X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=961c8e7e9a2891622fe588db9b4780919e2816e8;hb=bcce50eae2804247af45026ca20665a22ff073a3;hp=5c128578204ba3e1593da1d7e1ff9f8a5be9f995;hpb=aa4485dd557470a0a7a5e6c1891ddb255d88ee4d;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 5c12857..961c8e7 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -35,68 +35,153 @@ 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; - // 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; - - bool subjectFound; - canOpen =br_subject.LoadFile(subject); - if (!canOpen) + 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; + 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 ")); - - std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl; - subjectFound = false; - } - else - { - br_subject.FillMap(); - subjectFound = true; - } + 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' - 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_name=br_subject.GetFieldData("SUBJECT_name_string"); + subject_name = b_name.GetStringValue()[0]; + strPatientName = subject_name; + cleanString(subject_name); + DealWithSingleStudyDirectory (fileNames); + break; + } + + 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 *non recursive* 'set of studies' directory! (recursive 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; + } + } +} + +// ---------------------------------------------------------------------------------------------------------- + +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; @@ -105,15 +190,12 @@ bool Bruker2Dicom::Execute() 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) { + + std::cout << "===================================--===========nom dir [" << tempStringPatDir << "] subjectFound, studyName : " << subject_study_name<< std::endl; BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry"); subject_entry = b_entry.GetStringValue()[0]; //cleanString(subject_entry); @@ -136,6 +218,8 @@ bool Bruker2Dicom::Execute() } else // Desperate trick when file 'subject' is missing { + + std::cout << "==============================================nom dir [" << tempStringPatDir << "] subjectFound" << std::endl; subject_entry = "HeadFirst"; // Why not? subject_position = "Supine"; // Why not? strStudyTimeDate = "06_06_06_6_June_1666"; // Why not? @@ -168,6 +252,7 @@ bool Bruker2Dicom::Execute() // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie // ----------------------------------------------------- + /// \TODO better use directory iterator, from boost! // JPR GDCM_NAME_SPACE::DirListType::iterator it; for (it = fileNames.begin(); @@ -179,6 +264,10 @@ bool Bruker2Dicom::Execute() if (verbose) std::cout << "[" << *it << "] is a directory" << std::endl; + //if((*it) == "AdjResult") // avoid trouble with new version 'AdjResult' directory + if(GDCM_NAME_SPACE::Util::GetName(*it) == "AdjResult") + continue; + //BrukerDataSet br_acqp; std::string strAcqp; strAcqp = (*it) + @@ -221,7 +310,7 @@ bool Bruker2Dicom::Execute() + "." + acqp_scan_name + "." + acqp_method.c_str(); - sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(), //OutputDirName.c_str(), + sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(), //OutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, strSerieDescr.c_str() ); @@ -229,11 +318,11 @@ bool Bruker2Dicom::Execute() << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n" << " ================================================================================" << std::endl; - + std::string strOutputDirName(outputDirName); if (verbose) - printf ("outputDirName [%s]\n", outputDirName); + printf ("outputDirName [%s]\n", outputDirName); try { - DealWithNiveau1(*it, outputDirName); + DealWithNiveau1(*it, strOutputDirName); } catch (BrukerHopelessException &e) { @@ -246,7 +335,7 @@ bool Bruker2Dicom::Execute() // ===================================================================== -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 // @@ -305,6 +394,7 @@ 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; @@ -347,7 +437,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr 7 1 */ try { - DealWithNiveau2(*it, outputDirName); + DealWithNiveau2(*it, strOutputDirName); } catch (BrukerHopelessException &e) { @@ -360,7 +450,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr // ===================================================================== -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 // @@ -444,8 +534,9 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr GDCM_NAME_SPACE::Util::GetName(*it).c_str(), str_isa_func_name.c_str()); } + std::string strOutputDirName(outputDirName); try { - DealWithNiveau3(*it, outputDirName); + DealWithNiveau3(*it, strOutputDirName); } catch (BrukerHopelessException &e) { @@ -467,7 +558,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr // ===================================================================== // -void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){ +void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName){ // // e.g. at level 3, in @@ -667,7 +758,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr { 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'")); @@ -685,7 +778,7 @@ 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 @@ -757,7 +850,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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, "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" ); @@ -871,6 +964,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 1, fp); } fclose(fp); + // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl; } // end if mhd @@ -974,8 +1068,8 @@ 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 "" - char *separator[] = { "_", ".", "-", "" }; // add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with "" + 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; @@ -1105,9 +1199,47 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX } // end method +// ========================================================================================================== + +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; @@ -1116,8 +1248,7 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName) <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 @@ -1391,6 +1515,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, // 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"); @@ -1430,7 +1555,6 @@ std::cout << "charImageOrientation " << file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS"); - // 0020 0032 DS 3 Image Position (Patient) char charImagePosition[256]; @@ -1440,8 +1564,6 @@ 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)); @@ -1483,5 +1605,3 @@ std::cout << "charImageOrientation " << file->Delete(); fileH->Delete(); } - -