From c32795e40184854d8a60475b12954c45c36e2fc9 Mon Sep 17 00:00:00 2001 From: Frederic Cervenansky Date: Fri, 17 Sep 2010 12:05:04 +0000 Subject: [PATCH] run creaBruker with gdcm2 --- CMakeLists.txt | 4 +- lib/src1/CMakeLists.txt | 12 +- lib/src1/bruker2dicom2.cxx | 1894 ++++++++++++++++++++++++++++++++++++ lib/src1/bruker2dicom2.h | 161 +++ 4 files changed, 2068 insertions(+), 3 deletions(-) create mode 100644 lib/src1/bruker2dicom2.cxx create mode 100644 lib/src1/bruker2dicom2.h diff --git a/CMakeLists.txt b/CMakeLists.txt index f54d182..25ce48e 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -56,9 +56,9 @@ CREA_PREVENT_IN_SOURCE_BUILD() # if you need to LINK against crea # (and not only use its macros) SET(USE_CREA ON) -SET(USE_GDCM ON) +OPTION(USE_GDCM ON) SET(USE_GDCM_VTK ON) -SET(USE_GDCM2 OFF) +OPTION(USE_GDCM2 OFF) SET(USE_WXWIDGETS OFF) SET(USE_KWWIDGETS OFF) SET(USE_VTK OFF) diff --git a/lib/src1/CMakeLists.txt b/lib/src1/CMakeLists.txt index c5149f6..6cc702b 100644 --- a/lib/src1/CMakeLists.txt +++ b/lib/src1/CMakeLists.txt @@ -39,7 +39,17 @@ IF ( BUILD_${LIBRARY_NAME} ) # # ) #---------------------------------------------------------------------------- - + #TO SWITCH BETWEEN GDCM AND GDCM2 + message ("avant... ${creaBruker_SOURCES}") +if(USE_GDCM2) + LIST(REMOVE_ITEM ${LIBRARY_NAME}_SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/bruker2dicom.cxx") + LIST(REMOVE_ITEM ${LIBRARY_NAME}_HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/ bruker2dicom.h") +endif() +if(USE_GDCM) + LIST(REMOVE_ITEM ${LIBRARY_NAME}_SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/bruker2dicom2.cxx") + LIST(REMOVE_ITEM ${LIBRARY_NAME}_HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/ bruker2dicom2.h") +endif() + message ("apres... ${creaBruker_SOURCES}") #---------------------------------------------------------------------------- # LIBRARY DEPENDENCIES (LIBRARIES TO LINK WITH) SET ( ${LIBRARY_NAME}_LINK_LIBRARIES diff --git a/lib/src1/bruker2dicom2.cxx b/lib/src1/bruker2dicom2.cxx new file mode 100644 index 0000000..a05d413 --- /dev/null +++ b/lib/src1/bruker2dicom2.cxx @@ -0,0 +1,1894 @@ +#include "bruker2dicom2.h" +#include "brukerexception.h" + +#include +#include +#include + + +#ifndef PATH_MAX // If not defined yet : do it + #define PATH_MAX 2048 +#endif + + bool Bruker2Dicom::Execute() + { + + //--- first, Test the system----// + bool bigEndian = gdcm::ByteSwap::SystemIsBigEndian(); + gdcm::SwapCode sc = gdcm::SwapCode::Unknown; + if ( gdcm::ByteSwap::SystemIsBigEndian() ) + { + sc = gdcm::SwapCode::BigEndian; + } + else if ( gdcm::ByteSwap::SystemIsLittleEndian() ) + { + sc = gdcm::SwapCode::LittleEndian; + } + else // sc == gdcm::SwapCode::Unknown + { + return 1; + } + + // ----- Check input directory name ----- + if ( ! boost::filesystem::is_directory(InputDirName) ) + { + std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl; + return 0; + } + else + { + if (verbose) + std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl; + } + + // ----- Check output directory name ----- + if ( ! boost::filesystem::is_directory(OutputDirName) ) + { + bool res=CreateDirectory(OutputDirName); + if (!res) + { + std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl; + throw ( BrukerHopelessException ("Output directory creation failure ")); + } + } + else + { + if(verbose) + std::cout << "[" << OutputDirName << "] already exist " << std::endl; + } + + // Deal with level 0 + // Level 0 is the original directory + // who could contain "1 2 3 4 5 6" directories and "AdjStatePerStudy subject" files + std::string strDirNamein(InputDirName); + boost::filesystem::directory_iterator it(InputDirName), it_end; + subjectFound = false; + acqpFound = false; + for(; it != it_end; ++it) + { + if(! boost::filesystem::is_directory( (*it) ) ) + { + if( (*it).filename() == "subject") + { + subjectFound = true; + } + if( (*it).filename() == "acqp") + { + acqpFound = true; + } + } + } + + // 1 : if subjectFound : user passed a Single Study Directory + // 2 : if NOT subjectFound and acqpFound : user passed a Serie Directory + // 3 : if NOT subjectFound and NOT acqpFound : user passed a 'non Study Directory' (Hope it's a set of Single Study Directories) + int type; + if (subjectFound ) type = 1; // user passed a 'study + else if (acqpFound) type = 2; // user passed a 'serie' + else type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory! + + switch (type) + { + case 1: { + std::string subject = InputDirName + VALID_FILE_SEPARATOR; + subject += "subject"; + boost::algorithm::replace_all( subject, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + bool canOpen = br_subject.LoadFile(subject); + if (!canOpen) + { + std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl; + throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open")); + } + else + { + br_subject.FillMap(); + // get info for 'Study Description' + BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); + subject_name = b_name.GetStringValue()[0]; + strPatientName = subject_name; + cleanString(subject_name); + DealWithSingleStudyDirectory (InputDirName, OutputDirName); + } + break; + } + + case 2: + { + subject_name = "defaultPatName"; + strPatientName = subject_name; + DealWithSingleStudyDirectory (InputDirName,OutputDirName); + break; + } + + + case 3: { + std::cout << " User passed a 'non study' directory; Hope it's a *non recursive* 'set of studies' directory! (recursive not yet dealt with)" << std::endl; +// DealWithMultiStudyDirectory (fileNames); + break; + } + } +} + +// ---------------------------------------------------------------------------------------------------------- + +void Bruker2Dicom::DealWithMultiStudyDirectory (gdcm::Directory::FilenamesType &dirNames,const std::string ¤tOutputDirName) +{ + gdcm::Directory::FilenamesType::iterator it; + + for (it = dirNames.begin(); + it != dirNames.end(); + ++it) + { + if ( boost::filesystem::is_directory(*it) ) + { + subjectFound = false; + if (verbose) + std::cout << "in 'DealWithMultiStudyDirectory' [" << *it << "] is a directory" << std::endl; + + gdcm::Directory dirList; + dirList.Load(*it); + gdcm::Directory::FilenamesType fileNames; + fileNames = dirList.GetFilenames(); + + gdcm::Filename file(fileNames.begin()->c_str()); + std::string path = file.GetPath(); + std::string subject = path + + VALID_FILE_SEPARATOR + + "subject"; + boost::algorithm::replace_all( subject, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + if (! boost::filesystem::is_regular(subject) ) + { + std::cout << "no [" << subject << "] file found" << std::endl; + continue; + } + + bool canOpen = br_subject.LoadFile(subject); + if (!canOpen) + { + std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl; + throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open")); + } + else + { + br_subject.FillMap(); + subjectFound = true; // Hope so! (full checking needed!) + + BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); + subject_name = b_name.GetStringValue()[0]; + strPatientName = subject_name; + cleanString(subject_name); + + DealWithSingleStudyDirectory(dirList.GetDirectories().begin()->c_str(), currentOutputDirName); + } + } + else + { + if (verbose) + std::cout << "[" << *it << "] is NOT a directory; skipped!" << std::endl; + } + } +} + +// ---------------------------------------------------------------------------------------------------------- + +void Bruker2Dicom::DealWithSingleStudyDirectory (const std::string &dirname, const std::string &i_outputDir) //(gdcm::Directory::FilenamesType &fileNames) +{ + bool res; + // creation directory : 'nom du patient' + std::string output = createDirectory(subject_name.c_str(), i_outputDir); + + + if (subjectFound) + { + BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry"); + subject_entry = b_entry.GetStringValue()[0]; + //cleanString(subject_entry); + subject_entry = subject_entry.substr(11, subject_entry.size()-11); + + BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position"); + subject_position = b_position.GetStringValue()[0]; + //cleanString(subject_position); + subject_position = subject_position.substr(9, subject_position.size()-9); + + BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date"); + subject_date = b_date.GetStringValue()[0]; + strStudyTimeDate = subject_date; + cleanString(subject_date); + + BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name"); + subject_study_name = b_study_name.GetStringValue()[0]; + subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2); + cleanString(subject_study_name); + } + else // Desperate trick when file 'subject' is missing + { + subject_entry = "HeadFirst"; // Why not? + subject_position = "Supine"; // Why not? + strStudyTimeDate = "06_06_06_6_June_1666"; // Why not? + subject_date = "6_June_1666"; // Why not? + subject_study_name = "defStudyName"; // Why not? + } + // subject_name is already in 'Patient Name' + strStudyDescr = /*subject_name + "." + */ subject_study_name /*+ "." + subject_entry + "." + subject_position + "." + subject_date*/; + + // creation directory : 'nom de la Study' + output = createDirectory(strStudyDescr, output); + + gdcm::UIDGenerator uid; + strStudyUID = uid.Generate(); + serieNumber = 0; + instanceNumber = 0; + + // ----------------------------------------------------- + // Iterate to ALL the objets(files/directories) found in the input directory + // (this is level ZERO) + // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie + // ----------------------------------------------------- + boost::filesystem::directory_iterator it(dirname), end_iter; + for(; it != end_iter; ++it) + { + if(boost::filesystem::is_directory(*it)) + { + std::string fname = (*it).filename() ; + //if (fname == "AdjResult") continue; what's the point? + boost::filesystem::directory_iterator it_level((*it)); + bool bAcqp = false; + std::string nextLevel; + std::string strAcqp; + std::string nameAcqp; + for(; it_level != end_iter; ++it_level) + { + if( (*it_level).filename() == "acqp") + { + strAcqp = (*it_level).string(); + nameAcqp = (*it_level).filename(); + boost::algorithm::replace_all( strAcqp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + bAcqp = true; + } + else if (boost::filesystem::is_directory( (*it_level) ) && nextLevel == "") + { + nextLevel = (*it_level).string(); // Hope we found only one directory + } + else + { + // nothing + } + } + + if ( bAcqp) + { + std::string acqp_scan_name; + std::string acqp_method; + std::string acqp_protocol_location; + + br_acqp.LoadFile(strAcqp); + br_acqp.FillMap(); + BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location"); + acqp_protocol_location = b_protocol_location.GetStringValue()[0]; + cleanString(acqp_protocol_location); + + BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name"); + acqp_scan_name = b_scan_name.GetStringValue()[0]; + cleanString(acqp_scan_name); + + BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method"); + b_method.PrintSelf(); // why? + acqp_method = b_method.GetStringValue()[0]; + cleanString(acqp_method); + + BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size"); + nbSlices = b_list_size.GetIntValue()[0]; + strSerieDescr = fname + + "." + acqp_scan_name + + "." + acqp_method.c_str(); + + + /*sprintf(outputDirName, "%s%c%s", i_outputDir.c_str(), VALID_FILE_SEPARATOR, strSerieDescr.c_str() ); + std::string temp(outputDirName); + boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);*/ + output = createDirectory(strSerieDescr, output); + if (verbose) + printf ("outputDirName [%s]\n", output); + try { + + DealWithNiveau1( (*it).string(), output); + } + catch (BrukerHopelessException &e) + { + std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl; + continue; + } + } + } + } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it +} + +// ===================================================================== + +void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName) { +// +// e.g. : at level 1, in B67d1.Bp1/6 +// +// acqp fid imnd pdata pulseprogram spnam0 spnam1 + + + //gdcm::Directory dirList; + //dirList.Load(level1Directory); // DON'T get recursively the list of files + //gdcm::Directory::FilenamesType fileNames; + //fileNames = dirList.GetFilenames(); + + // ----------------------------------------------------- + // Iterate to ALL the objets(files/directories) found in the input directory + // ----------------------------------------------------- + bool bmethod = false; + //gdcm::Directory::FilenamesType::iterator it = fileNames.begin(); + boost::filesystem::directory_iterator it(level1Directory), it_end; + for(; it != it_end; it++) + { + if((*it).leaf() == "method") + { + bmethod = br_method.LoadFile((*it).string()); + break; + } + } + + // if method wasn't found or unable to load, try with imnd file + if(!bmethod) + { + for(; it != it_end; it++) + { + if((*it).leaf() == "imnd") + { + bmethod = br_method.LoadFile((*it).string()); + break; + } + } + } + if(!bmethod) + { + std::cout << "Hopeless! neither 'method' nor 'imnd' found in [" + << level1Directory << "]; we skip it!" << std::endl; + } + // if (verbose) + // std::cout << "open => [" << strMethod << "] successfully" << std::endl; + /* a recuperer : + ##$PVM_Fov (dimension) // ou plutot RECO_fov ! + */ + /* + dans method (pour perfusion seulement?) : + ##$PVM_ObjOrderList=( 8 ) + 0 2 4 6 1 3 5 7 + ##$PVM_NSPacks=2 + ##$PVM_SPackArrNSlices=( 2 ) + 7 1 + */ + br_method.FillMap(); + + try + { + boost::filesystem::directory_iterator itDir(level1Directory), it_end; + for(; itDir != it_end; ++itDir) + { + if ( boost::filesystem::is_directory(*itDir) && (*itDir).leaf() == "pdata") + { + std::string output = createDirectory( (*itDir).leaf() , currentOutputDirName); + // will be always "pdata" ... + boost::filesystem::directory_iterator itDirInside(*itDir), it_inside_end; + for(; itDirInside != it_end; ++it) + { + // we take the first and hope that we have only one! + if ( boost::filesystem::is_directory(*itDirInside)) + { + output = createDirectory( (*itDirInside).leaf() , output); + DealWithNiveau2( (*itDirInside).string(), output); + } + } + } + } + } + catch(BrukerHopelessException &e) + { + std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl; + } + +} + +// ===================================================================== + +void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName) { + +// e.g. : at level 2 in B67d1.Bp1/6/pdata +// +// acqp fid imnd pdata pulseprogram spnam0 spnam1 +// + std::string output = currentOutputDirName; + + bool bisa = false; + boost::filesystem::directory_iterator it(level2Directory), it_end; + for(; it != it_end; ++it) + { + if((*it).leaf() == "isa") + { + bisa = br_isa.LoadFile((*it).string()); + if (bisa) + { + br_isa.FillMap(); + BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name"); + + std::string str_isa_func_name = b_isa_func_name.GetStringValue()[0]; + cleanString(str_isa_func_name); + output = createDirectory(str_isa_func_name, currentOutputDirName); + + } + break; + } + } + try { + DealWithNiveau3(level2Directory, output); + } + catch (BrukerHopelessException &e) + { + std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); " + << " We skip [" << level2Directory << "]" << std::endl; + + } + catch (BrukerInitException &e) + { + std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); " + << " We skip [" << level2Directory << "]" << std::endl; + + } + +} + +// +// ===================================================================== +// + +void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName){ + +// +// e.g. at level 3, in + + // just to be able to go on checking // JP + gdcm::Filename file; + + bool res; + + + + gdcm::Directory dirList; + dirList.Load(level3Directory); // DON'T get recursively the list of files + gdcm::Directory::FilenamesType::iterator it; + gdcm::Directory::FilenamesType fileNames = dirList.GetFilenames(); + + char original2dseqName [(unsigned int) PATH_MAX+2]; + char original2dseqName_XXX [(unsigned int) PATH_MAX+2]; + char currentOutputMhdDirName [(unsigned int) PATH_MAX+2]; + + char outputMhdFileName [(unsigned int) PATH_MAX+2]; + char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm' + char output2dseqName [(unsigned int) PATH_MAX+6]; + char output2dseqCartoName [(unsigned int) PATH_MAX+6]; + + char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough! + std::string temp; + bool canOpen; + + //-------------- try d3proc; + + canOpen = br_d3proc.LoadFile(findFile( level3Directory,"d3proc")); + + if (!canOpen) + { + std::cout << "Hopeless! no 'd3proc' found" << std::endl; + throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found")); + //exit(0); /// \TODO throw an exception ! + } + else + { + canOpen = br_d3proc.FillMap(); + if (!canOpen) + { + std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl; + throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'")); + } + } + + //-------------- end try d3proc; + + + // -------------------try reco + + + std::string str_reco = level3Directory + VALID_FILE_SEPARATOR + "reco"; + canOpen = br_reco.LoadFile(findFile( level3Directory, "reco")); + if (!canOpen) + { + std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl; + throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'")); + //exit(0); /// \TODO throw an exception ! + } + + else { + if (verbose) + std::cout << "[" << str_reco << "] successfully Loaded " << std::endl; + canOpen = br_reco.FillMap(); + if (!canOpen) + { + std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl; + throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'")); + + } + else { + if (verbose) + std::cout << "[" << str_reco << "] successfully Mapped" << std::endl; + } + } + + //std::cout << "------------------------------------------------------------------------------------------------" << std::cout; + // br_reco.PrintSelf(); + // std::cout << "------------------------------------------------------------------------------------------------" << std::cout; + // -------------------end try reco + + + BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX"); + int NX = bX.GetIntValue()[0]; + + if (verbose) + std::cout << "IM_SIX " << NX << std::endl; + BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY"); + int NY = bY.GetIntValue()[0]; + + if (verbose) + std::cout << "IM_SIY " << NY << std::endl; + /// \todo : check if there are actually 3 dimensions or only 2 + + BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ"); + int nbFrames = bZ.GetIntValue()[0]; + if (verbose) + std::cout << "IM_SIZ " << nbFrames << std::endl; + + // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...} + + BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE"); + + std::string mhdDataPixelType; + int pixelSize; + getImhDataType(bDPT, mhdDataPixelType, pixelSize); + + + /* + + // See mail Denis : + // En regle generale il vaut mieux que l'on passe par RECO_* + // pour extraire les parametres de l'image + // + + BrukerFieldData fov = br_method.GetFieldData("PVM_Fov"); + double fovX = fov.GetDoubleValue()[0]; + double fovY = fov.GetDoubleValue()[1]; + if (verbose) + std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl; + + BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol"); + double spatResolX = spatResol.GetDoubleValue()[0]; + double spatResolY = spatResol.GetDoubleValue()[1]; + if (verbose) + std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl; + +*/ + +/* ------ */ +// Better we use 'get' accessors from BrukerImage class, as Denis wrote them + + BrukerFieldData fov = br_reco.GetFieldData("RECO_fov"); + double fovX = fov.GetDoubleValue()[0]; + double fovY = fov.GetDoubleValue()[1]; + if (verbose) + std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl; + + BrukerFieldData size = br_reco.GetFieldData("RECO_size"); + double sizeX = size.GetDoubleValue()[0]; + double sizeY = size.GetDoubleValue()[1]; + + if (verbose) + std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl; + + double spatResolX = fovX / sizeX; + double spatResolY = fovY / sizeY; + + if (verbose) + std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl; + +/* ------ */ + + /// \TODO probabely a more sophisticated accessor will be necessary : + /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc) + + BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance"); + double sliceDistance = bsliceDistance.GetDoubleValue()[0]; + + if (verbose) + std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl; + +// ---------------------------------------------------------------------------------------- + + if (mhd) + { + sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(), + VALID_FILE_SEPARATOR, "MhdFiles"); + std::string temp(currentOutputMhdDirName); + boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + sprintf(currentOutputMhdDirName, "%s", temp); + std::string strCurrentOutputMhdDirName(currentOutputMhdDirName); + res = CreateDirectory( strCurrentOutputMhdDirName ); + if (!res) { + std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; + throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'")); + //exit (0); + } + + if (verbose) + std::cout << "Directory creation [" << currentOutputDirName << "]" << std::endl; + } // end if mhd + + if (verbose) + std::cout << "nbFrames " << nbFrames << std::endl; + if (verbose) + std::cout << "nbSlices " << nbSlices << std::endl; + int k; + int nbInstants = nbFrames/nbSlices; + if (verbose) + std::cout << "nbInstants (deduced)" << nbInstants << std::endl; + int instantNb; + int sliceNb; + FILE *fp; // for MHD files + + sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(),VALID_FILE_SEPARATOR, "2dseq"); + temp = level3Directory + VALID_FILE_SEPARATOR + "2dseq" ; + boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + sprintf(original2dseqName, "%s", temp); + +/**/ + // \TODO : tenir compte du bazar precedent + + // load 2dseq in memory + + fp = fopen(temp.c_str(), "rb"); + if (!fp) + { + // try 2dseq_Angio2D ?!? + temp = original2dseqName_XXX; + sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D"); + sprintf(original2dseqName_XXX, "%s", temp); + fp = fopen(original2dseqName_XXX, "rb"); + if (!fp) + { + std::cout << "Cannot open [" << original2dseqName << "] nor [" << original2dseqName_XXX << "] for reading" << std::endl; + fclose(fp); + throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'")); + //exit (0); + } + } + + unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants]; + ///\ TODO : find a safer way to be sure to read everything! + size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp); + + // This one will be important! + // --------------------------- + try { + imageSet = CreateImageSet ( ); + } + catch (BrukerInitException& e) + { + if (verbose) + std::cout << "an Init Exception was thrown in CreateImageSet ( ); " << e.what() + << "catched in DealWithNiveau3" << std::endl; + //return; + throw (e); + } + + serieNumber++; + gdcm::UIDGenerator uid; + strSerieUID = uid.Generate(); + + if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives) + { + if (verbose) + std::cout << "Single instant : do not split" << std::endl; + if (mhd) + { + sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName, + VALID_FILE_SEPARATOR); + temp = currentOutputDirName + VALID_FILE_SEPARATOR + "MhdFiles" + VALID_FILE_SEPARATOR +"MhdData_All_the_Slices.mhd"; + boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + sprintf(outputMhdFileName,"%s", temp); + fp=fopen(temp.c_str(), "w"); + if (!fp) + { + std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl; + throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting")); + //exit(0); + } + else + { + fprintf(fp, "ObjectType = Image\n"); + fprintf(fp, "NDims = 3\n" ); + fprintf(fp, "BinaryData = True \n" ); + fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); + fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices ); + fprintf(fp, "HeaderSize = %d\n", 0); + //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance ); + fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance ); + fprintf(fp, "Position = 0 0 %d\n", 0 ); + fprintf(fp, "Offset = 0 0 0\n" ); + fprintf(fp, "CenterOfRotation = 0 0 0\n" ); + fprintf(fp, "ElementNumberOfChannels = 1\n" ); + fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() ); + fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" ); + fclose(fp); + } + sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices", + currentOutputDirName.c_str(), VALID_FILE_SEPARATOR); + temp = currentOutputDirName + VALID_FILE_SEPARATOR + "2dseq_All_the_Slices"; + boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + sprintf(output2dseqSliceFileName,"%s",temp); + fp=fopen(temp.c_str(), "wb"); + if (!fp) + { + std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl; + throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting")); + } + else + { + fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp); + } + fclose(fp); + serieNumber ++; + gdcm::UIDGenerator uid; + strSerieUID = uid.Generate(); + + } // end if mhd + if (dicom) + { + sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm", + VALID_FILE_SEPARATOR); + temp = currentOutputDirName + VALID_FILE_SEPARATOR + "2dseq_All_the_Slices.dcm"; + boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + sprintf(output2dseqSliceFileName, "%s", temp); + + /* ----------- Write Dicom Image ---------------*/ + MakeDicomImage(buffer_2dseq, + NX, + NY, + nbFrames, + pixelSize, + //fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, + temp.c_str(), + subject_name, + day, + strStudyUID, + strSerieUID, + strStudyDescr, + strSerieDescr, + strStudyTimeDate, + 0,// index frame number + 4 //GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE + ); + } // end if dicom + } // end if nbInstants = 1 + + else // more than ONE instant + { + // Interleaved ! + // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ... + unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants]; + + k = 0; + for (sliceNb=0; sliceNbc_str()); + std::string path = file.GetPath(); + + std::string subject = path + + VALID_FILE_SEPARATOR + + "subject"; + boost::algorithm::replace_all( subject, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + std::string acqp = path + + VALID_FILE_SEPARATOR + + "acqp"; + boost::algorithm::replace_all( acqp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + if ( boost::filesystem::is_regular(subject) ) + subjectFound = true; // user passed a 'study + else + subjectFound = false; // user didnt' pass a 'study + + if ( boost::filesystem::is_regular(acqp) ) + acqpFound= true; // user passes a 'serie', not a 'study' + else + acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory! + + int type; + if (subjectFound ) type = 1; // user passed a 'study + else if (acqpFound) type = 2; // user passed a 'serie' + else type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory! + + return type; +} + +// ========================================================================================================== + +bool Bruker2Dicom::CreateDirectory(const std::string &OutputDirName) +{ + std::string systemCommand; + + if (verbose) + std::cout << "Check for output directory :[" << OutputDirName << "]." + < Bruker2Dicom::CreateImageSet ( ) +{ + std::vector imageSet; + br_acqp.SetLoopStructure(); + std::vector tempVect = br_acqp.GetLoopStructure() ; + std::map map = br_acqp.GetBrukerHeaderMap(); + + bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect); + + if (result == false) + { + throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); + } + + br_acqp.SetImageLoopStructure(); + br_acqp.SetBrukerImageList(); + std::vector > brukerImageList = br_acqp.GetBrukerImageList(); + + BrukerImage image(br_acqp,br_reco); + image.Init(br_acqp,br_reco,1); + + for(int i=0;i > imageOrientation; + std::vector imagePosition; + for(int i=0;i at; + at.SetValue(X); + ds.Replace(at.GetAsDataElement()); + } + // rows + { + gdcm::Attribute<0x0028,0x0010, gdcm::VR::US> at; + at.SetValue(Y); + ds.Replace(at.GetAsDataElement()); + } + + //file.SetDataSet( createDataSet(str.str(),0x0028,0x0011,"US")); + // Set the image size + str.str(""); + str << X; + + // file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns + str.str(""); + str << Y; + // file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows + + if (nbFrames != 1) + { + gdcm::Attribute<0x0028,0x0008, gdcm::VR::IS> at; + at.SetValue(nbFrames); + ds.Replace(at.GetAsDataElement()); + // file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames + } + + // Set the pixel type + // Bits allocated + { + gdcm::Attribute<0x0028,0x0100, gdcm::VR::US> at; + at.SetValue(pixelSize*8); + ds.Replace(at.GetAsDataElement()); + } + // Bits stored + { + gdcm::Attribute<0x0028,0x0101, gdcm::VR::US> at; + at.SetValue(pixelSize*8); + ds.Replace(at.GetAsDataElement()); + } + // High Bit + { + gdcm::Attribute<0x0028,0x0102, gdcm::VR::US> at; + at.SetValue(pixelSize*8 -1); + ds.Replace(at.GetAsDataElement()); + } + + // pixel representation + { + gdcm::Attribute<0x0028,0x0103, gdcm::VR::US> at; + at.SetValue(1); + ds.Replace(at.GetAsDataElement()); + } + // sample per pixel + { + gdcm::Attribute<0x0028,0x0002, gdcm::VR::US> at; + at.SetValue(1); + ds.Replace(at.GetAsDataElement()); + } + + // pixel spacing + { + char temp[256]; + sprintf(temp,"%d%s%d",spacingX, "\\", spacingY); + std::string st; + st = temp; + gdcm::Attribute<0x0028,0x0030, gdcm::VR::DS> at; + // at.SetValue(st); + ds.Replace(at.GetAsDataElement()); + } + //Slice Thickness + { + gdcm::Attribute<0x0018,0x00500, gdcm::VR::DS> at; + + at.SetValue(sliceDistance); + ds.Replace(at.GetAsDataElement()); + } + // Series Number + { + gdcm::Attribute<0x0020,0x0011, gdcm::VR::IS> at; + at.SetValue(serieNumber); + ds.Replace(at.GetAsDataElement()); + } + //Instance Number + { + gdcm::Attribute<0x0020,0x00131,gdcm::VR::IS> at; + at.SetValue(++instanceNumber); + ds.Replace(at.GetAsDataElement()); + + } + // [Media Storage SOP Class UID] + { + /* + str.str(""); + str << "1.2.840.10008.5.1.4.1.1.4"; + gdcm::Tag tag(0x0002, 0x0002); + tag.Write(str); + at.SetValue(str); + ds.Replace(at.GetAsDataElement());*/ + } + // [SOP Class UID] + { + /* gdcm::Attribute<0x0008, 0x0162gdcm::VR::UI> at; + at.SetValue("1.2.840.10008.5.1.4.1.1.4"); + ds.Replace(at.GetAsDataElement());*/ + } + // Patient Name + { + gdcm::Attribute<0x0010,0x0010, gdcm::VR::PN> at; + at.SetValue(patientName); + ds.Replace(at.GetAsDataElement()); + } + // Patient's ID + { + gdcm::Attribute<0x0010,0x0020, gdcm::VR::LO> at; + at.SetValue(patientName); + ds.Replace(at.GetAsDataElement()); + } + // study UID + { + gdcm::Attribute< 0x0020, 0x000d, gdcm::VR::UI> at; + at.SetValue(studyUID); + ds.Replace(at.GetAsDataElement()); + } + // serieUID + { + gdcm::Attribute< 0x0020, 0x000e, gdcm::VR::UI> at; + at.SetValue(serieUID); + ds.Replace(at.GetAsDataElement()); + } + { + gdcm::Attribute< 0x0008,0x0020, gdcm::VR::DA> at; + at.SetValue(strStudyTimeDate.substr(10,11).c_str()); + ds.Replace(at.GetAsDataElement()); + } + { + gdcm::Attribute< 0x0008,0x0030, gdcm::VR::TM> at; + at.SetValue(strStudyTimeDate.substr(1,8).c_str()); + ds.Replace(at.GetAsDataElement()); + } + // Study Description + { + gdcm::Attribute< 0x0008,0x1030, gdcm::VR::LO> at; + at.SetValue(studyDescr); + ds.Replace(at.GetAsDataElement()); + } + // Series Description + { + gdcm::Attribute< 0x0008,0x103e, gdcm::VR::LO> at; + at.SetValue(serieDescr); + ds.Replace(at.GetAsDataElement()); + } + // Modalirty + { + gdcm::Attribute< 0x0008,0x0060, gdcm::VR::CS> at; + at.SetValue("MR"); + ds.Replace(at.GetAsDataElement()); + } + + + // //8, 16, 32, 64 (for double ?) + str.str(""); + str << pixelSize*8; + // file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated + + // file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored + + str.str(""); + str << pixelSize*8-1; + // file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit + + // Set the pixel representation // 0/1 , 0=unsigned + // file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation + + // Set the samples per pixel // 1:Grey level, 3:RGB + // file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel + +// 0028 0030 DS 2 Pixel Spacing + str.str(""); + str << spacingX << "\\" << spacingY; + // file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing + + // 0018 0050 DS 1 Slice Thickness + str.str(""); + str << sliceDistance; + // file->InsertEntryString(str.str(),0x0018,0x0050, "DS"); + +// 0020 0011 IS 1 Series Number + str.str(""); + str << serieNumber; +// file->InsertEntryString(str.str(),0x0020,0x0011, "IS"); + +// 0020|0013 [IS] [Instance Number] + instanceNumber++; + str.str(""); + str << instanceNumber; + // file->InsertEntryString(str.str(),0x0020,0x0013, "IS"); + + // 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage + // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID] + // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI"); // [SOP Class UID] + +// OK : MR is NOT multiframe, but I want just a quick an dirty solution +// +//// 1.2.840.10008.5.1.4.1.1.4 MR Image Storage +// file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID] +// file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI"); // [SOP Class UID] +// +// // if (strlen(patientName) != 0) +// file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name +// file->InsertEntryString(patientName.c_str(),0x0010,0x0020, "LO"); // Patient's ID +// +// file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI"); +// file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI"); +// +//// 0008 0020 DA 1 Study Date +//// 0008 0030 TM 1 Study Time +// +///// \TODO split into 2 strings! +// file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA"); +// file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(), 0x0008,0x0030, "TM"); +// +// file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO"); // Study Description +// file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO"); // Series Description +// +////0008|0060 [CS] [Modality] +// file->InsertEntryString("MR",0x0008,0x0060, "CS"); +// +// 0020 0037 DS 6 Image Orientation (Patient) + char charImageOrientation[256]; + +/* +std::cout << "charImageOrientation " << + imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " << + imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " << + imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " << + imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " << + imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " << + imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ; +*/ + + { + gdcm::Attribute< 0x0020,0x0037, gdcm::VR::DS> at; + at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0], 0); + at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1], 1); + at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2], 2); + at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0], 3); + at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1], 4); + at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2], 4); + ds.Replace(at.GetAsDataElement()); + } +// file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS"); + + char charImagePosition[256]; + sprintf(charImagePosition,"%f\\%f\\%f", + imageSet[imgNum].getTranslationVectorRPS2XYZ()[0], + imageSet[imgNum].getTranslationVectorRPS2XYZ()[1], + imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]); + + //file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient) + +// 0020 0032 DS 3 Image Position (Patient) + { + gdcm::Attribute< 0x0020,0x0032,gdcm::VR::DS> at; + at.SetValue( imageSet[imgNum].getTranslationVectorRPS2XYZ()[0], 0); + at.SetValue( imageSet[imgNum].getTranslationVectorRPS2XYZ()[1], 1); + at.SetValue(imageSet[imgNum].getTranslationVectorRPS2XYZ()[2], 2); + ds.Replace(at.GetAsDataElement()); + } + + + // Private creator + /* + +0029|0010 [LO] [Private Creator] [CREATIS HEADER ] +0029|0011 [LO] [Private Creator] [CREATIS for BRUKER to DICOM] +0029|1031 [LO] [] [4.0.7571167 ] +0029|1032 [UL] [] [1440000] =0x(15f900) + +> $$ Thu Jul 30 17:29:46 2009 CEST (UT+2h) mwiart +> $$ /opt/PV4.0/data/mwiart/nmr/dha80.Uw1/4/method +> ##$Method=DtiEpi +> ##$PVM_DwNDiffDir=3 % 3 directions +> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b par direction +> ##$PVM_DwAoImages=1 % 1 image pour b=0 +> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b +> 1500.000000 3000.000000 +> +> $$ Wed Dec 2 09:56:01 2009 UTC (UT+0h) mwiart +> $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/4/method +> ##$Method=DtiEpi +> ##$PVM_DwNDiffDir=3 % 3 directions +> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b par direction +> ##$PVM_DwAoImages=1 % 1 image pour b=0 +> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b +> 1500 3000 +> +> $$ Wed Dec 2 10:14:27 2009 UTC (UT+0h) mwiart +> $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/5/method +> ##$Method=DtiStandard +> ##$PVM_DwNDiffDir=1 % 1 direction +> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b +> ##$PVM_DwAoImages=0 % 0 image pour b=0 +> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b +> 138 1600 +> + */ + { + gdcm::Attribute< 0x0029,0x0010, gdcm::VR::LO> at; + at.SetValue( "CREATIS HEADER"); + ds.Replace(at.GetAsDataElement()); + } + { + gdcm::Attribute< 0x0029,0x0011, gdcm::VR::LO> at; + at.SetValue( "CREATIS FOR BRUKER-TO-DICOM"); + ds.Replace(at.GetAsDataElement()); + } + + // file->InsertEntryString("CREATIS HEADER", 0x0029,0x0010, "LO"); + //file->InsertEntryString("CREATIS FOR BRUKER-TO-DICOM", 0x0029,0x0011, "LO"); + + BrukerFieldData brf_method = br_method.GetFieldData("Method"); + const std::vector method = brf_method.GetStringValue(); + + // std::string method = br_method.GetFieldData("Method").GetStringValue(); + //{ + // gdcm::Attribute< 0x0029,0x0100, gdcm::VR::LO> at; + // at.SetValue(method[0]); + // ds.Replace(at.GetAsDataElement()); + //} + //file->InsertEntryString(method[0], 0x0029,0x0100, "LO"); + + std::cout << " method[" << method[0] << "]" << std::endl; + if (method[0] == "DtiEpi" || method[0] == "DtiStandard") + { + // const std::vector NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir").GetIntValue(); + BrukerFieldData brf_NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir"); + const std::vector NDiffDir = brf_NDiffDir.GetIntValue(); + + //const std::vector NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach").GetIntValue(); + BrukerFieldData brf_NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach"); + const std::vector NDiffExpEach =brf_NDiffExpEach.GetIntValue(); + +// const std::vector AoImages = br_method.GetFieldData("PVM_DwAoImages").GetIntValue(); + BrukerFieldData brf_AoImages = br_method.GetFieldData("PVM_DwAoImages"); + const std::vector AoImages = brf_AoImages.GetIntValue(); + + BrukerFieldData brf_DwBvalEach = br_method.GetFieldData("PVM_DwBvalEach"); + const std::vector DwBvalEach = brf_DwBvalEach.GetDoubleValue(); + + std::cout << "nb directions : " << NDiffDir[0] << " nb valeurs de b par direction : " << NDiffExpEach[0] + << " nb images for b=0 : " << AoImages[0] << std::endl; + + str.str(""); + str << NDiffDir[0]; + { + gdcm::Attribute< 0x0029,0x0101, gdcm::VR::US> at; + at.SetValue( NDiffDir[0]); + ds.Replace(at.GetAsDataElement()); + } + // file->InsertEntryString(str.str(),0x0029,0x0101,"US"); // directions + str.str(""); + str << NDiffExpEach[0]; + { + gdcm::Attribute< 0x0029,0x0102, gdcm::VR::US> at; + at.SetValue( NDiffExpEach[0]); + ds.Replace(at.GetAsDataElement()); + } + // file->InsertEntryString(str.str(),0x0029,0x0102,"US"); // valeurs de b par direction + str.str(""); + str << AoImages[0]; + { + gdcm::Attribute< 0x0029,0x0103, gdcm::VR::US> at; + at.SetValue( AoImages[0]); + ds.Replace(at.GetAsDataElement()); + } + // file->InsertEntryString(str.str(),0x0029,0x0103,"US"); // image pour b=0 + + { + gdcm::Attribute< 0x0029,0x0104,gdcm::VR::DS> at; + for (unsigned int i=0; iInsertEntryString(str.str(),0x0029,0x0104,"DS"); // Valeurs de b + } + file.SetDataSet(ds); + +// 0020 0x1041 DS 1 Slice Location +// sprintf(charImagePosition,"%f",float(imgNum)); +// file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS"); +/* + // Set Rescale Intercept + str.str(""); + str << div; + file->InsertEntryString(str.str(),0x0028,0x1052,"DS"); + + // Set Rescale Slope + str.str(""); + str << mini; + file->InsertEntryString(str.str(),0x0028,0x1053,"DS"); +*/ + // dcmImageName = "c:\\toto.dcm"; + boost::algorithm::replace_all( dcmImageName, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + FILE *fil=fopen("c:\\toto", "a"); + fclose(fil); + + gdcm::ImageWriter writer; + writer.SetFileName(dcmImageName.c_str()); + writer.SetFile(file); + gdcm::DataElement pixeldata( gdcm::Tag(0x7fe0,0x0010) ); + pixeldata.SetByteValue( (char*)tabPixels ,X*Y*nbFrames*pixelSize ); + gdcm::Image im; + im.SetDataElement(pixeldata); + writer.SetImage(im); + +// GDCM_NAME_SPACE::FileHelper *fileH; +// fileH = GDCM_NAME_SPACE::FileHelper::New(file); +// fileH->SetContentType(contentType); +// +// // cast is just to avoid warnings (*no* conversion is performed) +// //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float! +// +////std::cout << "-------------------------------- X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl; +// +// fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize); +// fileH->SetWriteModeToRaw(); +// fileH->SetWriteTypeToDcmExplVR(); +// if( !fileH->Write(dcmImageName)) { +// std::cout << "Failed for [" << dcmImageName << "]\n" +// << " File is unwrittable" << std::endl; +// file->Delete(); +// fileH->Delete(); +// throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file ")); +// } +// //if (verbose) +// // file->Print(); +// +// file->Delete(); +// fileH->Delete(); +} + +////////////////////////////////////////////////////////////////////// +// Generic