/* # --------------------------------------------------------------------- # # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image # pour la Santé) # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton # Previous Authors : Laurent Guigues, Jean-Pierre Roux # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil # # This software is governed by the CeCILL-B license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL-B # license as circulated by CEA, CNRS and INRIA at the following URL # http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html # or in the file LICENSE.txt. # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL-B license and that you accept its terms. # ------------------------------------------------------------------------ */ #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) void Bruker2Dicom::DealWithSingleStudyDirectory (const std::string dirname, const std::string i_outputDir) { 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.c_str()); 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 currentOutputDirName) { // // 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 currentOutputDirName) { // 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.c_str()); 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.c_str()); /**/ // \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.c_str()); 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.c_str()); 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.c_str()); 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.c_str()); /* ----------- 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<0x0018,0x0050, 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<0x0020,0x0013,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(.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(dcmImageName.c_str(), "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; //}