X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=813fdc5f8850cfc829aac495ebd64d25c5d1c686;hb=aa5fda796c3871968581d68fb26a13723370d5fc;hp=eac2702eb6f9c6d6e2c6901efdb822b757552f1c;hpb=11a9650af17244f38034d70edf3c638274c8a01c;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index eac2702..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() ); @@ -403,7 +426,13 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr 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; + } } } } @@ -437,6 +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]; @@ -509,13 +539,12 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (!canOpen) { std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl; - throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'")); + 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 @@ -549,6 +578,13 @@ 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 slices, etc) @@ -592,9 +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]; @@ -608,8 +652,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr } catch (BrukerInitException& e) { - std::cout << "an Exception was throw in CreateImageSet ( ); " << e.what() - << "catched in DealWithNiveau3" << std::endl; + if (verbose) + std::cout << "an Init Exception was thrown in CreateImageSet ( ); " << e.what() + << "catched in DealWithNiveau3" << std::endl; //return; throw (e); } @@ -639,7 +684,8 @@ 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" ); @@ -675,9 +721,10 @@ 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, @@ -694,7 +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; @@ -724,8 +770,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); 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 ); // slice distance : no meaning for temporal serie - fprintf(fp, "Position = 0 0 %d\n", sliceNb ); + //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // + 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" ); fprintf(fp, "ElementNumberOfChannels = 1\n" ); @@ -808,9 +855,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr NY, nbInstants, pixelSize, - fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, output2dseqSliceFileName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, @@ -837,7 +885,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // deal with MatLab-generated Carto file. // ----------------------------------------------------- - dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance, + dealWithCarto(fileNames, NX, NY, nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance, copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName); } @@ -845,7 +893,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // =========================================================================================== void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices, - double fovX, double fovY, double sliceDistance, + /*double fovX, double fovY, */ + double spatResolX, double spatResolY, double sliceDistance, char *copyFile, std::string ¤tOutputDirName, char *outputMhdFileName, char *output2dseqCartoName) { @@ -853,8 +902,10 @@ 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 "" - int icode; + 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 "" + int icode; + int iseparator; GDCM_NAME_SPACE::DirListType::iterator it; char file_name_ident[500]; FILE *fp; @@ -870,11 +921,15 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX if (verbose) std::cout << "--- [" << *it << "] is a file..." << std::endl; - icode = 0; - + icode = 0; while (code[icode][0] != 0) + { + iseparator = 0; + while (separator[iseparator][0] != 0) { - sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g "2dseq_ADC" + sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g "2dseq_ADC" + //if (verbose) + // std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl; std::string::size_type loc = (*it).rfind(file_name_ident); if ( loc != std::string::npos ) @@ -889,9 +944,10 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX } fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp); + // ?!? sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() , std::cout << "Deal with Carto file :[" <<*it << "], computed length : " << NX*NY*sizeof(double)*nbSlices << std::endl; - std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str()); + std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str()); if (mhd) { // Copy the data file in the new directory @@ -899,7 +955,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str()); system(copyFile); sprintf(outputMhdFileName, "%s%c%s%s", - currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" ); + currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" ); if (verbose) std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl; @@ -916,9 +972,8 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX fprintf(fp, "BinaryData = True \n" ); fprintf(fp, "BinaryDataByteOrderMSB = False\n" ); fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices); - fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance ); 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, "Position = 0 0 0\n" ); fprintf(fp, "Offset = 0 0 0\n" ); fprintf(fp, "CenterOfRotation = 0 0 0\n" ); @@ -948,9 +1003,10 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX NY, nbSlices, 8, // pixelSize - fovX/NY, fovY/NY, sliceDistance, + //fovX/NY, fovY/NY, sliceDistance, + spatResolX, spatResolY, sliceDistance, output2dseqCartoName, - strPatientName, + subject_name, day, strStudyUID, strSerieUID, @@ -966,13 +1022,15 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX if (verbose) std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl; break; // don't check for more ident on same file name! - - } - icode++; - } - } - } // end iterate on files -} + + } // end deal with _ADC, -adc, etc + iseparator ++; + } // end iterate speparators + icode++; + } // end iterate code + } // end boost::filesystem::is_regular(*it) + } // end iterate on all objects (files, dir, etc) +} // end method // ========================================================================================================== @@ -1007,7 +1065,7 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName) else { if (verbose) - std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl; + std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl; } return 1; @@ -1118,11 +1176,12 @@ std::vector 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 ("Bruker2Dicom::CreateImageSet failure ") ); + throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); } br_acqp.SetImageLoopStructure(); @@ -1153,7 +1212,7 @@ 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(); @@ -1346,8 +1405,8 @@ std::cout << "charImageOrientation " << fileH->Delete(); throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file ")); } - if (verbose) - file->Print(); + //if (verbose) + // file->Print(); file->Delete(); fileH->Delete();