repertory creation // +////////////////////////////////////////////////////////////////////// +const std::string Bruker2Dicom::createDirectory(const std::string &i_name, const std::string &i_dir) +{ + + // creation directory : 'nom du patient' + std::string tempString(i_dir); + tempString = tempString + VALID_FILE_SEPARATOR + i_name; + boost::algorithm::replace_all( tempString, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR); + if (!CreateDirectory(tempString)) + { + std::cout << "[" << tempString << "] Directory creation failure " << std::endl; + throw ( BrukerHopelessException ("Patient directory creation failure ")); + } + return tempString.c_str(); +} + + std::string Bruker2Dicom::findFile(const std::string &i_dir, const std::string i_name) +{ + bool bres = false; + std::string file; + boost::filesystem::directory_iterator it(i_dir), it_end; + for(; it != it_end; ++it) + { + if((*it).leaf() == i_name) + { + file = (*it).string(); + bres = true; + break; + } + } + + if(!bres) + { + boost::filesystem::path pth (i_dir); + boost::filesystem::directory_iterator itless(pth.branch_path()), it_end; + for(; itless != it_end; ++itless) + { + if((*itless).leaf() == i_name) + { + file = (*itless).string(); + bres = true; + break; + } + } + } + return file.c_str(); +} + + +//const gdcm::DataSet Bruker2Dicom::createDataSet(const std::string &i_val, +// const uint16_t &i_gr, const uint16_t &i_el, +// const gdcm::VR &i_vr) +// +//{ +// gdcm::Attribute at; +// at.SetValue(i_val.c_str()); +// +// +// gdcm::DataElement de; +// de.Clear(); +// de.SetVR(i_vr); +// de.SetTag( gdcm::Tag(i_gr, i_el) ); +// +// gdcm::DataSet ds; +// ds.Clear(); +// ds.Replace(at.GetAsDataElement()); +// return ds; +//} diff --git a/lib/src1/bruker2dicom2.h b/lib/src1/bruker2dicom2.h new file mode 100644 index 0000000..d047865 --- /dev/null +++ b/lib/src1/bruker2dicom2.h @@ -0,0 +1,161 @@ +#ifndef BRUKER2DICOM2_H +#define BRUKER2DICOM2_H + +#include +#include "gdcmDirectory.h" +#include +#include + +#include "gdcmByteSwap.h" +#include "gdcmSwapCode.h" +#include "gdcmFilename.h" +#include "gdcmDataSet.h" + +#include "gdcmImageWriter.h" +#include "gdcmImage.h" +#include "gdcmWriter.h" +#include "gdcmReader.h" +#include "gdcmUIDGenerator.h" +// +//#include "gdcmFile.h" +//#include "gdcmFileHelper.h" +//#include "gdcmCommon.h" +//#include "gdcmDebug.h" +//#include "gdcmUtil.h" +//#include "gdcmDirList.h" +// +//#include "gdcmArgMgr.h" +#include "brukerSystem.h" +#include "brukerdataset.h" +#include "brukerkspaceobject.h" +#include "brukerimage.h" +#include +#include +#include + + // file separator +#if defined(_WIN32) +#define VALID_FILE_SEPARATOR "\\" +#define INVALID_FILE_SEPARATOR "/" +#else +#define INVALID_FILE_SEPARATOR "\\" +#define VALID_FILE_SEPARATOR "/" +#endif + +class __declspec( dllexport ) Bruker2Dicom { + +public: + /*! \brief Constructor +*/ + Bruker2Dicom () /* : verbose(0), mhd(0), dicom(0), day(O)*/ {}; +/*! \brief Destructor +*/ + ~Bruker2Dicom (){}; + + void SetInputDirectory (const std::string &i) { InputDirName = i;} + void SetOutputDirectory(const std::string &o) { OutputDirName = o;} + void SetConvertModeToDicom() { dicom = 1; mhd = 0;} + void SetConvertModeToMhd() { dicom = 0; mhd = 1;} + bool Execute(); + + /* + // For debugging pupose only. + //Don't need accessors : Attributes are 'public' + + void SetVerbose(int v) { verbose = v;} + void SetMhd(int m) { mhd = m; } + void SetDicom(int d) { dicom = d; } + */ + +private : + +void MakeDicomImage(unsigned char *tabPixels, + int X, + int Y, + int nbFrames, + int pixelSize, + double spacingX, double spacingY, double sliceDistance, + std::string dcmImageName, + const std::string &patientName, + const char *day, + std::string &studyUID, + std::string &serieUID, + std::string &studyDescr, + std::string &serieDescr, + std::string &strStudyTimeDate, + int imgNum, int imagecontenttype//gdcm2 dont have such things, I think, as ImageContentTYpe + ); + +std::vector CreateImageSet ( ); + +void getImhDataType(BrukerFieldData &bDPT, + std::string &mhdDataPixelType, + int &pixelSize); + +void cleanString(std::string &s); + +bool CreateDirectory(const std::string &dirNameout); + +int CheckUserDirectory(std::string &userDirName); +void DealWithMultiStudyDirectory(gdcm::Directory::FilenamesType &fileNames,const std::string ¤tOutputDirName); +void DealWithSingleStudyDirectory (const std::string &dirname,const std::string ¤tOutputDirName) ; + +void DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName); +void DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName); +void DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName); + +void dealWithCarto(gdcm::Directory::FilenamesType &fileNames, int NX, int NY, int nbSlices, + double fovX, double fovY, double sliceDistance, + char *copyFile, std::string ¤tOutputDirName, + char *outputMhdFileName, char *output2dseqCartoName); + +const std::string createDirectory(const std::string &i_name,const std::string &i_dir); + std::string findFile(const std::string &i_dir, const std::string i_name); +public: + +// these ones are for debugging only +// don't bbfy the accessors. + + int verbose; + const char *day; + +private : + std::string InputDirName; + std::string OutputDirName; + + bool subjectFound; + bool acqpFound; + + std::string subject_entry; + std::string subject_position; + std::string subject_date; + std::string subject_study_name; + + int mhd; + int dicom; + + int nbSlices; + BrukerDataSet br_subject; + BrukerDataSet br_acqp; + BrukerDataSet br_method; + BrukerDataSet br_d3proc; + BrukerDataSet br_isa; + BrukerDataSet br_reco; + + std::vector imageSet; + +// For DICOM images. + + std::string strStudyUID; + std::string strSerieUID; + std::string strStudyDescr; + std::string strSerieDescr; + std::string strStudyTimeDate; + std::string strPatientName; + std::string subject_name; // cleaned strPatientName + + int serieNumber; + int instanceNumber; +}; + +#endif -- 2.47.1