X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=6e97c5bd0f59c0afaab7a1a7971d11bc56ea328c;hb=1d72babed2631bf4c953b43164d6088149bc3e4e;hp=87997d991c067abd2b43f827606ab68f7cb569da;hpb=c23d68fe2d14a4c4f4b164fdc447f38247f0efc3;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 87997d9..6e97c5b 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -1,18 +1,22 @@ #include "bruker2dicom.h" +#include +#include +#include "brukerexception.h" #ifndef PATH_MAX // If not defined yet : do it - #define PATH_MAX 2048 + #define PATH_MAX 2048 #endif bool Bruker2Dicom::Execute() { - // ----- Begin Processing ----- + // ----- Check input directory name ----- bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(); - if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) ) + //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) ) + if ( ! boost::filesystem::is_directory(InputDirName) ) { std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl; return 0; @@ -23,18 +27,21 @@ 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) { std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl; - exit (0); + //exit (0); + 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; @@ -55,6 +62,7 @@ bool Bruker2Dicom::Execute() bool canOpen; std::string outputFileName; + // BrukerDataSet br_subject; std::string subject; subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+ @@ -62,69 +70,114 @@ bool Bruker2Dicom::Execute() "subject"; if (verbose) std::cout << " Subject : [" << subject << "]" << std::endl; - canOpen =br_subject.LoadFile(subject); - + + bool subjectFound; + canOpen =br_subject.LoadFile(subject); if (!canOpen) { - std::cout << "Hopeless! no 'subject' found" << std::endl; - exit(0); /// \TODO throw an exception ! + //std::cout << "Hopeless! no 'subject' found" << std::endl; + //throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory ")); + + std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl; + subjectFound = false; } else { - br_subject.FillMap(); + br_subject.FillMap(); + subjectFound = true; } //br_subject.PrintSelf(); - // get info for 'Study Description' - - /* - BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location"); - acqp_protocol_location = b_protocol_location.GetStringValue()[0]; - cleanString(acqp_protocol_location); -*/ - BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); - std::string subject_name = b_name.GetStringValue()[0]; - strPatientName = subject_name; - cleanString(subject_name); - - 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); + // get info for 'Study Description' + + if (subjectFound) + { + BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); + subject_name = b_name.GetStringValue()[0]; + strPatientName = subject_name; + cleanString(subject_name); + } + else + subject_name ="defaultPatName"; - 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); + // creation directory : 'nom du patient' + std::string tempStringPatDir(OutputDirName); + tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name; - 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); + res=CreateDirectory(tempStringPatDir); + if (!res) { + std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl; + throw ( BrukerHopelessException ("Patient directory creation failure ")); + } + + std::string subject_entry; + std::string subject_position; + std::string subject_date; + std::string subject_study_name; + + 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; - strStudyDescr = subject_name + "-" + subject_study_name + "-" + subject_entry + "-" + subject_position + "-" + subject_date; - + 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(); - + 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(); it != fileNames.end(); ++it) { - if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_directory(*it) ) { if (verbose) std::cout << "[" << *it << "] is a directory" << std::endl; @@ -138,6 +191,7 @@ 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; @@ -145,47 +199,55 @@ 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 - + "-" + acqp_scan_name - + "-" + acqp_method.c_str(); + /* + "." + 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() ); - + std::cout << " ================================================================================\n" - << " ========================= [" << GDCM_NAME_SPACE::Util::GetName(*it).c_str() - << acqp_protocol_location.c_str() - << acqp_scan_name.c_str() - << acqp_method.c_str() - << "]\n" + << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n" << " ================================================================================" << std::endl; + if (verbose) printf ("outputDirName [%s]\n", outputDirName); - - DealWithNiveau1(*it, outputDirName); + try { + DealWithNiveau1(*it, outputDirName); + } + 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) { @@ -198,7 +260,8 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; - exit (0); + throw ( BrukerHopelessException ("Level 1 output directory creation failure ")); + // exit (0); } GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files GDCM_NAME_SPACE::DirListType fileNames; @@ -212,10 +275,11 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr it != fileNames.end(); ++it) { - if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_regular(*it) ) + //if ( ! boost::filesystem::is_directory(*it) ) { if (verbose) - std::cout << "--- [" << *it << "] is a file" << std::endl; + std::cout << "--- [" << *it << "] is a file." << std::endl; } } @@ -226,7 +290,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr it != fileNames.end(); ++it) { - if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_directory(*it) ) { // will be always "pdata" ... if (verbose) @@ -264,8 +328,11 @@ 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; - exit(0); /// \TODO throw an exception ! + 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 ! } } if (verbose) @@ -283,7 +350,14 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr ##$PVM_SPackArrNSlices=( 2 ) 7 1 */ - DealWithNiveau2(*it,outputDirName ); + try { + DealWithNiveau2(*it, outputDirName); + } + catch (BrukerHopelessException &e) + { + std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl; + continue; + } } } } @@ -301,7 +375,8 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; - exit (0); + 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 @@ -322,9 +397,9 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr it != fileNames.end(); ++it) { - if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( ! boost::filesystem::is_directory(*it) ) { - std::cout << "--- --- [" << *it << "] is a file" << std::endl; + std::cout << "--- --- [" << *it << "] is a file.." << std::endl; } } @@ -333,7 +408,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr it != fileNames.end(); ++it) { - if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_directory(*it) ) { if (verbose) @@ -369,12 +444,26 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr str_isa_func_name = b_isa_func_name.GetStringValue()[0]; cleanString(str_isa_func_name); - sprintf(outputDirName, "%s%c%s-%s", currentOutputDirName.c_str(), + sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, GDCM_NAME_SPACE::Util::GetName(*it).c_str(), str_isa_func_name.c_str()); - } - DealWithNiveau3(*it, outputDirName); + } + try { + DealWithNiveau3(*it, outputDirName); + } + 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; + } } } } @@ -398,7 +487,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; - exit (0); + throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure")); + //exit (0); } GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files @@ -407,6 +497,7 @@ 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]; @@ -423,21 +514,23 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" ); if (verbose) - std::cout << "--- => [" << char_d3proc << "]" << std::endl; + std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl; std::string str_d3proc(char_d3proc); canOpen = br_d3proc.LoadFile(str_d3proc); if (!canOpen) { std::cout << "Hopeless! no 'd3proc' found" << std::endl; - exit(0); /// \TODO throw an exception ! + throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found")); + //exit(0); /// \TODO throw an exception ! } canOpen = br_d3proc.FillMap(); if (!canOpen) { std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl; - exit(0); /// \TODO throw an exception ! + throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'")); + //exit(0); /// \TODO throw an exception ! } //-------------- end try d3proc; @@ -452,7 +545,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // GDCM_NAME_SPACE::GDCM_FILESEPARATOR + // "d3proc"; if (verbose) - std::cout << "--- => [" << char_reco << "]" << std::endl; + std::cout << "reco --- => [" << char_reco << "]" << std::endl; std::string str_reco(char_reco); canOpen = br_reco.LoadFile(str_reco); @@ -467,8 +560,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr canOpen = br_reco.LoadFile(str_reco); if (!canOpen) { - std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl; - exit(0); /// \TODO throw an exception ! + std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl; + throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'")); + //exit(0); /// \TODO throw an exception ! } } @@ -476,28 +570,31 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (!canOpen) { std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl; - exit(0); /// \TODO throw an exception ! + throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'")); + //exit(0); /// \TODO throw an exception ! } //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]; - std::cout << "IM_SIX " << NX << std::endl; + if (verbose) + std::cout << "IM_SIX " << NX << std::endl; BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY"); int NY = bY.GetIntValue()[0]; - std::cout << "IM_SIY " << NY << std::endl; + 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]; - std::cout << "IM_SIZ " << nbFrames << std::endl; + 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, ...} @@ -512,9 +609,16 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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; + /// \TODO probabely a more sophisticated accessor will be necessary : - /// (cf : non contiguous slices, overlapping, slice thickness, space between clices, etc) + /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc) BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance"); double sliceDistance = bsliceDistance.GetDoubleValue()[0]; @@ -525,18 +629,22 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr res = CreateDirectory( currentOutputMhdDirName ); if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; - exit (0); + throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'")); + //exit (0); } if (verbose) std::cout << "Directory creation [" << currentOutputDirName << "]" << std::endl; } // end if mhd - std::cout << "nbFrames " << nbFrames << std::endl; - std::cout << "nbSlices " << nbSlices << std::endl; + if (verbose) + std::cout << "nbFrames " << nbFrames << std::endl; + if (verbose) + std::cout << "nbSlices " << nbSlices << std::endl; int k; int nbInstants = nbFrames/nbSlices; - std::cout << "nbInstants (deduced )" << nbInstants << std::endl; + if (verbose) + std::cout << "nbInstants (deduced )" << nbInstants << std::endl; int instantNb; int sliceNb; FILE *fp; // for MHD files @@ -551,31 +659,53 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr fp = fopen(original2dseqName, "rb"); if (!fp) { - std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl; - 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]; + 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! // --------------------------- - imageSet = CreateImageSet ( ); + 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++; strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives) { - std::cout << "Single instant : do not split" << std::endl; + if (verbose) + std::cout << "Single instant : do not split" << std::endl; if (mhd) { - sprintf(outputMhdFileName, "%s%cMhdData_Toutes_les_Slices.mhd", currentOutputMhdDirName, + sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName, GDCM_NAME_SPACE::GDCM_FILESEPARATOR); fp=fopen(outputMhdFileName, "w"); if (!fp) { std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl; - exit(0); + throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting")); + //exit(0); } else { @@ -585,32 +715,35 @@ 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" ); fprintf(fp, "ElementNumberOfChannels = 1\n" ); fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() ); - fprintf(fp, "ElementDataFile = %s\n", "../2dseq_toutes_les_Slices" ); + fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" ); fclose(fp); } - sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices", + sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR); fp=fopen(output2dseqSliceFileName, "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 ++; strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); } // end if mhd if (dicom) { - sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices.dcm", + sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR); /* ----------- Write Dicom Image ---------------*/ @@ -619,15 +752,16 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr NY, nbFrames, pixelSize, - fovX/NY, fovY/NY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, output2dseqSliceFileName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, - strStudyDescr, + strStudyDescr, strSerieDescr, - strStudyTimeDate, + strStudyTimeDate, 0,// index frame number GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE ); @@ -638,14 +772,13 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr { // Interleaved ! // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ... - - unsigned char * pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants]; + unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants]; k = 0; for (sliceNb=0; sliceNb 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 ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); + } br_acqp.SetImageLoopStructure(); br_acqp.SetBrukerImageList(); @@ -1087,7 +1243,7 @@ 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(); @@ -1101,7 +1257,6 @@ std::vector Bruker2Dicom::CreateImageSet ( ) return imageSet; } - // =========================================================================================== void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, @@ -1117,7 +1272,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, std::string &serieUID, std::string &studyDescr, std::string &serieDescr, - std::string &strStudyTimeDate, + std::string &strStudyTimeDate, int imgNum, GDCM_NAME_SPACE::ImageContentType contentType ) @@ -1168,14 +1323,27 @@ 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] @@ -1191,10 +1359,10 @@ 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"); @@ -1203,7 +1371,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, char charImageOrientation[256]; /* -std::cout << "try charImageOrientation " << +std::cout << "charImageOrientation " << imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " << imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " << imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " << @@ -1261,12 +1429,15 @@ std::cout << "try 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();