSeriesFileNames;
auto nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->AddSeriesRestriction("0008|0021");
nameGenerator->SetDirectory(argv[1]);
try
{
std::cout << std::endl << "The directory: " << std::endl;
std::cout << std::endl << argv[1] << std::endl << std::endl;
std::cout << "Contains the following DICOM Series: ";
std::cout << std::endl << std::endl;
using SeriesIdContainer = std::vector<std::string>;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
auto seriesItr = seriesUID.begin();
auto seriesEnd = seriesUID.end();
while (seriesItr != seriesEnd)
{
std::cout << seriesItr->c_str() << std::endl;
++seriesItr;
}
std::string seriesIdentifier;
if (argc > 4) // If no optional series identifier
{
seriesIdentifier = argv[4];
}
else
{
seriesIdentifier = seriesUID.begin()->c_str();
}
std::cout << std::endl << std::endl;
std::cout << "Now reading series: " << std::endl << std::endl;
std::cout << seriesIdentifier << std::endl;
std::cout << std::endl << std::endl;
using FileNamesContainer = std::vector<std::string>;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetFileNames(seriesIdentifier);
reader->SetFileNames(fileNames);
try
{
reader->Update();
}
catch (const itk::ExceptionObject & ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
using FilterType =
itk::SmoothingRecursiveGaussianImageFilter<ImageType, ImageType>;
auto filter = FilterType::New();
filter->SetInput(reader->GetOutput());
const double sigma = std::stod(argv[3]);
filter->SetSigma(sigma);
using WriterType = itk::ImageFileWriter<ImageType>;
auto writer = WriterType::New();
writer->SetFileName(argv[2]);
writer->SetInput(filter->GetOutput());
std::cout << "Writing the image as " << std::endl << std::endl;
std::cout << argv[2] << std::endl << std::endl;
try
{
writer->Update();
}
catch (const itk::ExceptionObject & ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
}
catch (const itk::ExceptionObject & ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}