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| ==ResampleDICOM.cxx==
| | {{warning|1=The media wiki content on this page is no longer maintained. The examples presented on the https://itk.org/Wiki/* pages likely require ITK version 4.13 or earlier releases. In many cases, the examples on this page no longer conform to the best practices for modern ITK versions. |
| <source lang="cpp">
| | }} |
| // Resample a DICOM study
| |
| // Usage: ResampleDICOM InputDirectory OutputDirectory
| |
| // xSpacing ySpacing zSpacing
| |
| //
| |
| // Example: ResampleDICOM CT CTResample 0 0 1.5
| |
| // will read a series from the CT directory and create a
| |
| // new series in the CTResample directory. The new series
| |
| // will have the same x,y spacing as the input series, but
| |
| // will have a z-spacing of 1.5.
| |
| //
| |
| // Description:
| |
| // ResampleDICOM resamples a DICOM series with user-specified
| |
| // spacing. The program outputs a new DICOM series with a series
| |
| // number set to 1001. All non-private DICOM tags are moved from the input
| |
| // series to the output series. The Image Position Patient is adjusted
| |
| // for each slice to reflect the z-spacing. The number of slices in
| |
| // the output series may be larger or smaller due to changes in the
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| // z-spacing. To retain the spacing for a given dimension, specify 0.
| |
| //
| |
| // The program progresses as follows:
| |
| // 1) Read the input series
| |
| // 2) Resample the series according to the user specified x-y-z
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| // spacing.
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| // 3) Create a MetaDataDictionary for each slice.
| |
| // 4) Shift data to undo the effect of a rescale intercept by the
| |
| // DICOM reader
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| // 5) Write the new DICOM series
| |
| //
| |
| | |
| #include "itkVersion.h"
| |
| | |
| #include "itkImage.h"
| |
| #include "itkMinimumMaximumImageFilter.h"
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| | |
| #include "itkGDCMImageIO.h"
| |
| #include "itkGDCMSeriesFileNames.h"
| |
| #include "itkNumericSeriesFileNames.h"
| |
| | |
| #include "itkImageSeriesReader.h"
| |
| #include "itkImageSeriesWriter.h"
| |
| | |
| #include "itkResampleImageFilter.h"
| |
| #include "itkShiftScaleImageFilter.h"
| |
| | |
| #include "itkIdentityTransform.h"
| |
| #include "itkLinearInterpolateImageFunction.h"
| |
| | |
| #include <itksys/SystemTools.hxx>
| |
| | |
| #if ITK_VERSION_MAJOR >= 4
| |
| #include "gdcmUIDGenerator.h"
| |
| #else
| |
| #include "gdcm/src/gdcmFile.h"
| |
| #include "gdcm/src/gdcmUtil.h"
| |
| #endif
| |
| | |
| #include <string>
| |
| | |
| static void CopyDictionary (itk::MetaDataDictionary &fromDict,
| |
| itk::MetaDataDictionary &toDict);
| |
| | |
| | |
| int main( int argc, char* argv[] )
| |
| { | |
| // Validate input parameters
| |
| if( argc < 4 )
| |
| {
| |
| std::cerr << "Usage: "
| |
| << argv[0]
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| << " InputDicomDirectory OutputDicomDirectory spacing_x spacing_y spacing_z"
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| << std::endl;
| |
| return EXIT_FAILURE;
| |
| }
| |
| | |
| const unsigned int InputDimension = 3;
| |
| const unsigned int OutputDimension = 2;
| |
| | |
| typedef signed short PixelType;
| |
| | |
| typedef itk::Image< PixelType, InputDimension >
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| InputImageType;
| |
| typedef itk::Image< PixelType, OutputDimension >
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| OutputImageType;
| |
| typedef itk::ImageSeriesReader< InputImageType >
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| ReaderType;
| |
| typedef itk::GDCMImageIO
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| ImageIOType;
| |
| typedef itk::GDCMSeriesFileNames
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| InputNamesGeneratorType;
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| typedef itk::NumericSeriesFileNames
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| OutputNamesGeneratorType;
| |
| typedef itk::IdentityTransform< double, InputDimension >
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| TransformType;
| |
| typedef itk::LinearInterpolateImageFunction< InputImageType, double >
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| InterpolatorType;
| |
| typedef itk::ResampleImageFilter< InputImageType, InputImageType >
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| ResampleFilterType;
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| typedef itk::ShiftScaleImageFilter< InputImageType, InputImageType >
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| ShiftScaleType;
| |
| typedef itk::ImageSeriesWriter< InputImageType, OutputImageType >
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| SeriesWriterType;
| |
| | |
| ////////////////////////////////////////////////
| |
| // 1) Read the input series
| |
| | |
| ImageIOType::Pointer gdcmIO = ImageIOType::New();
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| InputNamesGeneratorType::Pointer inputNames = InputNamesGeneratorType::New();
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| inputNames->SetInputDirectory( argv[1] );
| |
| | |
| const ReaderType::FileNamesContainer & filenames =
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| inputNames->GetInputFileNames();
| |
| | |
| ReaderType::Pointer reader = ReaderType::New();
| |
| | |
| reader->SetImageIO( gdcmIO );
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| reader->SetFileNames( filenames );
| |
| try
| |
| {
| |
| reader->Update();
| |
| }
| |
| catch (itk::ExceptionObject &excp)
| |
| {
| |
| std::cerr << "Exception thrown while reading the series" << std::endl;
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| std::cerr << excp << std::endl;
| |
| return EXIT_FAILURE;
| |
| }
| |
| | |
| ////////////////////////////////////////////////
| |
| // 2) Resample the series
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| InterpolatorType::Pointer interpolator = InterpolatorType::New();
| |
| | |
| TransformType::Pointer transform = TransformType::New();
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| transform->SetIdentity();
| |
| | |
| const InputImageType::SpacingType& inputSpacing =
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| reader->GetOutput()->GetSpacing();
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| const InputImageType::RegionType& inputRegion =
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| reader->GetOutput()->GetLargestPossibleRegion();
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| const InputImageType::SizeType& inputSize =
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| inputRegion.GetSize();
| |
| | |
| std::cout << "The input series in directory " << argv[1]
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| << " has " << filenames.size() << " files with spacing "
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| << inputSpacing
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| << std::endl;
| |
| | |
| // Compute the size of the output. The user specifies a spacing on
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| // the command line. If the spacing is 0, the input spacing will be
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| // used. The size (# of pixels) in the output is recomputed using
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| // the ratio of the input and output sizes.
| |
| InputImageType::SpacingType outputSpacing;
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| outputSpacing[0] = atof(argv[3]);
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| outputSpacing[1] = atof(argv[4]);
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| outputSpacing[2] = atof(argv[5]);
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| | |
| bool changeInSpacing = false;
| |
| for (unsigned int i = 0; i < 3; i++)
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| {
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| if (outputSpacing[i] == 0.0)
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| {
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| outputSpacing[i] = inputSpacing[i];
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| }
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| else
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| {
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| changeInSpacing = true;
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| }
| |
| }
| |
| InputImageType::SizeType outputSize;
| |
| typedef InputImageType::SizeType::SizeValueType SizeValueType;
| |
| outputSize[0] = static_cast<SizeValueType>(inputSize[0] * inputSpacing[0] / outputSpacing[0] + .5);
| |
| outputSize[1] = static_cast<SizeValueType>(inputSize[1] * inputSpacing[1] / outputSpacing[1] + .5);
| |
| outputSize[2] = static_cast<SizeValueType>(inputSize[2] * inputSpacing[2] / outputSpacing[2] + .5);
| |
| | |
| ResampleFilterType::Pointer resampler = ResampleFilterType::New();
| |
| resampler->SetInput( reader->GetOutput() );
| |
| resampler->SetTransform( transform );
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| resampler->SetInterpolator( interpolator );
| |
| resampler->SetOutputOrigin ( reader->GetOutput()->GetOrigin());
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| resampler->SetOutputSpacing ( outputSpacing );
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| resampler->SetOutputDirection ( reader->GetOutput()->GetDirection());
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| resampler->SetSize ( outputSize );
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| resampler->Update ();
| |
| | |
| | |
| ////////////////////////////////////////////////
| |
| // 3) Create a MetaDataDictionary for each slice.
| |
| | |
| // Copy the dictionary from the first image and override slice
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| // specific fields
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| ReaderType::DictionaryRawPointer inputDict = (*(reader->GetMetaDataDictionaryArray()))[0];
| |
| ReaderType::DictionaryArrayType outputArray;
| |
|
| |
| // To keep the new series in the same study as the original we need
| |
| // to keep the same study UID. But we need new series and frame of
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| // reference UID's.
| |
| #if ITK_VERSION_MAJOR >= 4
| |
| gdcm::UIDGenerator suid;
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| std::string seriesUID = suid.Generate();
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| gdcm::UIDGenerator fuid;
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| std::string frameOfReferenceUID = fuid.Generate();
| |
| #else
| |
| std::string seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
| |
| std::string frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); | |
| #endif
| |
| std::string studyUID;
| |
| std::string sopClassUID;
| |
| itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
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| itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
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| gdcmIO->KeepOriginalUIDOn();
| |
| | |
| for (unsigned int f = 0; f < outputSize[2]; f++)
| |
| {
| |
| // Create a new dictionary for this slice
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| ReaderType::DictionaryRawPointer dict = new ReaderType::DictionaryType;
| |
| | |
| // Copy the dictionary from the first slice
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| CopyDictionary (*inputDict, *dict);
| |
| | |
| // Set the UID's for the study, series, SOP and frame of reference
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| itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0020|0052", frameOfReferenceUID);
| |
| | |
| #if ITK_VERSION_MAJOR >= 4
| |
| gdcm::UIDGenerator sopuid;
| |
| std::string sopInstanceUID = sopuid.Generate();
| |
| #else
| |
| std::string sopInstanceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
| |
| #endif
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0008|0018", sopInstanceUID);
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0002|0003", sopInstanceUID);
| |
| | |
| // Change fields that are slice specific
| |
| itksys_ios::ostringstream value;
| |
| value.str("");
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| value << f + 1;
| |
| | |
| // Image Number
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| itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());
| |
| | |
| // Series Description - Append new description to current series
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| // description
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| std::string oldSeriesDesc;
| |
| itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);
| |
| | |
| value.str("");
| |
| value << oldSeriesDesc
| |
| << ": Resampled with pixel spacing "
| |
| << outputSpacing[0] << ", "
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| << outputSpacing[1] << ", "
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| << outputSpacing[2];
| |
| // This is an long string and there is a 64 character limit in the
| |
| // standard
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| unsigned lengthDesc = value.str().length();
| |
|
| |
| std::string seriesDesc( value.str(), 0,
| |
| lengthDesc > 64 ? 64
| |
| : lengthDesc);
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0008|103e", seriesDesc);
| |
| | |
| // Series Number
| |
| value.str("");
| |
| value << 1001;
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0020|0011", value.str());
| |
| | |
| // Derivation Description - How this image was derived
| |
| value.str("");
| |
| for (int i = 0; i < argc; i++)
| |
| {
| |
| value << argv[i] << " ";
| |
| }
| |
| value << ": " << ITK_SOURCE_VERSION;
| |
| | |
| lengthDesc = value.str().length();
| |
| std::string derivationDesc( value.str(), 0,
| |
| lengthDesc > 1024 ? 1024
| |
| : lengthDesc);
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0008|2111", derivationDesc);
| |
|
| |
| // Image Position Patient: This is calculated by computing the
| |
| // physical coordinate of the first pixel in each slice.
| |
| InputImageType::PointType position;
| |
| InputImageType::IndexType index;
| |
| index[0] = 0;
| |
| index[1] = 0;
| |
| index[2] = f;
| |
| resampler->GetOutput()->TransformIndexToPhysicalPoint(index, position);
| |
| | |
| value.str("");
| |
| value << position[0] << "\\" << position[1] << "\\" << position[2];
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str());
| |
| // Slice Location: For now, we store the z component of the Image
| |
| // Position Patient.
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| value.str("");
| |
| value << position[2];
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());
| |
| | |
| if (changeInSpacing)
| |
| {
| |
| // Slice Thickness: For now, we store the z spacing
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| value.str("");
| |
| value << outputSpacing[2];
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0018|0050",
| |
| value.str());
| |
| // Spacing Between Slices
| |
| itk::EncapsulateMetaData<std::string>(*dict,"0018|0088",
| |
| value.str());
| |
| }
| |
|
| |
| // Save the dictionary
| |
| outputArray.push_back(dict);
| |
| }
| |
|
| |
| ////////////////////////////////////////////////
| |
| // 4) Shift data to undo the effect of a rescale intercept by the
| |
| // DICOM reader
| |
| std::string interceptTag("0028|1052");
| |
| typedef itk::MetaDataObject< std::string > MetaDataStringType;
| |
| itk::MetaDataObjectBase::Pointer entry = (*inputDict)[interceptTag];
| |
|
| |
| MetaDataStringType::ConstPointer interceptValue =
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| dynamic_cast<const MetaDataStringType *>( entry.GetPointer() ) ;
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|
| |
| int interceptShift = 0;
| |
| if( interceptValue )
| |
| {
| |
| std::string tagValue = interceptValue->GetMetaDataObjectValue();
| |
| interceptShift = -atoi ( tagValue.c_str() );
| |
| }
| |
| | |
| ShiftScaleType::Pointer shiftScale = ShiftScaleType::New();
| |
| shiftScale->SetInput( resampler->GetOutput());
| |
| shiftScale->SetShift( interceptShift );
| |
| | |
| ////////////////////////////////////////////////
| |
| // 5) Write the new DICOM series
| |
| | |
| // Make the output directory and generate the file names.
| |
| itksys::SystemTools::MakeDirectory( argv[2] );
| |
| | |
| // Generate the file names
| |
| OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
| |
| std::string seriesFormat(argv[2]);
| |
| seriesFormat = seriesFormat + "/" + "IM%d.dcm";
| |
| outputNames->SetSeriesFormat (seriesFormat.c_str());
| |
| outputNames->SetStartIndex (1);
| |
| outputNames->SetEndIndex (outputSize[2]);
| |
|
| |
| SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
| |
| seriesWriter->SetInput( shiftScale->GetOutput() );
| |
| seriesWriter->SetImageIO( gdcmIO );
| |
| seriesWriter->SetFileNames( outputNames->GetFileNames() );
| |
| seriesWriter->SetMetaDataDictionaryArray( &outputArray );
| |
| try
| |
| {
| |
| seriesWriter->Update();
| |
| }
| |
| catch( itk::ExceptionObject & excp )
| |
| {
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| std::cerr << "Exception thrown while writing the series " << std::endl;
| |
| std::cerr << excp << std::endl;
| |
| return EXIT_FAILURE;
| |
| }
| |
| std::cout << "The output series in directory " << argv[2]
| |
| << " has " << outputSize[2] << " files with spacing "
| |
| << outputSpacing
| |
| << std::endl;
| |
| return EXIT_SUCCESS;
| |
| }
| |
| | |
| void CopyDictionary (itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict)
| |
| {
| |
| typedef itk::MetaDataDictionary DictionaryType;
| |
| | |
| DictionaryType::ConstIterator itr = fromDict.Begin();
| |
| DictionaryType::ConstIterator end = fromDict.End();
| |
| typedef itk::MetaDataObject< std::string > MetaDataStringType;
| |
| | |
| while( itr != end )
| |
| {
| |
| itk::MetaDataObjectBase::Pointer entry = itr->second;
| |
| | |
| MetaDataStringType::Pointer entryvalue =
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| dynamic_cast<MetaDataStringType *>( entry.GetPointer() ) ;
| |
| if( entryvalue )
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| {
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| std::string tagkey = itr->first;
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| std::string tagvalue = entryvalue->GetMetaDataObjectValue();
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| itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
| |
| }
| |
| ++itr;
| |
| }
| |
| }
| |
| </source>
| |
| | |
| ==CMakeLists.txt==
| |
| <source lang="cmake">
| |
| cmake_minimum_required(VERSION 2.6)
| |
| | |
| PROJECT(ResampleDICOM)
| |
| | |
| FIND_PACKAGE(ITK REQUIRED)
| |
| INCLUDE(${ITK_USE_FILE})
| |
| | |
| ADD_EXECUTABLE(ResampleDICOM ResampleDICOM.cxx)
| |
| TARGET_LINK_LIBRARIES(ResampleDICOM ${ITK_LIBRARIES})
| |
| </source>
| |
