X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=6e97c5bd0f59c0afaab7a1a7971d11bc56ea328c;hb=1d72babed2631bf4c953b43164d6088149bc3e4e;hp=bdf1e4d73aa2b32dbe31c3bfd62061df758d9059;hpb=4733eef5b89801ea0b0e799569677b1c4abc3203;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index bdf1e4d..6e97c5b 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -11,7 +11,7 @@ bool Bruker2Dicom::Execute() { - // ----- Check input values ----- + // ----- Check input directory name ----- bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(); @@ -27,6 +27,8 @@ 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) { @@ -68,61 +70,107 @@ 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; - throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory ")); - //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_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); + 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"; + + // 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 ")); + } + + std::string subject_entry; + std::string subject_position; + std::string subject_date; + std::string subject_study_name; - 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); + 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"); - std::string subject_date = b_date.GetStringValue()[0]; - strStudyTimeDate = subject_date; - cleanString(subject_date); + 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"); - 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); - - // subject_name is already in 'Patient Name' - strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + 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(); @@ -143,6 +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; @@ -150,26 +199,32 @@ 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() ); @@ -193,7 +248,6 @@ bool Bruker2Dicom::Execute() } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it } - // ===================================================================== void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) { @@ -297,7 +351,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr 7 1 */ try { - DealWithNiveau2(*it,outputDirName ); + DealWithNiveau2(*it, outputDirName); } catch (BrukerHopelessException &e) { @@ -443,6 +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]; @@ -521,7 +576,6 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr //std::cout << "------------------------------------------------------------------------------------------------" << std::cout; // br_reco.PrintSelf(); // std::cout << "------------------------------------------------------------------------------------------------" << std::cout; - // -------------------end try reco @@ -605,9 +659,17 @@ 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]; @@ -654,7 +716,7 @@ 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, spatResolX, 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" ); @@ -691,9 +753,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr nbFrames, pixelSize, //fovX/NY, fovY/NY, sliceDistance, - spatResolX, spatResolX, sliceDistance, + spatResolX, spatResolY, sliceDistance, output2dseqSliceFileName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, @@ -710,7 +772,6 @@ 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]; k = 0; @@ -741,7 +802,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 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 ); // - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolX, 1.0 ); //slice distance : no meaning for temporal serie + 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" ); @@ -828,7 +889,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr spatResolX, spatResolY, sliceDistance, //fovX/NY, fovY/NY, sliceDistance, output2dseqSliceFileName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, @@ -976,7 +1037,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX //fovX/NY, fovY/NY, sliceDistance, spatResolX, spatResolY, sliceDistance, output2dseqCartoName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID,