#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
+#if GDCM_MAJOR_VERSION >= 2
// ImageTypes
typedef itk::Image<PixelType, Dimension> InputImageType;
typedef itk::Image<PixelType, Dimension> OutputImageType;
// Read Dicom model file
- typename ReaderType::Pointer reader = ReaderType::New();
typename ReaderSeriesType::Pointer readerSeries = ReaderSeriesType::New();
ImageIOType::Pointer gdcmIO = ImageIOType::New();
std::string filename_out = m_ArgsInfo.outputFilename_arg;
gdcmIO->LoadPrivateTagsOn();
gdcmIO->KeepOriginalUIDOn();
- 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 model file !!" << std::endl;
typename InputImageType::Pointer input = volumeReader->GetOutput();
+ //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
-/* 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;
- }
- }
-*/
-
-
- //Read the dicom file to find the energy, the head & the steps (TODO: do it on the mhd filetext)
- gdcm::Reader hreader;
- hreader.SetFileName(m_ArgsInfo.inputModelFilename_arg);
- hreader.Read();
- gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
- int energyNumber, headNumber, rotationNumber; //Read the number of energy, of head and rotation steps
- gdcm::Attribute<0x54,0x11> energyNumber_att;
- energyNumber_att.SetFromDataSet(hreader.GetFile().GetDataSet());
- energyNumber = energyNumber_att.GetValue();
-
- gdcm::Attribute<0x54,0x21> headNumber_att;
- headNumber_att.SetFromDataSet(hreader.GetFile().GetDataSet());
- headNumber = headNumber_att.GetValue();
-
- gdcm::Tag squenceTag(0x54,0x52); //rotation, read a sequence first
- const gdcm::DataElement &sequence = hreader.GetFile().GetDataSet().GetDataElement( squenceTag );
- gdcm::DataSet &sequenceDataSet = sequence.GetValueAsSQ()->GetItem(1).GetNestedDataSet();
- gdcm::Tag rotationNumber_Tag(0x54,0x53);
- const gdcm::DataElement &rotationNumber_Element = sequenceDataSet.GetDataElement( rotationNumber_Tag );
- gdcm::Attribute<0x54,0x53> rotationNumber_att;
- rotationNumber_att.SetFromDataElement(rotationNumber_Element);
- rotationNumber = rotationNumber_att.GetValue();
-
-energyNumber = 3;
-headNumber = 4;
-rotationNumber = 6;
- // Create a new mhd image with the dicom order slices
+ // Create a new mhd image with the correct dicom order slices
typename InputImageType::Pointer mhdCorrectOrder = InputImageType::New();
mhdCorrectOrder->SetRegions(input->GetLargestPossibleRegion());
mhdCorrectOrder->Allocate();
// update output dicom keys/tags
+ // 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);
- std::string entryId, value;
- entryId = "0054|0011";
- value = NumberToString(energyNumber);
- itk::EncapsulateMetaData<std::string>(*outputDict, "0054|0011", value );
- entryId = "0054|0021";
- value = NumberToString(headNumber);
- itk::EncapsulateMetaData<std::string>(*outputDict, "0054|0021", value );
-outputArray.push_back(outputDict);
// Output directory and filenames
- //itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputFilename_arg ); // create if it doesn't exist
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
typedef itk::ImageSeriesWriter<OutputImageType, OutputImageType> WriterSerieType;
- typename WriterType::Pointer writer = WriterType::New();
typename WriterSerieType::Pointer writerSerie = WriterSerieType::New();
-
- writer->SetInput( mhdCorrectOrder );
- writer->SetImageIO( gdcmIO );
-
- writer->SetFileName( filename_out );
- //writer->SetMetaDataDictionary(outputDict);
writerSerie->SetInput( mhdCorrectOrder );
writerSerie->SetImageIO( gdcmIO );
typename ReaderSeriesType::FileNamesContainer fileNamesOutput;
writerSerie->SetFileNames( fileNamesOutput );
writerSerie->SetMetaDataDictionaryArray(&outputArray);
+
// Write
try {
if (m_ArgsInfo.verbose_flag)
- std::cout << writer << std::endl;
- //writer->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;
++itr;
}
}
+//---------------------------------------------------------------------------
+
+
+//---------------------------------------------------------------------------
+template <typename T> std::string NumberToString ( T Number )
+{
+ std::ostringstream ss;
+ ss << Number;
+ return ss.str();
+}
+//---------------------------------------------------------------------------
-template <typename T>
- std::string NumberToString ( T Number )
- {
- std::ostringstream ss;
- ss << Number;
- return ss.str();
- }
}//end clitk
#endif //#define clitkGateSimulation2DicomGenericFilter_txx