X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=813fdc5f8850cfc829aac495ebd64d25c5d1c686;hb=aa5fda796c3871968581d68fb26a13723370d5fc;hp=bdf1e4d73aa2b32dbe31c3bfd62061df758d9059;hpb=4733eef5b89801ea0b0e799569677b1c4abc3203;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index bdf1e4d..813fdc5 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) { @@ -84,45 +86,66 @@ bool Bruker2Dicom::Execute() // 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); + BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); + subject_name = b_name.GetStringValue()[0]; + strPatientName = subject_name; + cleanString(subject_name); + + // 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 ")); + } + + 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_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_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); - - // 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"); + 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_study_name); + // 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(); @@ -169,7 +192,7 @@ bool Bruker2Dicom::Execute() + "." + 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() ); @@ -443,6 +466,7 @@ 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 +545,6 @@ 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 +628,17 @@ 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 +685,7 @@ 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 +722,9 @@ 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 +741,6 @@ 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 +771,7 @@ 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 +858,7 @@ 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 +1006,7 @@ 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,