X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=eac2702eb6f9c6d6e2c6901efdb822b757552f1c;hb=11a9650af17244f38034d70edf3c638274c8a01c;hp=710129b778aaac8994e8f5d27330b037def324b2;hpb=64f789199d7c134627b31cfaee6e67eb012f48bb;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 710129b..eac2702 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -1,9 +1,10 @@ #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 @@ -30,7 +31,8 @@ bool Bruker2Dicom::Execute() 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); @@ -71,7 +73,8 @@ bool Bruker2Dicom::Execute() if (!canOpen) { std::cout << "Hopeless! no 'subject' found" << std::endl; - exit(0); /// \TODO throw an exception ! + throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory ")); + //exit(0); /// \TODO throw an exception ! } else { @@ -79,40 +82,41 @@ bool Bruker2Dicom::Execute() } //br_subject.PrintSelf(); - // get info for 'Study Description' - + // get info for 'Study Description' BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); std::string subject_name = b_name.GetStringValue()[0]; - strPatientName = subject_name; + 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); - + 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); - + 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; + 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); + subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2); cleanString(subject_date); - - strStudyDescr = subject_name + "." + subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; + + // subject_name is already in 'Patient Name' + strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; char outputDirName[(unsigned int) PATH_MAX+2]; 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) @@ -156,38 +160,35 @@ bool Bruker2Dicom::Execute() cleanString(acqp_method); BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size"); - b_list_size.PrintSelf(); //JP + //b_list_size.PrintSelf(); //JP nbSlices = b_list_size.GetIntValue()[0]; strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it) - + "." + acqp_protocol_location + /* + "." + acqp_protocol_location */ // always the same (in each acquisition) + "." + acqp_scan_name + "." + acqp_method.c_str(); sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, strSerieDescr.c_str() ); - + std::cout << " ================================================================================\n" - << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n" + << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n" << " ================================================================================" << std::endl; -/* - 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" - << " ================================================================================" - << 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 } @@ -205,7 +206,8 @@ 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; @@ -272,8 +274,11 @@ 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) @@ -291,7 +296,14 @@ 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; + } } } } @@ -309,7 +321,8 @@ 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 @@ -381,8 +394,16 @@ 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); + } + try { + DealWithNiveau3(*it, outputDirName); + } + catch (BrukerHopelessException &e) + { + std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); " + << " We skip [" << level2Directory << "]" << std::endl; + continue; + } } } } @@ -406,7 +427,8 @@ 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 @@ -431,21 +453,23 @@ 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 << "try d3proc: --- => [" << 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; @@ -460,7 +484,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // GDCM_NAME_SPACE::GDCM_FILESEPARATOR + // "d3proc"; if (verbose) - std::cout << "try reco --- => [" << char_reco << "]" << std::endl; + std::cout << "reco --- => [" << char_reco << "]" << std::endl; std::string str_reco(char_reco); canOpen = br_reco.LoadFile(str_reco); @@ -475,8 +499,9 @@ 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 ! } } @@ -484,7 +509,8 @@ 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(); @@ -496,16 +522,19 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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, ...} @@ -533,18 +562,22 @@ 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 @@ -560,7 +593,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (!fp) { std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl; - exit (0); + throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'")); + //exit (0); } unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants]; @@ -569,12 +603,23 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // This one will be important! // --------------------------- - imageSet = CreateImageSet ( ); + try { + imageSet = CreateImageSet ( ); + } + catch (BrukerInitException& e) + { + std::cout << "an Exception was throw 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_All_the_Slices.mhd", currentOutputMhdDirName, @@ -583,7 +628,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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 { @@ -608,12 +654,14 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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) @@ -633,9 +681,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr day, strStudyUID, strSerieUID, - strStudyDescr, + strStudyDescr, strSerieDescr, - strStudyTimeDate, + strStudyTimeDate, 0,// index frame number GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE ); @@ -652,8 +700,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr k = 0; for (sliceNb=0; sliceNb Bruker2Dicom::CreateImageSet ( ) 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 ") ); + } br_acqp.SetImageLoopStructure(); br_acqp.SetBrukerImageList(); @@ -1125,7 +1182,7 @@ 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 ) @@ -1176,14 +1233,27 @@ 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] @@ -1199,10 +1269,10 @@ 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"); @@ -1211,7 +1281,7 @@ 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] << " " << @@ -1269,10 +1339,13 @@ 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; - + << " File is unwrittable" << std::endl; + file->Delete(); + fileH->Delete(); + throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file ")); + } if (verbose) file->Print();