#include "math.h"
-#include "clitkImageToDICOMRTDose.h"
-#include "clitkImageToDICOMRTDose_ggo.h"
+#include "clitkImage2DicomDoseGenericFilter.h"
+#include "clitkCommon.h"
+#include "itkMinimumMaximumImageCalculator.h"
+#include "itkImageRegionIterator.h"
+#include "itkImageRegionConstIterator.h"
#if GDCM_MAJOR_VERSION >= 2
#include "gdcmUIDGenerator.h"
#include <gdcmImageHelper.h>
Image2DicomDoseGenericFilter<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;
+ typedef unsigned short int OutputPixelType;
+ typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::ImageSeriesReader< InputImageType > ReaderSeriesType;
+ typedef itk::ImageSeriesWriter<OutputImageType, OutputImageType> WriterSerieType;
typedef itk::ImageRegionIterator< InputImageType > IteratorType;
+ typedef itk::MinimumMaximumImageCalculator <InputImageType> ImageCalculatorFilterType;
typedef itk::GDCMImageIO ImageIOType;
+ //-----------------------------------------------------------------------------
+ // opening image input file
+ typename ReaderType::Pointer reader = ReaderType::New();
+ const char * filename = m_ArgsInfo.input_arg;
+ reader->SetFileName( filename );
+ reader->Update();
+ typename InputImageType::Pointer image = reader->GetOutput();
+ std::ostringstream value;
+
// Read Dicom model file
typename ReaderSeriesType::Pointer readerSeries = ReaderSeriesType::New();
ImageIOType::Pointer gdcmIO = ImageIOType::New();
std::cerr << excp << std::endl;
}
-
-
-//-----------------------------------------------------------------------------------
-// opening dicom input file
- gdcm::Reader reader2;
- reader2.SetFileName( m_ArgsInfo.DicomInputFile_arg );
- reader2.Read();
- gdcm::File &mDCMFile = reader2.GetFile();
- gdcm::DataSet &ds = mDCMFile.GetDataSet();
-//mDCMFile.SetMaxSizeLoadEntry(1006384); // important size required, otherwise some data are not loaded
-//mDCMFile.AddForceLoadElement(0x7fe0,0x0010); //Load pixel data no matter its size
-
-std::cout << "File: "<< m_ArgsInfo.DicomInputFile_arg << " loaded !"<< std::endl;
-
-
-
-//-----------------------------------------------------------------------------
-// opening image input file
-typename ReaderType::Pointer reader = ReaderType::New();
-const char * filename = m_ArgsInfo.input_arg;
-reader->SetFileName( filename );
-reader->Update();
-typename InputImageType::Pointer image = reader->GetOutput();
-
-// origin
-typename InputImageType::PointType origin = image->GetOrigin();
-DD(origin);
-
-// size
-typename InputImageType::SizeType imageSize = image->GetLargestPossibleRegion().GetSize();
-//DD(imageSize);
-int NbCols=imageSize[0]; // col
-int NbRows=imageSize[1]; // row
-int NbFrames=imageSize[2]; // frame
-DD(NbCols);
-DD(NbRows);
-DD(NbFrames);
-
-// spacing
-typename InputImageType::SpacingType Spacing = image->GetSpacing();
-DD(Spacing);
-
-// scaling
-float highestValue=pow(10,-10);
-IteratorType out( image, image->GetRequestedRegion() );
-for (out.GoToBegin(); !out.IsAtEnd(); ++out){
-//DD(out.Get());
- if (out.Get()>highestValue) highestValue=out.Get();
-}
-double doseScaling = highestValue/(pow(2,16)-1);
-DD(doseScaling);
-
-// image data
-std::vector<unsigned short int> ImageData;
-typename InputImageType::IndexType pixelIndex;
-int l=0;
-unsigned short int pixelValue;
-//DD(highestValue);
-for (int i=0; i<NbFrames; i++){
- pixelIndex[2] = i;
- for (int j=0; j<NbRows; j++){
- pixelIndex[1] = j;
- for (int k=0; k<NbCols; k++){
- pixelIndex[0] = k;
- pixelValue=image->GetPixel(pixelIndex)/doseScaling;
-if(float(image->GetPixel(pixelIndex)/doseScaling)>(pow(2,16)-1.)) {
-std::cout<<"\n!!!!! WARNING !!!!! pixel index: "<<pixelIndex<<"unsigned short int capacity ful or overfuled => Highest value may become 0"<<std::endl;
-DD(pixelIndex);
-DD(image->GetPixel(pixelIndex));
-//DD(image->GetPixel(pixelIndex)/doseScaling);
-DD(pixelValue);
-std::cout<<"Pixel Value should be equal to "<<(pow(2,16)-1)<<" but should not be 0"<<std::endl;
-std::cout<<"\n"<<std::endl;
-//assert(pixelValue<=(pow(2,16)-1)); should work, but do not...
-}
-//DD(pixelValue);
- ImageData.push_back(pixelValue);
- l++;
- }
- }
-}
-DD(ImageData.size());
-
-// Relevant parameters inserted in the new dicom file
-/*
-ImagePosition
-NbCols
-NbRows
-NbFrames
-Spacing
-ImageData
-doseScaling
-*/
-
+ // update output dicom keys/tags
typename ReaderSeriesType::DictionaryRawPointer inputDict = (*(readerSeries->GetMetaDataDictionaryArray()))[0];
typename ReaderSeriesType::DictionaryArrayType outputArray;
typename ReaderSeriesType::DictionaryRawPointer outputDict = new typename ReaderSeriesType::DictionaryType;
CopyDictionary (*inputDict, *outputDict);
- outputArray.push_back(outputDict);
+
+ // origin
+ typename InputImageType::PointType origin = image->GetOrigin();
+ value.str("");
+ value<<origin[0]<<'\\'<<origin[1]<<'\\'<<origin[2];
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0020|0032", value.str());
+ DD(origin);
+
+ // orientation
+ typename InputImageType::DirectionType direction = image->GetDirection();
+ value.str("");
+ value<<direction[0][0]<<'\\'<<direction[0][1]<<'\\'<<direction[0][2]<<'\\'<<direction[1][0]<<'\\'<<direction[1][1]<<'\\'<<direction[1][2];
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0020|0037", value.str());
+ DD(direction);
+
+ // size
+ typename InputImageType::SizeType imageSize = image->GetLargestPossibleRegion().GetSize();
+ //DD(imageSize);
+ int NbCols=imageSize[0]; // col
+ int NbRows=imageSize[1]; // row
+ int NbFrames=imageSize[2]; // frame
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0028|0008", NumberToString(NbFrames));
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0028|0010", NumberToString(NbRows));
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0028|0011", NumberToString(NbCols));
+ DD(NbCols);
+ DD(NbRows);
+ DD(NbFrames);
+
+ // spacing
+ typename InputImageType::SpacingType Spacing = image->GetSpacing();
+ value.str("");
+ value<<Spacing[0]<<'\\'<<Spacing[1];
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0028|0030", value.str());
+ value.str("");
+ value<<Spacing[2];
+ itk::EncapsulateMetaData<std::string>(*outputDict, "0018|0050", value.str());
+ DD(Spacing);
+
+ // offset
+ float offset = 0.;
+ value.str("");
+ value << offset;
+ for (int i=1; i<NbFrames ; i++){
+ offset+=Spacing[2];
+ value << '\\';
+ value << offset;
+ }
+ itk::EncapsulateMetaData<std::string>(*outputDict, "3004|000c", value.str());
+ DD(value.str());
+
+ // scaling
+ typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
+ imageCalculatorFilter->SetImage(image);
+ imageCalculatorFilter->ComputeMaximum();
+ float highestValue=imageCalculatorFilter->GetMaximum();
+ double doseScaling = highestValue/(pow(2,16)-1);
+ value.str("");
+ value<<doseScaling;
+ itk::EncapsulateMetaData<std::string>(*outputDict, "3004|000e", value.str());
+ DD(value.str());
+
+ // image data
+ typename OutputImageType::Pointer imageOutput = OutputImageType::New();
+ imageOutput->SetRegions(image->GetLargestPossibleRegion());
+ imageOutput->SetSpacing(image->GetSpacing());
+ imageOutput->SetOrigin(image->GetOrigin());
+ imageOutput->SetDirection(image->GetDirection());
+ imageOutput->Allocate();
+
+ typename itk::ImageRegionConstIterator<InputImageType> imageIterator(image,image->GetLargestPossibleRegion());
+ typename itk::ImageRegionIterator<OutputImageType> imageOutputIterator(imageOutput,imageOutput->GetLargestPossibleRegion());
+ while(!imageIterator.IsAtEnd()) {
+ // Set the current pixel to white
+ imageOutputIterator.Set((signed short int)(imageIterator.Get()/doseScaling));
+
+ ++imageIterator;
+ ++imageOutputIterator;
+ }
// Output directory and filenames
- typedef itk::ImageSeriesWriter<OutputImageType, OutputImageType> WriterSerieType;
typename WriterSerieType::Pointer writerSerie = WriterSerieType::New();
- writerSerie->SetInput( image );
+ outputArray.push_back(outputDict);
+ writerSerie->SetInput( imageOutput );
writerSerie->SetImageIO( gdcmIO );
typename ReaderSeriesType::FileNamesContainer fileNamesOutput;
fileNamesOutput.push_back(filename_out);
writerSerie->SetFileNames( fileNamesOutput );
writerSerie->SetMetaDataDictionaryArray(&outputArray);
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-//--------------------------------------------------------------
-std::cout<<"\nECRITURE DU FICHIER DICOM !"<<std::endl;
-
-//gdcm::ValEntry *b;
-std::string Value("");
-
-
-gdcm::DataElement DE;
-
-DE = gdcm::Tag(0x20, 0x32);
-Value = origin[0];
-Value += "\\";
-Value += origin[1];
-Value += "\\";
-Value += origin[2];
-DE.SetVR( gdcm::VR::US );
-DE.SetByteValue(Value.c_str(), 1);
-ds.Insert(DE);
-DD(Value);
-Value = "";
-
-DE = gdcm::Tag(0x28, 0x11);
-Value = NbCols;
-DE.SetVR( gdcm::VR::US );
-DE.SetByteValue(Value.c_str(), 1);
-ds.Insert(DE);
-DD(Value);
-Value = "";
-
-DE = gdcm::Tag(0x28, 0x10);
-Value = NbRows;
-DE.SetVR( gdcm::VR::US );
-DE.SetByteValue(Value.c_str(), 1);
-ds.Insert(DE);
-DD(Value);
-Value = "";
-
-DE = gdcm::Tag(0x28, 0x08);
-Value = NbFrames;
-DE.SetVR( gdcm::VR::US );
-DE.SetByteValue(Value.c_str(), 1);
-ds.Insert(DE);
-DD(Value);
-Value = "";
-
-DE = gdcm::Tag(0x3004, 0x0e);
-Value = doseScaling;
-DE.SetVR( gdcm::VR::US );
-DE.SetByteValue(Value.c_str(), 1);
-ds.Insert(DE);
-DD(Value);
-Value = "";
-
-DE = gdcm::Tag(0x28, 0x30);
-Value = Spacing[0];
-Value += "\\";
-Value += Spacing[1];
-DE.SetVR( gdcm::VR::US );
-DE.SetByteValue(Value.c_str(), 1);
-ds.Insert(DE);
-DD(Value);
-Value = "";
-
-DE = gdcm::Tag(0x3004, 0x000c);
-float offset = 0.;
-Value = offset;
- for (int i=1; i<NbFrames ; i++){
- offset+=Spacing[2];
- Value += "\\";
- Value += offset;
+ // Write
+ try {
+ if (m_ArgsInfo.verbose_flag)
+ 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;
}
-DE.SetVR( gdcm::VR::US );
-DE.SetByteValue(Value.c_str(), 1);
-ds.Insert(DE);
-DD(Value);
-Value = "";
-
-/*
-// NbCols
-b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028,0x0011);
-Value<<NbCols;
-b->SetValue(Value.str());
-DD(Value.str());
-Value.str("");
-
-// NbRows
-b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028,0x0010);
-Value<<NbRows;
-b->SetValue(Value.str());
-DD(Value.str());
-Value.str("");
-//DD(Value.str());
-
-// NbFrames
-b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028,0x0008);
-Value<<NbFrames;
-b->SetValue(Value.str());
-DD(Value.str());
-Value.str("");
-
-// doseScaling
-b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x3004,0x000e);
-Value<<doseScaling;
-b->SetValue(Value.str());
-DD(Value.str());
-Value.str("");
-
-// Spacing X Y
-b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028, 0x0030);
-Value<<Spacing[0]<<'\\'<<Spacing[1];
-b->SetValue(Value.str());
-DD(Value.str());
-Value.str("");
-
-// Spacing Z ([Grid Frame Offset Vector])
-b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x3004, 0x000c);
-float offset=0.;
-Value<<offset;
- for (int i=1; i<NbFrames ; i++){
- offset+=Spacing[2];
- Value<<'\\'<<offset;
- }
-b->SetValue(Value.str());
-DD(Value.str());
-Value.str("");
-*/
-//ImageData
-//bool data = mDCMFile->SetBinEntry(reinterpret_cast<uint8_t*>( &(ImageData[0]) ) , (int)(sizeof(unsigned short int) * ImageData.size()) , 0x7fe0, 0x0010);
-//if (data) std::cout<<"\n DICOM dose data written !"<<std::endl;
+ //Read sequence dicom tag with gdcm
+ gdcm::Reader readerTemplateGDCM;
+ readerTemplateGDCM.SetFileName( fileNames[0].c_str() );
+ readerTemplateGDCM.Read();
+ gdcm::File &fileTemplate = readerTemplateGDCM.GetFile();
+ gdcm::DataSet &dsTemplate = fileTemplate.GetDataSet();
+ const unsigned int ptr_len = 42;
+ char *ptrTemplate = new char[ptr_len];
+ memset(ptrTemplate,0,ptr_len);
+
+ const gdcm::DataElement &referenceRTPlanSq = dsTemplate.GetDataElement(gdcm::Tag(0x300c, 0x02));
+
+ //Create the Dose Grid Scaling data element (ITK 4.13 do not take into account - it works well with ITK 4.5.1)
+ gdcm::DataElement deDoseGridScaling( gdcm::Tag(0x3004,0x0e) );
+ deDoseGridScaling.SetVR( gdcm::VR::DS );
+ deDoseGridScaling.SetByteValue(NumberToString(doseScaling).c_str(), (uint32_t)strlen(NumberToString(doseScaling).c_str()));
+
+ //Copy/Write sequence dicom tag with gdcm
+ gdcm::Reader readerOutputGDCM;
+ readerOutputGDCM.SetFileName( fileNamesOutput[0].c_str() );
+ readerOutputGDCM.Read();
+ gdcm::File &file = readerOutputGDCM.GetFile();
+ gdcm::DataSet &dsOutput = file.GetDataSet();
+
+ dsOutput.Insert(referenceRTPlanSq);
+ dsOutput.Replace(deDoseGridScaling);
+ gdcm::Writer w;
+ w.SetFile( file );
+ w.SetFileName( fileNamesOutput[0].c_str() );
+ w.Write();
-//---------------------------------------------------------------------------------------
-//WRITE DICOM
-/*gdcm::FileType type = mDCMFile->GetFileType();
-//type=(gdcm::FileType)2;
-bool ecriture = mDCMFile->Write (args_info.OutputFile_arg, type);
-if (ecriture) std::cout<<"\n DICOM File written !"<<std::endl;
-*/
//---------------------------------------------------------------------------------------
//WRITE DICOM BIS
// The previous way of writting DICOM-RT-DOSE works only for ITK
else std::cout<<"\n DICOM File re-written, using the FileHelper syntax, in order to be processed by commercial systems !"<<std::endl;
delete fh; */
- gdcm::Writer w;
+/* gdcm::Writer w;
w.SetFile(mDCMFile);
w.SetFileName(m_ArgsInfo.output_arg);
- w.Write();
+ w.Write();*/
// fh->Delete();
//---------------------------------------------------------------------------------------
//((gdcm::SQItem*)mDCMFile)->RemoveEntry(a);
//-----------------------------------------------------------------------------------
-std::cout <<"\n## DICOM Image to RT DOSE application is ended..."<<std::endl;
-std::cout <<"#########################################################\n" << std::endl;
+ std::cout <<"\n## DICOM Image to RT DOSE application is ended..."<<std::endl;
+ std::cout <<"#########################################################\n" << std::endl;
#else
std::cout << "Use GDCM2" << std::endl;
}
}
//---------------------------------------------------------------------------
+
+//---------------------------------------------------------------------------
+template <typename T> std::string NumberToString ( T Number )
+{
+ std::ostringstream ss;
+ ss << Number;
+ return ss.str();
+}
+//---------------------------------------------------------------------------
+
+
}//end clitk
#endif //#define clitkImage2DicomDoseGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff