Revision 02d622602e0552f8bf6df13762acf4446f02db47 authored by Konrad Werys on 14 November 2018, 11:57:33 UTC, committed by Konrad Werys on 14 November 2018, 12:01:08 UTC
1 parent 09dae69
Tomato_export.hxx
/*!
* \file Tomato.h
* \author Konrad Werys
* \date 2018/08/14
*/
#ifndef Tomato_Tomato_EXPORT_HXX
#define Tomato_Tomato_EXPORT_HXX
#include "CmakeConfigForTomato.h"
#ifdef USE_ITK
namespace Ox {
template< typename IType, typename EType >
class CastPixelAccessor
{
public:
typedef IType InternalType;
typedef EType ExternalType;
static void Set(InternalType & output, const ExternalType & input)
{
output = static_cast<InternalType>( input );
}
static ExternalType Get( const InternalType & input )
{
return static_cast<ExternalType>( input );
}
};
template< typename MeasureType >
int
Tomato<MeasureType>
::exportToDicom(){
if (_opts->dir_output_map.empty()){
printf("No DICOM export, dir_output_map not given.\n");
return EXIT_FAILURE;
}
// OxColorbarImageFilter
typedef itk::Colorbar2DImageFilter< ImageType2D > OxColorbarImageFilterType;
typename OxColorbarImageFilterType::Pointer OxColorbarFilter = OxColorbarImageFilterType::New();
OxColorbarFilter->SetInput(_imageCalculatorItk->GetT1Image());
// get the dictionary ready before export
//typedef itk::MetaDataDictionary DictionaryType;
//DictionaryType & _dictionaryInput = reader->GetDicomIO()->GetMetaDataDictionary();
// T1 map with color
DictionaryType dictionaryOutput_T1Color(_dictionaryInput);
// UIDs
gdcm::UIDGenerator sopuid;
std::string sopInstanceUID_T1Color = sopuid.Generate();
gdcm::UIDGenerator suid;
std::string seriesUID_T1 = suid.Generate();
// seriesNumber
std::string seriesNumber, newSeriesNumber_T1;
itk::ExposeMetaData<std::string>(_dictionaryInput, "0020|0011", seriesNumber);
if (_opts->output_map_series_number == 0){
newSeriesNumber_T1 = KWUtil::NumberToString(KWUtil::StringToNumber<int>(seriesNumber) + 10002);
// newSeriesNumber_T1 = std::to_string( stoi(seriesNumber) + 10002 ); // C++11 needed to do this
} else {
newSeriesNumber_T1 = KWUtil::NumberToString(_opts->output_map_series_number);
}
// dicom tags dependent on the MagneticFieldStrength
std::string MagneticFieldStrength;
itk::ExposeMetaData<std::string>(_dictionaryInput, "0018|0087", MagneticFieldStrength);
std::string ImageCommentsT1mapWithColormap, clutRedString, clutGreenString, clutBlueString;
if (MagneticFieldStrength.find("1.5") != std::string::npos){
ImageCommentsT1mapWithColormap = ImageCommentsT1mapWithColormap.append("OxShMOLLI color 980SD265ms");
clutRedString = getEncodedSting(getShmolliColormapRed15TArray());
clutGreenString = getEncodedSting(getShmolliColormapGreen15TArray());
clutBlueString = getEncodedSting(getShmolliColormapBlue15TArray());
printf("Colormap for MagneticFieldStrength 1.5T is used.\n");
} else if (MagneticFieldStrength.find("3") != std::string::npos){
ImageCommentsT1mapWithColormap = ImageCommentsT1mapWithColormap.append("OxShMOLLI color 1198SD175ms");
clutRedString = getEncodedSting(getShmolliColormapRed3TArray());
clutGreenString = getEncodedSting(getShmolliColormapGreen3TArray());
clutBlueString = getEncodedSting(getShmolliColormapBlue3TArray());
printf("Colormap for MagneticFieldStrength 3T is used.\n");
} else {
printf("MagneticFieldStrength not detected, colormap will not be used.\n");
}
// PaletteColorLookupTableUID
std::string PaletteColorLookupTableUID;
itk::ExposeMetaData<std::string>(_dictionaryInput, "0028|1199", PaletteColorLookupTableUID);
//std::cout << "PaletteColorLookupTableUID: " << PaletteColorLookupTableUID << std::endl;
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0008|0018"), sopInstanceUID_T1Color);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0002|0003"), sopInstanceUID_T1Color);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0020|000e"), seriesUID_T1);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1199"), PaletteColorLookupTableUID); // color look up table UID
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0020|0011"), newSeriesNumber_T1); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0020|4000"), ImageCommentsT1mapWithColormap); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0020|0013"), std::string("1")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1050"), std::string("2048")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1051"), std::string("4096")); // window width
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1101"), std::string("4096\\0\\16")); // red color look up table descriptor
