#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;
//-----------------------------------------------------------------------------
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::string filename_out = m_ArgsInfo.output_arg;
+ gdcmIO->LoadPrivateTagsOn();
+ gdcmIO->KeepOriginalUIDOn();
+ typename ReaderSeriesType::FileNamesContainer fileNames;
+ fileNames.push_back(m_ArgsInfo.DicomInputFile_arg);
+ readerSeries->SetImageIO( gdcmIO );
+ readerSeries->SetFileNames( fileNames );
+ try {
+ readerSeries->Update();
+ } catch (itk::ExceptionObject &excp) {
+ std::cerr << "Error: Exception thrown while reading the DICOM model file !!" << std::endl;
+ std::cerr << excp << std::endl;
+ }
+
+ // 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);
// 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.;
- std::stringstream strOffset;
- strOffset << offset;
+ value.str("");
+ value << offset;
for (int i=1; i<NbFrames ; i++){
offset+=Spacing[2];
- strOffset << "\\";
- strOffset << offset;
+ value << '\\';
+ value << offset;
}
- DD(strOffset.str().c_str());
+ itk::EncapsulateMetaData<std::string>(*outputDict, "3004|000c", value.str());
+ DD(value.str());
// 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();
- }
+ typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
+ imageCalculatorFilter->SetImage(image);
+ imageCalculatorFilter->ComputeMaximum();
+ float highestValue=imageCalculatorFilter->GetMaximum();
double doseScaling = highestValue/(pow(2,16)-1);
- DD(doseScaling);
+ value.str("");
+ value<<doseScaling;
+ itk::EncapsulateMetaData<std::string>(*outputDict, "3004|000e", value.str());
+ DD(value.str());
// 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());*/
-
- // Read Dicom model file
- typename ReaderSeriesType::Pointer readerSeries = ReaderSeriesType::New();
- ImageIOType::Pointer gdcmIO = ImageIOType::New();
- std::string filename_out = m_ArgsInfo.output_arg;
- gdcmIO->LoadPrivateTagsOn();
- gdcmIO->KeepOriginalUIDOn();
- typename ReaderSeriesType::FileNamesContainer fileNames;
- fileNames.push_back(m_ArgsInfo.DicomInputFile_arg);
- readerSeries->SetImageIO( gdcmIO );
- readerSeries->SetFileNames( fileNames );
- try {
- readerSeries->Update();
- } catch (itk::ExceptionObject &excp) {
- std::cerr << "Error: Exception thrown while reading the DICOM model file !!" << std::endl;
- std::cerr << excp << std::endl;
+ 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;
}
- // 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, "0020|0032", NumberToString(origin));
- 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));
- itk::EncapsulateMetaData<std::string>(*outputDict, "0028|0030", NumberToString(Spacing));
- itk::EncapsulateMetaData<std::string>(*outputDict, "3004|000e", NumberToString(doseScaling));
- itk::EncapsulateMetaData<std::string>(*outputDict, "3004|000c", strOffset.str());
- outputArray.push_back(outputDict);
-
// 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);
std::cerr << excp << 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 BIS
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff