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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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
*
* http://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;
}
typedef signed short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer dicomIO = ImageIOType::New();
reader->SetImageIO( dicomIO );
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer 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;
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator 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;
typedef std::vector< std::string > FileNamesContainer;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetFileNames( seriesIdentifier );
reader->SetFileNames( fileNames );
try
{
reader->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
typedef itk::SmoothingRecursiveGaussianImageFilter< ImageType, ImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( reader->GetOutput() );
const double sigma = atof( argv[3] );
filter->SetSigma( sigma );
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer 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 (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
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