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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.
*
*=========================================================================*/
//
// This example illustrates how to read a DICOM series into a volume
// and then save this volume into another DICOM series using the
// exact same name.
// It makes use of the GDCM library
//
#define ITK_LEGACY_TEST
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
int itkGDCMSeriesReadImageWriteTest( int argc, char* argv[] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << argv[0] <<
" DicomDirectory outputFile OutputDicomDirectory" << std::endl;
return EXIT_FAILURE;
}
#if ! defined ( ITK_LEGACY_REMOVE )
typedef itk::Image<unsigned short,3> ImageType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GDCMSeriesFileNames SeriesFileNames;
ImageIOType::Pointer gdcmIO = ImageIOType::New();
SeriesFileNames::Pointer it = SeriesFileNames::New();
// Get the DICOM filenames from the directory
// First add a restriction *before* selecting the input directory
// since SetInputDirectory has a side effect of executing
gdcm::SerieHelper *sh = it->GetSeriesHelper( );
sh->AddRestriction(0x0010, 0x0010, "Wes Turner", gdcm::GDCM_EQUAL);
sh->AddRestriction(0x0020, 0x0013, "75", gdcm::GDCM_GREATEROREQUAL);
sh->AddRestriction(0x0020, 0x0013, "77", gdcm::GDCM_LESSOREQUAL);
it->SetInputDirectory( argv[1] );
ReaderType::Pointer reader = ReaderType::New();
const ReaderType::FileNamesContainer & fileNames = it->GetInputFileNames();
const size_t numberOfFileNames = fileNames.size();
std::cout << numberOfFileNames << std::endl;
for( unsigned int fni = 0; fni < numberOfFileNames; ++fni )
{
std::cout << "filename # " << fni << " = ";
std::cout << fileNames[fni] << std::endl;
}
reader->SetFileNames( fileNames );
reader->SetImageIO( gdcmIO );
try
{
reader->Update();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( argv[2] );
writer->SetInput( reader->GetOutput() );
try
{
writer->Update();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Writing image afer downscaling to 8bits (unsigned char)
typedef itk::Image< unsigned short, 3> Image3DType;
typedef itk::Image< unsigned char, 3> RescaleImageType;
typedef itk::Image< unsigned char, 2> OutputImageType;
typedef itk::RescaleIntensityImageFilter<
Image3DType, RescaleImageType > RescaleFilterType;
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
rescaler->SetInput( reader->GetOutput() );
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 255 );
typedef itk::ImageSeriesWriter< RescaleImageType, OutputImageType > SeriesWriterRescaleType;
SeriesWriterRescaleType::Pointer swriter2 = SeriesWriterRescaleType::New();
it->SetOutputDirectory( argv[3] );
swriter2->SetInput( rescaler->GetOutput() );
swriter2->SetImageIO( gdcmIO );
gdcmIO->SetInternalComponentType( itk::ImageIOBase::UCHAR );
swriter2->SetFileNames( it->GetOutputFileNames() );
swriter2->SetMetaDataDictionaryArray( reader->GetMetaDataDictionaryArray() );
try
{
swriter2->Update();
}
catch (itk::ExceptionObject & e)
{
std::cerr << "exception in file writer " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
#endif
return EXIT_SUCCESS;
}
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