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1102"), std::string("4096\\0\\16")); // green color look up table descriptor
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1103"), std::string("4096\\0\\16")); // blue color look up table descriptor
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1201"), clutRedString);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1202"), clutGreenString);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1Color, std::string("0028|1203"), clutBlueString);
// T1 map no color
DictionaryType dictionaryOutput_T1(_dictionaryInput);
std::string sopInstanceUID_T1 = sopuid.Generate();
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0008|0018"), sopInstanceUID_T1);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0002|0003"), sopInstanceUID_T1);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0020|000e"), seriesUID_T1);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0020|0011"), newSeriesNumber_T1); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0020|4000"), std::string("OxShMOLLI T1 map")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0020|0013"), std::string("2")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0028|1050"), std::string("2048")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1, std::string("0028|1051"), std::string("4096")); // window width
// R2 map
DictionaryType dictionaryOutput_R2(_dictionaryInput);
std::string sopInstanceUID_R2 = sopuid.Generate();
std::string seriesUID_R2 = suid.Generate();
std::string newSeriesNumber_R2;
itk::ExposeMetaData<std::string>(_dictionaryInput, "0020|0011", seriesNumber);
if (_opts->output_fitparams_series_number == 0) {
newSeriesNumber_R2 = KWUtil::NumberToString(KWUtil::StringToNumber<int>(seriesNumber) + 10003);
//newSeriesNumber_R2 = std::to_string( std::stoi(seriesNumber) + 10003 ); // C++11
} else {
newSeriesNumber_R2 = KWUtil::NumberToString(_opts->output_fitparams_series_number);
}
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0008|0018"), sopInstanceUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0002|0003"), sopInstanceUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0020|000e"), seriesUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0020|0011"), newSeriesNumber_R2); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0020|4000"), std::string("Rsquare*4000 Map")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0020|0013"), std::string("3")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0028|1050"), std::string("3900")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_R2, std::string("0028|1051"), std::string("200")); // window width
// A map
DictionaryType dictionaryOutput_A(_dictionaryInput);
std::string sopInstanceUID_A = sopuid.Generate();
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0008|0018"), sopInstanceUID_A);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0002|0003"), sopInstanceUID_A);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0020|000e"), seriesUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0028|1199"), PaletteColorLookupTableUID); // color look up table UID
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0020|0011"), newSeriesNumber_R2); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0020|4000"), std::string("Signal(TI)=[___AMap___]-B*exp(-TI/T1star)")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0020|0013"), std::string("4")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0028|1050"), std::string("2000")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_A, std::string("0028|1051"), std::string("4000")); // window width
// B map
DictionaryType dictionaryOutput_B(_dictionaryInput);
std::string sopInstanceUID_B = sopuid.Generate();
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0008|0018"), sopInstanceUID_B);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0002|0003"), sopInstanceUID_B);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0020|000e"), seriesUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0020|0011"), newSeriesNumber_R2); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0020|4000"), std::string("Signal(TI)=A-[___BMap___]*exp(-TI/T1star)")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0020|0013"), std::string("5")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0028|1050"), std::string("2000")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_B, std::string("0028|1051"), std::string("4000")); // window width
// T1star map
DictionaryType dictionaryOutput_T1star(_dictionaryInput);
std::string sopInstanceUID_T1star = sopuid.Generate();
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0008|0018"), sopInstanceUID_T1star);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0002|0003"), sopInstanceUID_T1star);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0020|000e"), seriesUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0020|0011"), newSeriesNumber_R2); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0020|4000"), std::string("Signal(TI)=A-B*exp(-TI/[___T1starMap___])")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0020|0013"), std::string("6")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0028|1050"), std::string("2000")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_T1star, std::string("0028|1051"), std::string("4000")); // window width
// _ShMOLLIT1range map
DictionaryType dictionaryOutput_ShMolliT1Range(_dictionaryInput);
std::string sopInstanceUID_ShMolliT1Range = sopuid.Generate();
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0008|0018"), sopInstanceUID_ShMolliT1Range);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0002|0003"), sopInstanceUID_ShMolliT1Range);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0020|000e"), seriesUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0020|0011"), newSeriesNumber_R2); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0020|4000"), std::string("_ShMOLLIT1range")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0020|0013"), std::string("7")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0028|1050"), std::string("1500")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_ShMolliT1Range, std::string("0028|1051"), std::string("3000")); // window width
// _nAmebaCallFinal map
DictionaryType dictionaryOutput_nAmebaCallFinal(_dictionaryInput);
std::string sopInstanceUID_nAmebaCallFinal = sopuid.Generate();
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0008|0018"), sopInstanceUID_nAmebaCallFinal);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0002|0003"), sopInstanceUID_nAmebaCallFinal);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0020|000e"), seriesUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0020|0011"), newSeriesNumber_R2); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0020|4000"), std::string("_nAmebaCallFinal")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0020|0013"), std::string("8")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0028|1050"), std::string("2000")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_nAmebaCallFinal, std::string("0028|1051"), std::string("4000")); // window width
// _RelSNRFinal map
DictionaryType dictionaryOutput_RelSNRFinal(_dictionaryInput);
std::string sopInstanceUID_RelSNRFinal = sopuid.Generate();
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0008|0018"), sopInstanceUID_RelSNRFinal);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0002|0003"), sopInstanceUID_RelSNRFinal);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0020|000e"), seriesUID_R2);
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0020|0011"), newSeriesNumber_R2); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0020|4000"), std::string("_RelSNRFinal")); // series number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0020|0013"), std::string("9")); // instance number
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0028|0106"), std::string("0")); // smallest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0028|0107"), std::string("4096")); // largest pixel
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0028|1050"), std::string("2000")); // window center
itk::EncapsulateMetaData<std::string>( dictionaryOutput_RelSNRFinal, std::string("0028|1051"), std::string("4000")); // window width
// get GDCMImageIO ready before export
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
gdcmImageIO->KeepOriginalUIDOn();
// to cast
typedef itk::AdaptImageFilter < ImageType2D, OutputImageType, CastPixelAccessor< InputPixelType, OutputPixelType > > ImageAdaptorType;
typename ImageAdaptorType::Pointer adaptor = ImageAdaptorType::New();
// get the writer ready before export
typedef itk::ImageFileWriter<OutputImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetUseInputMetaDataDictionary(false);
// maybe this? http://www.cplusplus.com/reference/string/string/find_last_of/
if (!_opts->dir_output_map.empty()) {
printf("Saving to: %s ", _opts->dir_output_map.c_str());
//std::cout << "Saving to: " << _opts->dir_output_map << std::flush;
itk::FileTools::CreateDirectory(_opts->dir_output_map);
// export T1 color
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_T1Color);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_map + KWUtil::PathSeparator() + newSeriesNumber_T1 + "_T1color.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
// export T1 color
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_T1);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName( _opts->dir_output_map + KWUtil::PathSeparator() + newSeriesNumber_T1 + "_T1.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
std::cout << " Saved!" << std::endl;
}
if (!_opts->dir_output_fitparams.empty()) {
printf("Saving to: %s ", _opts->dir_output_fitparams.c_str());
//std::cout << "Saving to: " << _opts->dir_output_fitparams << std::flush;
// scaling R2 * 4000
typedef itk::MultiplyImageFilter< ImageType2D, ImageType2D, ImageType2D > MultiplyImageFilterType;
typename MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New();
multiplyFilter->SetInput( _imageCalculatorItk->GetR2Image() );
multiplyFilter->SetConstant( 4000 );
OxColorbarFilter->SetInput(multiplyFilter->GetOutput());
OxColorbarFilter->SetZerosInsteadOfColorbar(true);
// mkdir
itk::FileTools::CreateDirectory(_opts->dir_output_fitparams);
// export R2
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_R2);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_fitparams + KWUtil::PathSeparator() + newSeriesNumber_R2 + "_R2.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
// export A
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_A);
OxColorbarFilter->SetInput(_imageCalculatorItk->GetAImage());
OxColorbarFilter->SetZerosInsteadOfColorbar(true);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_fitparams + KWUtil::PathSeparator() + newSeriesNumber_R2 + "_A.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
// export B
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_B);
OxColorbarFilter->SetInput(_imageCalculatorItk->GetBImage());
OxColorbarFilter->SetZerosInsteadOfColorbar(true);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_fitparams + KWUtil::PathSeparator() + newSeriesNumber_R2 + "_B.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
// export T1star
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_T1star);
OxColorbarFilter->SetInput(_imageCalculatorItk->GetT1starImage());
OxColorbarFilter->SetZerosInsteadOfColorbar(true);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_fitparams + KWUtil::PathSeparator() + newSeriesNumber_R2 + "_T1star.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
// export ShMolliRange
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_ShMolliT1Range);
typedef itk::NShmolliSamplesUsedTo123ImageFilter <ImageType2D> nShmolliSamplesUsedTo123FilterType;
typename nShmolliSamplesUsedTo123FilterType::Pointer nShmolliSamplesUsedTo123Filter = nShmolliSamplesUsedTo123FilterType::New();
nShmolliSamplesUsedTo123Filter->SetInput(_imageCalculatorItk->GetNShmolliSamplesUsedImage());
OxColorbarFilter->SetInput(nShmolliSamplesUsedTo123Filter->GetOutput());
OxColorbarFilter->SetZerosInsteadOfColorbar(true);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_fitparams + KWUtil::PathSeparator() + newSeriesNumber_R2 + "_ShMolliRange.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
// TODO: change chisquare to final call value
// export nAmebaCalls
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_nAmebaCallFinal);
OxColorbarFilter->SetInput(_imageCalculatorItk->GetChiSqrtImage());
OxColorbarFilter->SetZerosInsteadOfColorbar(true);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_fitparams + KWUtil::PathSeparator() + newSeriesNumber_R2 + "_nAmebaCallFinal.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
// TODO: check, values seem a little low
// export RelSNRFinal
gdcmImageIO->SetMetaDataDictionary(dictionaryOutput_RelSNRFinal);
OxColorbarFilter->SetInput(_imageCalculatorItk->GetSNRImage());
OxColorbarFilter->SetZerosInsteadOfColorbar(true);
// export to dicom
adaptor->SetInput(OxColorbarFilter->GetOutput());
writer->SetFileName(_opts->dir_output_fitparams + KWUtil::PathSeparator() + newSeriesNumber_R2 + "_RelSNRFinal.dcm");
writer->SetInput(adaptor->GetOutput());
writer->SetImageIO(gdcmImageIO);
try {
writer->Update();
} catch (itk::ExceptionObject &e) {
std::cerr << "Exception in file writer " << std::endl;
std::cerr << e << std::endl;
}
std::cout << " Saved!" << std::endl;
}
return 0; // EXIT_SUCCESS
}
} // namespace Ox
#endif
#endif //Tomato_Tomato_EXPORT_HXX
Computing file changes ...
