*
===================================================*/
+#include <sstream>
// clitk
#include "clitkResampleImageWithOptionsFilter.h"
#if GDCM_MAJOR_VERSION >= 2
#include "gdcmUIDGenerator.h"
+#include <gdcmImageHelper.h>
+#include <gdcmAttribute.h>
+#include <gdcmReader.h>
+#include <gdcmWriter.h>
#else
#include "gdcmFile.h"
#include "gdcmUtil.h"
#endif
+#include "itkImageRegionIterator.h"
+#include "itkMetaImageIO.h"
+#include "itkMetaDataDictionary.h"
+
namespace clitk
{
GateSimulation2DicomGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
{
+#if GDCM_MAJOR_VERSION >= 2
// ImageTypes
typedef itk::Image<PixelType, Dimension> InputImageType;
typedef itk::Image<PixelType, Dimension> OutputImageType;
-
- // Read the dicom directory
typedef itk::ImageFileReader< InputImageType > ReaderType;
+ typedef itk::ImageSeriesReader< InputImageType > ReaderSeriesType;
typedef itk::GDCMImageIO ImageIOType;
- typedef itk::GDCMSeriesFileNames NamesGeneratorType;
+
+ // Read Dicom model file
+ typename ReaderSeriesType::Pointer readerSeries = ReaderSeriesType::New();
ImageIOType::Pointer gdcmIO = ImageIOType::New();
std::string filename_out = m_ArgsInfo.outputFilename_arg;
-
- // Output the dicom files
- unsigned int numberOfFilenames = 1;
- if (m_Verbose) {
- std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputModelFilename_arg<<"..."<<std::endl<<std::endl;
- }
-
- // Read the series
- typename ReaderType::Pointer reader = ReaderType::New();
-#if GDCM_MAJOR_VERSION >= 2
gdcmIO->LoadPrivateTagsOn();
gdcmIO->KeepOriginalUIDOn();
-#endif
- reader->SetImageIO( gdcmIO );
- reader->SetFileName( m_ArgsInfo.inputModelFilename_arg );
+ typename ReaderSeriesType::FileNamesContainer fileNames;
+ fileNames.push_back(m_ArgsInfo.inputModelFilename_arg);
+ readerSeries->SetImageIO( gdcmIO );
+ readerSeries->SetFileNames( fileNames );
try {
- reader->Update();
+ readerSeries->Update();
} catch (itk::ExceptionObject &excp) {
- std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
+ std::cerr << "Error: Exception thrown while reading the DICOM model file !!" << std::endl;
std::cerr << excp << std::endl;
}
+
// Read the input (MHD file)
typedef typename InputImageType::RegionType RegionType;
typedef typename RegionType::SizeType SizeType;
typename InputReaderType::Pointer volumeReader = InputReaderType::New();
volumeReader->SetFileName( m_InputFileName);
volumeReader->Update();
-
typename InputImageType::Pointer input = volumeReader->GetOutput();
- if (input->GetLargestPossibleRegion().GetSize() != reader->GetOutput()->GetLargestPossibleRegion().GetSize()) {
-
- // resampling is carried out on the fly if resolution or size between
- // the input mhd and input dicom series is different
-
- // Filter
- typedef clitk::ResampleImageWithOptionsFilter<InputImageType, InputImageType> ResampleImageFilterType;
- typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New();
- filter->SetInput(input);
- filter->SetVerboseOptions(m_Verbose);
- filter->SetGaussianFilteringEnabled(false);
- filter->SetDefaultPixelValue(0);
-
- const SizeType& input_size = input->GetLargestPossibleRegion().GetSize();
- SizeType output_size;
- for (unsigned int i = 0; i < Dimension; i++)
- output_size[i] = input_size[i];
- filter->SetOutputSize(output_size);
- if (m_Verbose) {
- std::cout << "Warning: The image size differs between the MHD file and the input dicom series. Performing resampling with default options using mhd size as reference (for advanced options, use clitkResampleImage)." << std::endl;
- std::cout << "MHD -> " << input->GetLargestPossibleRegion().GetSize() << std::endl;
- std::cout << "dicom -> " << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl;
- }
- try {
- filter->Update();
- input = filter->GetOutput();
- } catch( itk::ExceptionObject & excp ) {
- std::cerr << "Error: Exception thrown while resampling!!" << std::endl;
- std::cerr << excp << std::endl;
- }
- }
-#if GDCM_MAJOR_VERSION < 2
- gdcmIO->SetKeepOriginalUID(true);
-#endif
-
-
- //Read the dicom file to find the energy, the head & the steps (TODO: do it on the mhd filetext)
+ //Read the metadata informations in the mhd
+ MetaObject tObj(3);
+ tObj.AddUserField("NumberOfEnergyWindows", MET_STRING);
+ tObj.AddUserField("NbOfHeads", MET_STRING);
+ tObj.AddUserField("NbOfProjections", MET_STRING);
+ tObj.Read(m_InputFileName.c_str());
+ char *p_energyNumber, *p_headNumber, *p_rotationNumber;
+ int energyNumber, headNumber, rotationNumber;
+ p_energyNumber = static_cast<char*>(tObj.GetUserField("NumberOfEnergyWindows"));
+ p_headNumber = static_cast<char*>(tObj.GetUserField("NbOfHeads"));
+ p_rotationNumber = static_cast<char*>(tObj.GetUserField("NbOfProjections"));
+ energyNumber = atoi(p_energyNumber);
+ headNumber = atoi(p_headNumber);
+ rotationNumber = atoi(p_rotationNumber);
+ for (unsigned int i=0; i<energyNumber; ++i) {
+ std::string tagEnergyName("EnergyWindow_");
+ tagEnergyName += NumberToString(i).c_str();
+ std::string tagEnergyThreshold(tagEnergyName), tagEnergyUphold(tagEnergyName);
+ tagEnergyThreshold += "_threshold";
+ tagEnergyUphold += "_uphold";
+ tObj.AddUserField(tagEnergyName.c_str(), MET_STRING);
+ tObj.AddUserField(tagEnergyThreshold.c_str(), MET_STRING);
+ tObj.AddUserField(tagEnergyUphold.c_str(), MET_STRING);
+ }
+ tObj.Read(m_InputFileName.c_str());
+ std::vector<char*> p_EnergyWindowName(energyNumber), p_EnergyWindowThreshold(energyNumber), p_EnergyWindowUphold(energyNumber);
+ std::vector<int> energyWindowThreshold(energyNumber), energyWindowUphold(energyNumber);
+ for (unsigned int i=0; i<energyNumber; ++i) {
+ std::string tagEnergyName("EnergyWindow_");
+ tagEnergyName += NumberToString(i).c_str();
+ std::string tagEnergyThreshold(tagEnergyName), tagEnergyUphold(tagEnergyName);
+ tagEnergyThreshold += "_threshold";
+ tagEnergyUphold += "_uphold";
+ p_EnergyWindowName[i] = static_cast<char*>(tObj.GetUserField(tagEnergyName.c_str()));
+ p_EnergyWindowThreshold[i] = static_cast<char*>(tObj.GetUserField(tagEnergyThreshold.c_str()));
+ p_EnergyWindowUphold[i] = static_cast<char*>(tObj.GetUserField(tagEnergyUphold.c_str()));
+ energyWindowThreshold[i] = atoi(p_EnergyWindowThreshold[i]);
+ energyWindowUphold[i] = atoi(p_EnergyWindowUphold[i]);
+ }
+//TODO if the input size/spacing and dicom model ones are different
+
+ // Create a new mhd image with the correct dicom order slices
+ typename InputImageType::Pointer mhdCorrectOrder = InputImageType::New();
+ mhdCorrectOrder->SetRegions(input->GetLargestPossibleRegion());
+ mhdCorrectOrder->Allocate();
+ unsigned int zAxis(0); //z value for the input mhd image
+ for (unsigned int energy = 0; energy < energyNumber; ++energy) {
+ for (unsigned int head = 0; head < headNumber; ++head) {
+ for (unsigned int rotation = 0; rotation < rotationNumber; ++rotation) {
+ std::cout << "Energy " << energy << " Head " << head << " Rotation " << rotation << std::endl;
+
+ typename InputImageType::IndexType startIteratorIndexCorrectOrder; //pixel index of mhdCorrectOrder
+ startIteratorIndexCorrectOrder[0] = 0;
+ startIteratorIndexCorrectOrder[1] = 0;
+ startIteratorIndexCorrectOrder[2] = rotation + head*rotationNumber + energy*headNumber;
+
+ typename InputImageType::IndexType startIteratorIndexOriginalOrder; //pixel index of input mhd
+ startIteratorIndexOriginalOrder[0] = 0;
+ startIteratorIndexOriginalOrder[1] = 0;
+ startIteratorIndexOriginalOrder[2] = head + energy*headNumber + rotation*energyNumber;
+
+ typename InputImageType::SizeType regionSizeIterator;
+ regionSizeIterator[0] = input->GetLargestPossibleRegion().GetSize()[0];
+ regionSizeIterator[1] = input->GetLargestPossibleRegion().GetSize()[1];
+ regionSizeIterator[2] = 1;
+
+ typename InputImageType::RegionType regionIteratorCorrectOrder;
+ regionIteratorCorrectOrder.SetSize(regionSizeIterator);
+ regionIteratorCorrectOrder.SetIndex(startIteratorIndexCorrectOrder);
+
+ typename InputImageType::RegionType regionIteratorOriginalOrder;
+ regionIteratorOriginalOrder.SetSize(regionSizeIterator);
+ regionIteratorOriginalOrder.SetIndex(startIteratorIndexOriginalOrder);
+
+ itk::ImageRegionIterator<InputImageType> CorrectOrderIterator(mhdCorrectOrder,regionIteratorCorrectOrder);
+ itk::ImageRegionIterator<InputImageType> OriginalOrderIterator(input,regionIteratorOriginalOrder);
+ while(!CorrectOrderIterator.IsAtEnd()) {
+ CorrectOrderIterator.Set(OriginalOrderIterator.Get());
+ ++CorrectOrderIterator;
+ ++OriginalOrderIterator;
+ }
+
+ ++zAxis;
+ }
+ }
+ }
-/*
// update output dicom keys/tags
- //std::string seriesUIDkey = "0020|000e";
- for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
- std::string entryId(m_ArgsInfo.key_arg[i] );
- std::string value( m_ArgsInfo.tag_arg[i] );
+ // string for distinguishing items inside sequence:
+ const std::string ITEM_ENCAPSULATE_STRING("DICOM_ITEM_ENCAPSULATE");
+ std::string tempString = ITEM_ENCAPSULATE_STRING + "01";
+ typename ReaderSeriesType::DictionaryRawPointer inputDict = (*(readerSeries->GetMetaDataDictionaryArray()))[0];
+ typename ReaderSeriesType::DictionaryArrayType outputArray;
+ typename ReaderSeriesType::DictionaryRawPointer outputDict = new typename ReaderSeriesType::DictionaryType;
+ CopyDictionary (*inputDict, *outputDict);
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0054|0011", NumberToString(energyNumber));
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0054|0021", NumberToString(headNumber));
+ outputArray.push_back(outputDict);
+
- itk::EncapsulateMetaData<std::string>(reader->GetMetaDataDictionary(), entryId, value );
- }
-*/
// Output directory and filenames
- //itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputFilename_arg ); // create if it doesn't exist
- typedef itk::ImageFileWriter<OutputImageType> SeriesWriterType;
- typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
+ typedef itk::ImageSeriesWriter<OutputImageType, OutputImageType> WriterSerieType;
+ typename WriterSerieType::Pointer writerSerie = WriterSerieType::New();
+ writerSerie->SetInput( mhdCorrectOrder );
+ writerSerie->SetImageIO( gdcmIO );
+ typename ReaderSeriesType::FileNamesContainer fileNamesOutput;
+ fileNamesOutput.push_back(filename_out);
+ writerSerie->SetFileNames( fileNamesOutput );
+ writerSerie->SetMetaDataDictionaryArray(&outputArray);
- seriesWriter->SetInput( input );
- seriesWriter->SetImageIO( gdcmIO );
-
- seriesWriter->SetFileName( filename_out );
- seriesWriter->SetMetaDataDictionary(reader->GetMetaDataDictionary());
// Write
try {
if (m_ArgsInfo.verbose_flag)
- std::cout << seriesWriter << std::endl;
- seriesWriter->Update();
+ std::cout << writerSerie << std::endl;
+ writerSerie->Update();
} catch( itk::ExceptionObject & excp ) {
std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
std::cerr << excp << std::endl;
}
+
+ //Write sequence dicom tag with gdcm
+ gdcm::Reader reader;
+ reader.SetFileName( fileNamesOutput[0].c_str() );
+ reader.Read();
+ gdcm::File &file = reader.GetFile();
+ gdcm::DataSet &ds2 = file.GetDataSet();
+ const unsigned int ptr_len = 42;
+ char *ptr = new char[ptr_len];
+ memset(ptr,0,ptr_len);
+
+ //Write rotation tag
+ // Create a Sequence
+ gdcm::SmartPointer<gdcm::SequenceOfItems> rotationSq = new gdcm::SequenceOfItems();
+ rotationSq->SetLengthToUndefined();
+ // Create a dataelement
+ gdcm::DataElement rotationDE( gdcm::Tag(0x54, 0x53) );
+ rotationDE.SetVR( gdcm::VR::US );
+ char essai = (char)rotationNumber;
+ char *p_essai = &essai;
+ rotationDE.SetByteValue(p_essai, 1);
+ // Create an item
+ gdcm::Item rotationIt;
+ rotationIt.SetVLToUndefined();
+ gdcm::DataSet &rotationDS = rotationIt.GetNestedDataSet();
+ rotationDS.Insert(rotationDE);
+ rotationSq->AddItem(rotationIt);
+ // Insert sequence into data set
+ gdcm::DataElement rotationDEParent( gdcm::Tag(0x54, 0x52) );
+ rotationDEParent.SetVR(gdcm::VR::SQ);
+ rotationDEParent.SetValue(*rotationSq);
+ rotationDEParent.SetVLToUndefined();
+
+ //Write energy
+ gdcm::DataElement energyDEParent( gdcm::Tag(0x54, 0x12) );
+ energyDEParent.SetVR(gdcm::VR::SQ);
+ // Create a Sequence
+ gdcm::SmartPointer<gdcm::SequenceOfItems> energySq = new gdcm::SequenceOfItems();
+ energySq->SetLengthToUndefined();
+ for (unsigned int i=0; i<energyNumber; ++i) {
+ gdcm::SmartPointer<gdcm::SequenceOfItems> energyThresholdSq = new gdcm::SequenceOfItems();
+ energyThresholdSq->SetLengthToUndefined();
+ // Create a dataelement
+ gdcm::DataElement energyThresholdDE( gdcm::Tag(0x54, 0x14) );
+ gdcm::DataElement energyUpholdDE( gdcm::Tag(0x54, 0x15) );
+ energyThresholdDE.SetVR( gdcm::VR::DS );
+ energyUpholdDE.SetVR( gdcm::VR::DS );
+ energyThresholdDE.SetByteValue(p_EnergyWindowThreshold[i], (uint32_t)strlen(p_EnergyWindowThreshold[i]));
+ energyUpholdDE.SetByteValue(p_EnergyWindowUphold[i], (uint32_t)strlen(p_EnergyWindowUphold[i]));
+ // Create an item
+ gdcm::Item energyThresholdIt;
+ energyThresholdIt.SetVLToUndefined();
+ gdcm::DataSet &energyThresholdDS = energyThresholdIt.GetNestedDataSet();
+ energyThresholdDS.Insert(energyThresholdDE);
+ energyThresholdDS.Insert(energyUpholdDE);
+ energyThresholdSq->AddItem(energyThresholdIt);
+ // Insert sequence into data set
+ gdcm::DataElement energyThresholdDEParent( gdcm::Tag(0x54, 0x13) );
+ energyThresholdDEParent.SetVR(gdcm::VR::SQ);
+ energyThresholdDEParent.SetValue(*energyThresholdSq);
+ energyThresholdDEParent.SetVLToUndefined();
+ // Create a dataelement
+ gdcm::DataElement energyNameDE( gdcm::Tag(0x54, 0x18) );
+ energyNameDE.SetVR( gdcm::VR::SH );
+ energyNameDE.SetByteValue(p_EnergyWindowName[i], (uint32_t)strlen(p_EnergyWindowName[i]));
+ // Create an item
+ gdcm::Item energyIt;
+ energyIt.SetVLToUndefined();
+ gdcm::DataSet &energyDS = energyIt.GetNestedDataSet();
+ energyDS.Insert(energyNameDE);
+ energyDS.Insert(energyThresholdDEParent);
+ energySq->AddItem(energyIt);
+ }
+ // Insert sequence into data set
+ energyDEParent.SetValue(*energySq);
+ energyDEParent.SetVLToUndefined();
+ ds2.Insert(energyDEParent);
+ ds2.Insert(rotationDEParent);
+
+ gdcm::Writer w;
+ w.SetFile( file );
+ w.SetFileName( fileNamesOutput[0].c_str() );
+ w.Write();
+
+#else
+ std::cout << "Use GDCM2" << std::endl;
+#endif
+}
+//---------------------------------------------------------------------------
+
+
+//---------------------------------------------------------------------------
+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;
+ }
+}
+//---------------------------------------------------------------------------
+
+
+//---------------------------------------------------------------------------
+template <typename T> std::string NumberToString ( T Number )
+{
+ std::ostringstream ss;
+ ss << Number;
+ return ss.str();
}
+//---------------------------------------------------------------------------
}//end clitk
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff