*
===================================================*/
-// clitk
-#include "clitkResampleImageWithOptionsFilter.h"
-#if GDCM_MAJOR_VERSION >= 2
-#include "gdcmUIDGenerator.h"
-#else
-#include "gdcmFile.h"
-#include "gdcmUtil.h"
-#endif
#include "itkVersion.h"
-
#include "itkImage.h"
-#include "itkMinimumMaximumImageFilter.h"
-
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkNumericSeriesFileNames.h"
-
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"
-#include <itkThresholdImageFilter.h>
-
-#include "itkResampleImageFilter.h"
-
+#include "itkThresholdImageFilter.h"
+
#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
#include "itkShiftScaleImageFilter.h"
#endif
-
-#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>
#include <sstream>
#if GDCM_MAJOR_VERSION >= 2
-#include "gdcmUIDGenerator.h"
+#include <gdcmUIDGenerator.h>
#include <gdcmImageHelper.h>
#include <gdcmAttribute.h>
#include <gdcmReader.h>
#include <gdcmWriter.h>
#include <gdcmDataElement.h>
#include <gdcmTag.h>
+#else
+#include "gdcmFile.h"
+#include "gdcmUtil.h"
#endif
namespace clitk
void
Spect2DicomGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
{
+ // Validate input parameters
+ const unsigned int InputDimension = Dimension;
+ const unsigned int OutputDimension = Dimension;
-// 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
-// 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
-// spacing.
-// 3) Create a MetaDataDictionary for each slice.
-// 4) Shift data to undo the effect of a rescale intercept by the
-// DICOM reader (only for ITK < 4.6)
-// 5) Write the new DICOM series
-//
-
-
-
-
- // Validate input parameters
-
- const unsigned int InputDimension = 3;
- const unsigned int OutputDimension = 3;
-
-
- typedef itk::Image< PixelType, InputDimension >
- InputImageType;
- typedef itk::Image< PixelType, OutputDimension >
- OutputImageType;
- typedef itk::ImageSeriesReader< InputImageType >
- ReaderType;
- typedef itk::GDCMImageIO
- ImageIOType;
- typedef itk::GDCMSeriesFileNames
- InputNamesGeneratorType;
- typedef itk::NumericSeriesFileNames
- OutputNamesGeneratorType;
- typedef itk::IdentityTransform< double, InputDimension >
- TransformType;
- typedef itk::LinearInterpolateImageFunction< InputImageType, double >
- InterpolatorType;
- typedef itk::ResampleImageFilter< InputImageType, InputImageType >
- ResampleFilterType;
+ typedef itk::Image< PixelType, InputDimension > InputImageType;
+ typedef itk::Image< PixelType, OutputDimension > OutputImageType;
+ typedef itk::ImageSeriesReader< InputImageType > ReaderType;
+ typedef itk::GDCMImageIO ImageIOType;
#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
- typedef itk::ShiftScaleImageFilter< InputImageType, InputImageType >
- ShiftScaleType;
+ typedef itk::ShiftScaleImageFilter< InputImageType, InputImageType > ShiftScaleType;
#endif
- typedef itk::ImageSeriesWriter< InputImageType, OutputImageType >
- SeriesWriterType;
-
+ typedef itk::ImageSeriesWriter< InputImageType, OutputImageType > SeriesWriterType;
+
////////////////////////////////////////////////
// 1) Read the input series
typedef typename RegionType::SizeType SizeType;
typedef itk::ImageFileReader<InputImageType> InputReaderType;
typename InputReaderType::Pointer volumeReader = InputReaderType::New();
- volumeReader->SetFileName( m_ArgsInfo.input_arg );
+ volumeReader->SetFileName(m_ArgsInfo.input_arg);
volumeReader->Update();
-
typename InputImageType::Pointer input = volumeReader->GetOutput();
-
+
ImageIOType::Pointer gdcmIO = ImageIOType::New();
gdcmIO->LoadPrivateTagsOn();
- InputNamesGeneratorType::Pointer inputNames = InputNamesGeneratorType::New();
- inputNames->SetInputDirectory( m_ArgsInfo.inputDir_arg );
-
- const typename ReaderType::FileNamesContainer & filenames =
- inputNames->GetInputFileNames();
-
+ typename ReaderType::FileNamesContainer filenames;
+ filenames.push_back(m_ArgsInfo.inputDcm_arg);
typename ReaderType::Pointer reader = ReaderType::New();
-
- reader->SetImageIO( gdcmIO );
- reader->SetFileNames( filenames );
- try
- {
+ reader->SetImageIO(gdcmIO);
+ reader->SetFileNames(filenames);
+ try {
reader->Update();
- }
- catch (itk::ExceptionObject &excp)
- {
+ } catch (itk::ExceptionObject &excp) {
std::cerr << "Exception thrown while reading the series" << std::endl;
std::cerr << excp << std::endl;
return;
- }
- typename InputImageType::SpacingType outputSpacing;
- typename InputImageType::SizeType outputSize;
- for (unsigned int i = 0; i < 3; i++)
- {
+ }
+
+ typename InputImageType::SpacingType outputSpacing;
+ typename InputImageType::SizeType outputSize;
+ for (unsigned int i = 0; i < 3; i++) {
outputSpacing[i] = input->GetSpacing()[i];
outputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
- }
+ }
////////////////////////////////////////////////
// 2) Ensure to have value >= -1024
input=thresholdFilter->GetOutput();
-
-
-////////////////////////////////////////////////
-// 2) Resample the series
-/* typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
-
- TransformType::Pointer transform = TransformType::New();
- transform->SetIdentity();
-
- const typename InputImageType::SpacingType& inputSpacing =
- reader->GetOutput()->GetSpacing();
- const typename InputImageType::RegionType& inputRegion =
- reader->GetOutput()->GetLargestPossibleRegion();
- const typename InputImageType::SizeType& inputSize =
- inputRegion.GetSize();
-
- std::cout << "The input series in directory " << m_ArgsInfo.inputDir_arg
- << " has " << filenames.size() << " files with spacing "
- << inputSpacing
- << std::endl;
-
- // Compute the size of the output. The user specifies a spacing on
- // the command line. If the spacing is 0, the input spacing will be
- // used. The size (# of pixels) in the output is recomputed using
- // the ratio of the input and output sizes.
- typename InputImageType::SpacingType outputSpacing;
-
- bool changeInSpacing = false;
- for (unsigned int i = 0; i < 3; i++)
- {
- outputSpacing[i] = inputSpacing[i];
- }
- typename InputImageType::SizeType outputSize;
- typedef typename 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);
-
- typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
- resampler->SetInput( reader->GetOutput() );
- resampler->SetTransform( transform );
- resampler->SetInterpolator( interpolator );
- resampler->SetOutputOrigin ( reader->GetOutput()->GetOrigin());
- resampler->SetOutputSpacing ( outputSpacing );
- resampler->SetOutputDirection ( reader->GetOutput()->GetDirection());
- resampler->SetSize ( outputSize );
- resampler->Update ();
-
- */
-
////////////////////////////////////////////////
// 3) Create a MetaDataDictionary for each slice.
-
+
// Copy the dictionary from the first image and override slice
// specific fields
typename ReaderType::DictionaryRawPointer inputDict = (*(reader->GetMetaDataDictionaryArray()))[0];
typename 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
// reference UID's.
itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
gdcmIO->KeepOriginalUIDOn();
- int nbFile(1);
- for (unsigned int f = 0; f < nbFile; f++)
- {
- // Create a new dictionary for this slice
- typename ReaderType::DictionaryRawPointer dict = new typename ReaderType::DictionaryType;
-
- // Copy the dictionary from the first slice
- //CopyDictionary (*inputDict, *dict);
-
- typedef itk::MetaDataDictionary DictionaryType;
-
- DictionaryType::ConstIterator itrDic = (*inputDict).Begin();
- DictionaryType::ConstIterator endDic = (*inputDict).End();
- typedef itk::MetaDataObject< std::string > MetaDataStringType;
-
- while( itrDic != endDic )
+
+ // Create a new dictionary for this slice
+ typename ReaderType::DictionaryRawPointer dict = new typename ReaderType::DictionaryType;
+
+ typedef itk::MetaDataDictionary DictionaryType;
+
+ DictionaryType::ConstIterator itrDic = (*inputDict).Begin();
+ DictionaryType::ConstIterator endDic = (*inputDict).End();
+ typedef itk::MetaDataObject< std::string > MetaDataStringType;
+
+ while( itrDic != endDic )
+ {
+ itk::MetaDataObjectBase::Pointer entry = itrDic->second;
+
+ MetaDataStringType::Pointer entryvalue =
+ dynamic_cast<MetaDataStringType *>( entry.GetPointer() ) ;
+ if( entryvalue )
{
- itk::MetaDataObjectBase::Pointer entry = itrDic->second;
-
- MetaDataStringType::Pointer entryvalue =
- dynamic_cast<MetaDataStringType *>( entry.GetPointer() ) ;
- if( entryvalue )
- {
- std::string tagkey = itrDic->first;
- std::string tagvalue = entryvalue->GetMetaDataObjectValue();
- itk::EncapsulateMetaData<std::string>(*dict, tagkey, tagvalue);
- }
- ++itrDic;
+ std::string tagkey = itrDic->first;
+ std::string tagvalue = entryvalue->GetMetaDataObjectValue();
+ itk::EncapsulateMetaData<std::string>(*dict, tagkey, tagvalue);
}
-
- // Set the UID's for the study, series, SOP and frame of reference
- itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);
- itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);
- itk::EncapsulateMetaData<std::string>(*dict,"0020|0052", frameOfReferenceUID);
-
+ ++itrDic;
+ }
+
+ // Set the UID's for the study, series, SOP and frame of reference
+ 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();
+ gdcm::UIDGenerator sopuid;
+ std::string sopInstanceUID = sopuid.Generate();
#else
- std::string sopInstanceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+ 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
- std::ostringstream value;
- value.str("");
- //unsigned int f = 0;
- value << f + 1;
-
- // Image Number
- itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());
-
- // Series Description - Append new description to current series
- // description
- std::string oldSeriesDesc;
- itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);
-
- value.str("");
- value << oldSeriesDesc
- << ": Resampled with pixel spacing "
- << outputSpacing[0] << ", "
- << outputSpacing[1] << ", "
- << outputSpacing[2];
- // This is an long string and there is a 64 character limit in the
- // standard
- 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("");
-
- 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.
- typename InputImageType::PointType position;
- typename InputImageType::IndexType index;
- index[0] = 0;
- index[1] = 0;
- index[2] = f;
- input->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.
- value.str("");
- value << position[2];
- itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());
-
-
- // Slice Thickness: For now, we store the z spacing
- 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());
-
- /*
- value.str("");
- value << 0.999987 << "\\" << -0.005061 << "\\" << 0.000000 << "\\" << 0.000000 << "\\" << 0.000000 << "\\" << -1.000000;
- itk::EncapsulateMetaData<std::string>(*dict, "0020|0037", value.str());
-
- value.str("");
- value << 196;
- itk::EncapsulateMetaData<std::string>(*dict, "0002|0000", value.str());
- value.str("");
- value << 510;
- itk::EncapsulateMetaData<std::string>(*dict, "0008|0000", value.str());
- value.str("");
- value << 362;
- itk::EncapsulateMetaData<std::string>(*dict, "0009|0000", value.str());
- value.str("");
- value << 116;
- itk::EncapsulateMetaData<std::string>(*dict, "0010|0000", value.str());
- value.str("");
- value << 1008;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|0000", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1011", value.str());
- value.str("");
- value << 1 << "\\" << 1;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1015", value.str());
- value.str("");
- value << 1 << "\\" << 2;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1016", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1017", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1018", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1019", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|101a", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|101f", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1026", value.str());
- value.str("");
- value << 0 << "\\" << 0 << "\\" << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1027", value.str());
- value.str("");
- value << 0 << "\\" << 0 << "\\" << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1028", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|102c", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|102d", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|102e", value.str());
- std::ostringstream valueVec[2];
- valueVec[0].str("");
- valueVec[0] << 32767;
- valueVec[1].str("");
- valueVec[1] << 32767;
- std::string valueVec2[2];
- valueVec2[0]=valueVec[0].str();
- valueVec2[1]=valueVec[1].str();
- itk::EncapsulateMetaData<std::string*>(*dict, "0011|102f", valueVec2);
- value.str("");
- value << 1 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0020|1011", value.str());
- value.str("");
- value << 63 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0028|0107", value.str());
-
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1130", value.str());
- value.str("");
- value << 563.7 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1131", value.str());
- value.str("");
- value << "CC" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1140", value.str());
- value.str("");
- value << 243.5 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1142", value.str());
- value.str("");
- value << 360 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1143", value.str());
- value.str("");
- value << 6 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1144", value.str());
- value.str("");
- value << 10000 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1242", value.str());
- value.str("");
- value << 60 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0054|0053", value.str());
- value.str("");
- value << 180.29 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0054|0200", value.str());
- value.str("");
- value << "F-10450" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0008|0100", value.str());
- value.str("");
- value << "99SDM" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0008|0102", value.str());
- value.str("");
- value << "recumbent" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0008|0104", value.str());
- value.str("");
- value << 114 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0054|0014", value.str());
- value.str("");
- value << 126 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0054|0015", value.str());
- value.str("");
- value << "Tc99m_SC" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0054|0018", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1120", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1145", value.str());
- value.str("");
- value << 0 << "\\" << 0;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1149", value.str());
- value.str("");
- value << "LEHR" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1180", value.str());
- value.str("");
- value << "PARA" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1181", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1182", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1183", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0018|1184", value.str());
- value.str("");
- value << 1.000000 << "\\" << 1.000000 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0028|0031", value.str());
- value.str("");
- value << 0.000000 << "\\" << 0.000000 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0028|0032", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|101c", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|101d", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0013|1016", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0013|1017", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1023", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1024", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1025", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|1029", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0011|103e", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0013|1018", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0013|1019", value.str());
- value.str("");
- value << 0 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0013|101a", value.str());
- value.str("");
- value << "GEMS_GENIE_1" ;
- itk::EncapsulateMetaData<std::string>(*dict, "0035|0010", value.str());
- value.str("");
- value << 29 ;
- itk::EncapsulateMetaData<std::string>(*dict, "0035|1001", value.str());
-
- */
- // Save the dictionary
- outputArray.push_back(inputDict);
- }
-
+ itk::EncapsulateMetaData<std::string>(*dict,"0008|0018", sopInstanceUID);
+ itk::EncapsulateMetaData<std::string>(*dict,"0002|0003", sopInstanceUID);
+
+ // Change fields that are slice specific
+ std::ostringstream value;
+ value.str("1");
+
+ // Image Number
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());
+
+ // Series Description - Append new description to current series
+ // description
+ std::string oldSeriesDesc;
+ itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);
+
+ value.str("");
+ value << oldSeriesDesc
+ << ": Resampled with pixel spacing "
+ << outputSpacing[0] << ", "
+ << outputSpacing[1] << ", "
+ << outputSpacing[2];
+ // This is an long string and there is a 64 character limit in the
+ // standard
+ 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("");
+
+ 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.
+ typename InputImageType::PointType position;
+ typename InputImageType::IndexType index;
+ index[0] = 0;
+ index[1] = 0;
+ index[2] = 0;
+ input->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.
+ value.str("");
+ value << position[2];
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());
+
+ // Slice Thickness: For now, we store the z spacing
+ 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(inputDict);
+
#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
////////////////////////////////////////////////
// 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;
+ typedef itk::MetaDataObject<std::string> MetaDataStringType;
itk::MetaDataObjectBase::Pointer entry = (*inputDict)[interceptTag];
-
+
MetaDataStringType::ConstPointer interceptValue =
- dynamic_cast<const MetaDataStringType *>( entry.GetPointer() ) ;
-
+ dynamic_cast<const MetaDataStringType *>(entry.GetPointer());
+
int interceptShift = 0;
- if( interceptValue )
- {
+ if(interceptValue ) {
std::string tagValue = interceptValue->GetMetaDataObjectValue();
- interceptShift = -atoi ( tagValue.c_str() );
- }
-
+ interceptShift = -atoi (tagValue.c_str());
+ }
+
ShiftScaleType::Pointer shiftScale = ShiftScaleType::New();
- shiftScale->SetInput( resampler->GetOutput());
- shiftScale->SetShift( interceptShift );
+ shiftScale->SetInput(resampler->GetOutput());
+ shiftScale->SetShift(interceptShift );
#endif
-
+
////////////////////////////////////////////////
// 5) Write the new DICOM series
-
- // Make the output directory and generate the file names.
- itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg );
-
// Generate the file names
- OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
- std::string seriesFormat(m_ArgsInfo.outputDir_arg);
- seriesFormat = seriesFormat + "/" + "IM%03d.dcm";
- outputNames->SetSeriesFormat (seriesFormat.c_str());
- outputNames->SetStartIndex (1);
- outputNames->SetEndIndex (nbFile);
- //outputNames->SetEndIndex (outputSize[2]);
typename ReaderType::FileNamesContainer fileNamesOutput;
- std::string extension = "output.dcm";
- fileNamesOutput.push_back(extension);
- //seriesWriter->SetFileNames( fileNamesOutput );
-
+ fileNamesOutput.push_back(m_ArgsInfo.outputDcm_arg);
+
typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
- seriesWriter->SetInput( input );
+ seriesWriter->SetInput(input);
#else
- seriesWriter->SetInput( input );
+ seriesWriter->SetInput(input);
#endif
- seriesWriter->SetImageIO( gdcmIO );
- seriesWriter->SetFileNames( outputNames->GetFileNames() );
- seriesWriter->SetMetaDataDictionaryArray( &outputArray );
- try
- {
+ seriesWriter->SetImageIO(gdcmIO);
+ seriesWriter->SetFileNames(fileNamesOutput);
+ seriesWriter->SetMetaDataDictionaryArray(&outputArray);
+ try {
seriesWriter->Update();
- }
- catch( itk::ExceptionObject & excp )
- {
+ } catch(itk::ExceptionObject & excp) {
std::cerr << "Exception thrown while writing the series " << std::endl;
std::cerr << excp << std::endl;
return;
- }
- std::cout << "The output series in directory " << m_ArgsInfo.outputDir_arg
- << " has " << nbFile << " files with spacing "
- << outputSpacing
- << std::endl;
+ }
+////////////////////////////////////////////////
+// 5) Read the new dicom data tag and copy it in the model data tag to have all dicom tags
gdcm::Reader readerModel, readerOutput;
- readerModel.SetFileName( inputNames->GetInputFileNames()[0].c_str() );
- readerOutput.SetFileName( outputNames->GetFileNames()[0].c_str() );
+ readerModel.SetFileName(filenames[0].c_str());
+ readerOutput.SetFileName(fileNamesOutput[0].c_str());
readerModel.Read();
readerOutput.Read();
gdcm::File &fileModel = readerModel.GetFile();
const gdcm::DataElement &dataOutput = dsOutput.GetDataElement(gdcm::Tag(0x7fe0, 0x10));
dsModel.Replace(dataOutput);
gdcm::Writer w;
- w.SetFile( fileModel );
- w.SetFileName( outputNames->GetFileNames()[0].c_str() );
+ w.SetFile(fileModel);
+ w.SetFileName(fileNamesOutput[0].c_str());
w.Write();
return;
}
-
-
-/*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 =
- dynamic_cast<MetaDataStringType *>( entry.GetPointer() ) ;
- if( entryvalue )
- {
- std::string tagkey = itr->first;
- std::string tagvalue = entryvalue->GetMetaDataObjectValue();
- itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
- }
- ++itr;
- }
-} */
-
-
}//end clitk
#endif //#define clitkSpect2DicomGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff