X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=05695f43927ab5da979b16a535df6c41b20dea40;hb=2da5837d36be6ef2a73036715343d436231556ff;hp=3dc9cbefc91a74057c9a43ab26cbfcc460749ecc;hpb=e290be9f28dc24bfb58f239c098b67c2a76cfbd9;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 3dc9cbe..05695f4 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -7,11 +7,9 @@ #define PATH_MAX 2048 #endif - - bool Bruker2Dicom::Execute() { - // ----- Check input values ----- + // ----- Check input directory name ----- bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(); @@ -27,6 +25,8 @@ bool Bruker2Dicom::Execute() std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl; } + // ----- Check output directory name ----- + std::string strDirNameOut(OutputDirName); bool res=CreateDirectory(strDirNameOut); if (!res) { @@ -35,93 +35,219 @@ bool Bruker2Dicom::Execute() throw ( BrukerHopelessException ("Output directory creation failure ")); } - std::string strDirNamein(InputDirName); - GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files - std::string strDirNameout(OutputDirName); - -/* - if (listonly) - { - std::cout << "------------List of found files ------------" << std::endl; - dirList.Print(); - std::cout << std::endl; - return 1; - } -*/ - // // e.g : at level 0, in : B67d1.Bp1 // // 1 2 3 4 5 6 AdjStatePerStudy subject // + std::string strDirNamein(InputDirName); + +/* */ + GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files + GDCM_NAME_SPACE::DirListType fileNames; fileNames = dirList.GetFilenames(); - bool canOpen; - std::string outputFileName; + std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())); - // BrukerDataSet br_subject; - std::string subject; - subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+ - GDCM_NAME_SPACE::GDCM_FILESEPARATOR + - "subject"; - if (verbose) - std::cout << " Subject : [" << subject << "]" << std::endl; - canOpen =br_subject.LoadFile(subject); + std::string subject = path + + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + + "subject"; - if (!canOpen) + std::string acqp = path + + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + + "acqp"; + + if ( boost::filesystem::is_regular(subject) ) + subjectFound = true; + else + subjectFound = false; // user passed only a 'serie', not a 'study + + if ( boost::filesystem::is_regular(acqp) ) + acqpFound= true; + 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! + /* */ + + + // 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 = CheckUserDirectory(InputDirName); + + switch (type) { - std::cout << "Hopeless! no 'subject' found" << std::endl; - throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory ")); - //exit(0); /// \TODO throw an exception ! - } - else - { - br_subject.FillMap(); - } + case 1: { + 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(); + } //br_subject.PrintSelf(); // get info for 'Study Description' BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); - std::string subject_name = b_name.GetStringValue()[0]; + subject_name = b_name.GetStringValue()[0]; strPatientName = subject_name; cleanString(subject_name); + DealWithSingleStudyDirectory (fileNames); + break; + } - BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry"); - std::string 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"); - std::string 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"); - std::string subject_date = b_date.GetStringValue()[0]; - strStudyTimeDate = subject_date; - cleanString(subject_date); - - BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name"); - std::string subject_study_name = b_study_name.GetStringValue()[0]; - subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2); - cleanString(subject_date); + case 2: { + subject_name = "defaultPatName"; + strPatientName = subject_name; + DealWithSingleStudyDirectory (fileNames); + break; + } + + case 3: { + std::cout << " user passed a 'non study' directory; Hope it's a 'set of studies' directory!, not yet dealt with" << std::endl; + DealWithMultiStudyDirectory (fileNames); + break; + } + } +} + +// ---------------------------------------------------------------------------------------------------------- + +void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames) +{ + GDCM_NAME_SPACE::DirListType::iterator it; + + for (it = dirNames.begin(); + it != dirNames.end(); + ++it) + { + if ( boost::filesystem::is_directory(*it) ) + { + if (verbose) + std::cout << "[" << *it << "] is a directory" << std::endl; + + GDCM_NAME_SPACE::DirList dirList(*it, false, true); // DON'T get recursively the list of files + GDCM_NAME_SPACE::DirListType fileNames; + fileNames = dirList.GetFilenames(); + + std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())); + std::string subject = path + + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + + "subject"; + 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(); + } + + BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); + subject_name = b_name.GetStringValue()[0]; + strPatientName = subject_name; + cleanString(subject_name); + + DealWithSingleStudyDirectory(fileNames); + } + else + { + if (verbose) + std::cout << "[" << *it << "] is NOT a directory; skipped!" << std::endl; + } + } +} + +// ---------------------------------------------------------------------------------------------------------- - // subject_name is already in 'Patient Name' - strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; +void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames) +{ + bool res; + // creation directory : 'nom du patient' + std::string tempStringPatDir(OutputDirName); + tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name; + + res=CreateDirectory(tempStringPatDir); + if (!res) { + std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl; + throw ( BrukerHopelessException ("Patient directory creation failure ")); + } + 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' + + std::string tempStringStudyDir(OutputDirName); + tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr; + + res=CreateDirectory(tempStringStudyDir); + if (!res) { + std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl; + throw ( BrukerHopelessException ("Study directory creation failure ")); + } + char outputDirName[(unsigned int) PATH_MAX+2]; - strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); - serieNumber = 0; + strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); + 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 // ----------------------------------------------------- - + GDCM_NAME_SPACE::DirListType::iterator it; for (it = fileNames.begin(); @@ -133,6 +259,9 @@ bool Bruker2Dicom::Execute() if (verbose) std::cout << "[" << *it << "] is a directory" << std::endl; + if((*it) == "AdjStatePerStudy") // avoid trouble with new version 'AdjStatePerStudy' directory + continue; + //BrukerDataSet br_acqp; std::string strAcqp; strAcqp = (*it) + @@ -142,6 +271,7 @@ bool Bruker2Dicom::Execute() br_acqp.LoadFile(strAcqp); br_acqp.FillMap(); +//std::cout << "out of br_acqp.FillMap " << std::endl; std::string acqp_scan_name; std::string acqp_method; std::string acqp_protocol_location; @@ -149,26 +279,32 @@ bool Bruker2Dicom::Execute() BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location"); acqp_protocol_location = b_protocol_location.GetStringValue()[0]; cleanString(acqp_protocol_location); - + +//std::cout << "out of br_acqp.FillMap 1" << std::endl; BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name"); +//std::cout << "out of br_acqp.FillMap 11" << std::endl; acqp_scan_name = b_scan_name.GetStringValue()[0]; +//std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl; cleanString(acqp_scan_name); +//std::cout << "out of br_acqp.FillMap 2" << std::endl; + BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method"); + b_method.PrintSelf(); + acqp_method = b_method.GetStringValue()[0]; - BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method"); - acqp_method = b_method.GetStringValue()[0]; cleanString(acqp_method); - +//std::cout << "out of br_acqp.FillMap 3" << std::endl; BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size"); - b_list_size.PrintSelf(); //JP +//std::cout << "out of br_acqp.FillMap 4" << std::endl; + //b_list_size.PrintSelf(); //JP nbSlices = b_list_size.GetIntValue()[0]; - +//std::cout << "out of br_acqp.FillMap 5" << std::endl; strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it) /* + "." + acqp_protocol_location */ // always the same (in each acquisition) + "." + acqp_scan_name + "." + acqp_method.c_str(); - sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(), + sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(), //OutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, strSerieDescr.c_str() ); @@ -176,20 +312,24 @@ bool Bruker2Dicom::Execute() << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n" << " ================================================================================" << std::endl; - - + std::string strOutputDirName(outputDirName); if (verbose) - printf ("outputDirName [%s]\n", outputDirName); - - DealWithNiveau1(*it, outputDirName); + printf ("outputDirName [%s]\n", outputDirName); + try { + DealWithNiveau1(*it, strOutputDirName); + } + 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) { +void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName) { // // e.g. : at level 1, in B67d1.Bp1/6 // @@ -248,6 +388,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, GDCM_NAME_SPACE::Util::GetName(*it).c_str()); + std::string strOutputDirName(outputDirName); //br1.PrintSelf(); std::string strMethod; @@ -267,8 +408,10 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr canOpen = br_method.LoadFile(strMethod); if (!canOpen) { - std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl; - throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found ")); + std::cout << "Hopeless! neither 'method' nor 'imnd' found in [" + << level1Directory << "]; we skip it!" << std::endl; + continue; + //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found ")); //exit(0); /// \TODO throw an exception ! } } @@ -277,7 +420,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr br_method.FillMap(); /* a recuperer : - ##$PVM_Fov (dimension) + ##$PVM_Fov (dimension) // ou plutot RECO_fov ! */ /* dans method (pour perfusion seulement?) : @@ -287,15 +430,22 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr ##$PVM_SPackArrNSlices=( 2 ) 7 1 */ - DealWithNiveau2(*it,outputDirName ); + try { + DealWithNiveau2(*it, strOutputDirName); + } + catch (BrukerHopelessException &e) + { + std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl; + continue; + } } } } // ===================================================================== -void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) { - +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 @@ -308,7 +458,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure")); //exit (0); } - + GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files GDCM_NAME_SPACE::DirListType fileNames; @@ -331,7 +481,6 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr { std::cout << "--- --- [" << *it << "] is a file.." << std::endl; } - } for (it = fileNames.begin(); @@ -343,7 +492,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr if (verbose) std::cout << "--- --- [" << *it << "] is a directory" << std::endl; - + // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), // GDCM_NAME_SPACE::GDCM_FILESEPARATOR, // GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); @@ -378,18 +527,32 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr GDCM_NAME_SPACE::GDCM_FILESEPARATOR, GDCM_NAME_SPACE::Util::GetName(*it).c_str(), str_isa_func_name.c_str()); - } - DealWithNiveau3(*it, outputDirName); + } + std::string strOutputDirName(outputDirName); + try { + DealWithNiveau3(*it, strOutputDirName); + } + catch (BrukerHopelessException &e) + { + std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); " + << " We skip [" << level2Directory << "]" << std::endl; + continue; + } + catch (BrukerInitException &e) + { + std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); " + << " We skip [" << level2Directory << "]" << std::endl; + continue; + } } } } - // // ===================================================================== // -void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){ +void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName){ // // e.g. at level 3, in @@ -403,7 +566,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; - throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure")); + throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure")); //exit (0); } @@ -413,6 +576,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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]; @@ -422,12 +586,12 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough! bool canOpen; - + //-------------- try d3proc; char char_d3proc[(unsigned int) PATH_MAX+2]; sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" ); - + if (verbose) std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl; std::string str_d3proc(char_d3proc); @@ -447,10 +611,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'")); //exit(0); /// \TODO throw an exception ! } - + //-------------- end try d3proc; - - + + // -------------------try reco char char_reco[(unsigned int) PATH_MAX+2]; @@ -460,8 +624,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // GDCM_NAME_SPACE::GDCM_FILESEPARATOR + // "d3proc"; if (verbose) - std::cout << "reco --- => [" << char_reco << "]" << std::endl; - std::string str_reco(char_reco); + std::cout << "reco: --- => [" << char_reco << "]" << std::endl; + + std::string str_reco(char_reco); canOpen = br_reco.LoadFile(str_reco); if (!canOpen) // we try in directory ../1 @@ -471,7 +636,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory); //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName); sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" ); - str_reco=char_reco; + //str_reco=char_reco; canOpen = br_reco.LoadFile(str_reco); if (!canOpen) { @@ -479,19 +644,25 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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'")); - //exit(0); /// \TODO throw an exception ! - } + throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'")); + //exit(0); /// \TODO throw an exception ! + } 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 @@ -506,36 +677,84 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles"); - res = CreateDirectory( currentOutputMhdDirName ); + std::string strCurrentOutputMhdDirName(currentOutputMhdDirName); + + res = CreateDirectory( strCurrentOutputMhdDirName ); if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'")); @@ -553,7 +772,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr int k; int nbInstants = nbFrames/nbSlices; if (verbose) - std::cout << "nbInstants (deduced )" << nbInstants << std::endl; + std::cout << "nbInstants (deduced)" << nbInstants << std::endl; int instantNb; int sliceNb; FILE *fp; // for MHD files @@ -568,11 +787,19 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr fp = fopen(original2dseqName, "rb"); if (!fp) { - std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl; - throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'")); - //exit (0); + // try 2dseq_Angio2D ?!? + + sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D"); + 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); @@ -584,10 +811,13 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr } catch (BrukerInitException& e) { - std::cout << "Exception " << e.what() << std::endl; - return; + if (verbose) + std::cout << "an Init Exception was thrown in CreateImageSet ( ); " << e.what() + << "catched in DealWithNiveau3" << std::endl; + //return; + throw (e); } - + serieNumber++; strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives) @@ -613,7 +843,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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",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" ); @@ -642,16 +873,17 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr { sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR); - + /* ----------- Write Dicom Image ---------------*/ MakeDicomImage(buffer_2dseq, NX, NY, nbFrames, pixelSize, - fovX/NY, fovY/NY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, output2dseqSliceFileName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, @@ -663,12 +895,11 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr ); } // 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; @@ -698,8 +929,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants); fprintf(fp, "HeaderSize = %d\n", 0); - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie - fprintf(fp, "Position = 0 0 %d\n", sliceNb ); + //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // + fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie + fprintf(fp, "Position = 0 0 %d\n", sliceNb ); fprintf(fp, "Offset = 0 0 0\n" ); fprintf(fp, "CenterOfRotation = 0 0 0\n" ); fprintf(fp, "ElementNumberOfChannels = 1\n" ); @@ -726,6 +958,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 1, fp); } fclose(fp); + // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl; } // end if mhd @@ -782,9 +1015,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr NY, nbInstants, pixelSize, - fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, output2dseqSliceFileName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, @@ -805,13 +1039,13 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr } // end nbInstants == 1 delete [] buffer_2dseq; /**/ - - + + // ----------------------------------------------------- // deal with MatLab-generated Carto file. // ----------------------------------------------------- - - dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance, + + dealWithCarto(fileNames, NX, NY, nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance, copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName); } @@ -819,7 +1053,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // =========================================================================================== void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices, - double fovX, double fovY, double sliceDistance, + /*double fovX, double fovY, */ + double spatResolX, double spatResolY, double sliceDistance, char *copyFile, std::string ¤tOutputDirName, char *outputMhdFileName, char *output2dseqCartoName) { @@ -827,12 +1062,14 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX // deal with MatLab-generated Carto file. // ----------------------------------------------------- - char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak" , ""}; // add more carto file name identifiers if necessary; end with "" - int icode; + const char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with "" + const char *separator[] = { "_", ".", "-", "" }; // add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with "" + int icode; + int iseparator; GDCM_NAME_SPACE::DirListType::iterator it; char file_name_ident[500]; FILE *fp; - + // Iterate to ALL the objets(files/directories) found in the input directory for (it = fileNames.begin(); it != fileNames.end(); @@ -844,28 +1081,33 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX if (verbose) std::cout << "--- [" << *it << "] is a file..." << std::endl; - icode = 0; - + icode = 0; while (code[icode][0] != 0) + { + iseparator = 0; + while (separator[iseparator][0] != 0) { - sprintf(file_name_ident, "2dseq_%s",code[icode]); // e.g "2dseq_ADC" + sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g "2dseq_ADC" + //if (verbose) + // std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl; std::string::size_type loc = (*it).rfind(file_name_ident); if ( loc != std::string::npos ) { - + ///\ TODO : find a safer way to be sure to read everything! unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices]; fp = fopen ( (*it).c_str(), "rb"); if (!fp){ std::cout << "Cannot open [" << *it << "] for reading" << std::endl; - + throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file ")); } fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp); + // ?!? sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() , std::cout << "Deal with Carto file :[" <<*it << "], computed length : " << NX*NY*sizeof(double)*nbSlices << std::endl; - std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str()); + std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str()); if (mhd) { // Copy the data file in the new directory @@ -873,10 +1115,10 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str()); system(copyFile); sprintf(outputMhdFileName, "%s%c%s%s", - currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" ); + currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" ); if (verbose) std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl; - + FILE *fp; fp=fopen(outputMhdFileName, "w"); if (!fp) @@ -890,9 +1132,8 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX fprintf(fp, "BinaryData = True \n" ); fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices); - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance ); 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 0\n" ); fprintf(fp, "Offset = 0 0 0\n" ); fprintf(fp, "CenterOfRotation = 0 0 0\n" ); @@ -922,9 +1163,10 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX NY, nbSlices, 8, // pixelSize - fovX/NY, fovY/NY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, output2dseqCartoName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, @@ -940,18 +1182,58 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX if (verbose) std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl; break; // don't check for more ident on same file name! + + } // end deal with _ADC, -adc, etc + iseparator ++; + } // end iterate speparators + icode++; + } // end iterate code + } // end boost::filesystem::is_regular(*it) + } // end iterate on all objects (files, dir, etc) +} // end method - } - icode++; - } - } - } // end iterate on files + +// ========================================================================================================== + +int Bruker2Dicom::CheckUserDirectory(std::string &userDirName) +{ + GDCM_NAME_SPACE::DirList dirList(userDirName, false, true); // DON'T get recursively the list of files + + GDCM_NAME_SPACE::DirListType fileNames; + fileNames = dirList.GetFilenames(); + + std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())); + + std::string subject = path + + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + + "subject"; + + std::string acqp = path + + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + + "acqp"; + + 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(std::string OutputDirName) +bool Bruker2Dicom::CreateDirectory(std::string &OutputDirName) { std::string systemCommand; @@ -960,8 +1242,7 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName) < Bruker2Dicom::CreateImageSet ( ) 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 ("Bruker2Dicom::CreateImageSet failure ") ); + throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); } br_acqp.SetImageLoopStructure(); @@ -1126,7 +1404,7 @@ std::vector Bruker2Dicom::CreateImageSet ( ) imageOrientation = imageSet[i].getRotationMatrixRPS2XYZ(); std::cout << "\t Orientation " ; for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++) - std::cout << imageOrientation[i1][i2] << " "; + std::cout << imageOrientation[i1][i2] << " ";CreateImageSet //std::cout << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition(); std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition(); @@ -1206,20 +1484,32 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, // 0018 0050 DS 1 Slice Thickness str.str(""); str << sliceDistance; - file->InsertEntryString(str.str(),0x0018,0x0050, "DS"); + 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"); @@ -1229,10 +1519,10 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, /// \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(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 + 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"); @@ -1259,7 +1549,6 @@ std::cout << "charImageOrientation " << file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS"); - // 0020 0032 DS 3 Image Position (Patient) char charImagePosition[256]; @@ -1269,8 +1558,6 @@ std::cout << "charImageOrientation " << imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]); file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient) - - // 0020 0x1041 DS 1 Slice Location // sprintf(charImagePosition,"%f",float(imgNum)); @@ -1299,15 +1586,16 @@ std::cout << "charImageOrientation " << fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize); fileH->SetWriteModeToRaw(); fileH->SetWriteTypeToDcmExplVR(); - if( !fileH->Write(dcmImageName)) + if( !fileH->Write(dcmImageName)) { std::cout << "Failed for [" << dcmImageName << "]\n" - << " File is unwrittable" << std::endl; - - if (verbose) - file->Print(); + << " 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(); } - -