X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=02419461abdf7ba848809af178db1d87b7e0b56f;hb=40ddbaaf47ea11957bb59444f4a8d6aa57d75c2b;hp=5c128578204ba3e1593da1d7e1ff9f8a5be9f995;hpb=aa4485dd557470a0a7a5e6c1891ddb255d88ee4d;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 5c12857..0241946 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -12,7 +12,7 @@ bool Bruker2Dicom::Execute() // ----- Check input directory name ----- bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(); - + //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) ) if ( ! boost::filesystem::is_directory(InputDirName) ) { @@ -35,83 +35,161 @@ 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(); + + // get info for 'Study Description' + 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; + } } - //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"; - +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) ) + { + subjectFound = false; + if (verbose) + std::cout << "in 'DealWithMultiStudyDirectory' [" << *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(); + subjectFound = true; // Hope so! (full checking needed!) + + 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; - + 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; - if (subjectFound) { BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry"); @@ -143,19 +221,22 @@ bool Bruker2Dicom::Execute() 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; - + if (0) // We don't realy need so much information for 'Study' + strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; + else + 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(); @@ -167,7 +248,8 @@ bool Bruker2Dicom::Execute() // (this is level ZERO) // 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 +261,10 @@ 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) + @@ -207,13 +293,13 @@ bool Bruker2Dicom::Execute() BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method"); b_method.PrintSelf(); 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"); //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) @@ -221,19 +307,19 @@ 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() ); - + std::cout << " ================================================================================\n" << " === [" << 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 +332,7 @@ 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 +391,7 @@ 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; @@ -345,9 +432,9 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr ##$PVM_NSPacks=2 ##$PVM_SPackArrNSlices=( 2 ) 7 1 - */ + */ try { - DealWithNiveau2(*it, outputDirName); + DealWithNiveau2(*it, strOutputDirName); } catch (BrukerHopelessException &e) { @@ -360,7 +447,7 @@ 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 // @@ -398,38 +485,38 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr std::cout << "--- --- [" << *it << "] is a file.." << std::endl; } } - + for (it = fileNames.begin(); it != fileNames.end(); ++it) { if ( boost::filesystem::is_directory(*it) ) - { - + { + if (verbose) std::cout << "--- --- [" << *it << "] is a directory" << std::endl; - // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), + // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), // GDCM_NAME_SPACE::GDCM_FILESEPARATOR, // GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); // MUST be 'pdata'! // // (interest of previous method : -// If unaware user changed the pdata name, it goes on working +// If unaware user changed the pdata name, it goes on working // std::string str_isa; str_isa = (*it) + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + "isa"; - std::string str_isa_func_name; + std::string str_isa_func_name; canOpen = br_isa.LoadFile(str_isa); if (!canOpen) { sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, - GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); + GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); } else { @@ -444,8 +531,9 @@ 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) { @@ -458,7 +546,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); " << " We skip [" << level2Directory << "]" << std::endl; continue; - } + } } } } @@ -467,7 +555,7 @@ 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 @@ -509,7 +597,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (verbose) std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl; - std::string str_d3proc(char_d3proc); + std::string str_d3proc(char_d3proc); canOpen = br_d3proc.LoadFile(str_d3proc); if (!canOpen) @@ -524,7 +612,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr { std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl; throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'")); - //exit(0); /// \TODO throw an exception ! + //exit(0); /// \TODO throw an exception ! } //-------------- end try d3proc; @@ -540,7 +628,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // "d3proc"; if (verbose) std::cout << "reco: --- => [" << char_reco << "]" << std::endl; - + std::string str_reco(char_reco); canOpen = br_reco.LoadFile(str_reco); @@ -563,7 +651,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (verbose) std::cout << "[" << str_reco << "] successfully Loaded " << std::endl; } - + canOpen = br_reco.FillMap(); if (!canOpen) { @@ -573,8 +661,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr } else { if (verbose) std::cout << "[" << str_reco << "] successfully Mapped" << std::endl; - } - + } + //std::cout << "------------------------------------------------------------------------------------------------" << std::cout; // br_reco.PrintSelf(); // std::cout << "------------------------------------------------------------------------------------------------" << std::cout; @@ -625,7 +713,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr double spatResolY = spatResol.GetDoubleValue()[1]; if (verbose) std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl; - + */ /* ------ */ @@ -640,13 +728,13 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr BrukerFieldData size = br_reco.GetFieldData("RECO_size"); double sizeX = size.GetDoubleValue()[0]; double sizeY = size.GetDoubleValue()[1]; - + if (verbose) std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl; - + double spatResolX = fovX / sizeX; double spatResolY = fovY / sizeY; - + if (verbose) std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl; @@ -654,10 +742,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr /// \TODO probabely a more sophisticated accessor will be necessary : /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc) - + BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance"); double sliceDistance = bsliceDistance.GetDoubleValue()[0]; - + if (verbose) std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl; @@ -667,7 +755,9 @@ 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 +775,7 @@ 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 +847,7 @@ 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 +961,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 1, fp); } fclose(fp); + // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl; } // end if mhd @@ -895,7 +986,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr 1, fp); } fclose(fp); - + fp=fopen(output2dseqSliceFileName, "rb"); if (!fp) { @@ -910,7 +1001,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr */ /* ----------- Write Dicom Image ---------------*/ - + int frameSize = NX*NY*pixelSize; for (instantNb=0; instantNb 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 ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); + throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") ); } br_acqp.SetImageLoopStructure(); @@ -1262,22 +1381,22 @@ std::vector Bruker2Dicom::CreateImageSet ( ) BrukerImage image(br_acqp,br_reco); image.Init(br_acqp,br_reco,1); - + for(int i=0;i > imageOrientation; std::vector imagePosition; for(int i=0;i Bruker2Dicom::CreateImageSet ( ) std::cout << "\t Orientation " ; for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++) std::cout << imageOrientation[i1][i2] << " ";CreateImageSet - + //std::cout << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition(); std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition(); @@ -1315,14 +1434,14 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, std::string &serieDescr, std::string &strStudyTimeDate, int imgNum, - GDCM_NAME_SPACE::ImageContentType contentType + GDCM_NAME_SPACE::ImageContentType contentType ) { std::ostringstream str; GDCM_NAME_SPACE::File *file; - file = GDCM_NAME_SPACE::File::New(); - + file = GDCM_NAME_SPACE::File::New(); + // Set the image size str.str(""); str << X; @@ -1341,7 +1460,9 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, // Set the pixel type // //8, 16, 32, 64 (for double ?) str.str(""); - str << pixelSize*8; + str << pixelSize*8; + + // Bits Allocated file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored @@ -1352,7 +1473,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, // Set the pixel representation // 0/1 , 0=unsigned file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation - + // Set the samples per pixel // 1:Grey level, 3:RGB file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel @@ -1360,29 +1481,27 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, str.str(""); str << spacingX << "\\" << spacingY; file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing - + // 0018 0050 DS 1 Slice Thickness str.str(""); str << sliceDistance; 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" , 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 @@ -1391,10 +1510,11 @@ 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"); - + // 0008 0020 DA 1 Study Date // 0008 0030 TM 1 Study Time @@ -1427,9 +1547,8 @@ std::cout << "charImageOrientation " << imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0], imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1], imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ; - - file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS"); + file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS"); // 0020 0032 DS 3 Image Position (Patient) @@ -1438,10 +1557,94 @@ std::cout << "charImageOrientation " << imageSet[imgNum].getTranslationVectorRPS2XYZ()[0], imageSet[imgNum].getTranslationVectorRPS2XYZ()[1], imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]); - + file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient) - + // Private creator + /* + +0029|0010 [LO] [Private Creator] [CREATIS HEADER ] +0029|0011 [LO] [Private Creator] [CREATIS for BRUKER to DICOM] +0029|1031 [LO] [] [4.0.7571167 ] +0029|1032 [UL] [] [1440000] =0x(15f900) + +> $$ Thu Jul 30 17:29:46 2009 CEST (UT+2h) mwiart +> $$ /opt/PV4.0/data/mwiart/nmr/dha80.Uw1/4/method +> ##$Method=DtiEpi +> ##$PVM_DwNDiffDir=3 % 3 directions +> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b par direction +> ##$PVM_DwAoImages=1 % 1 image pour b=0 +> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b +> 1500.000000 3000.000000 +> +> $$ Wed Dec 2 09:56:01 2009 UTC (UT+0h) mwiart +> $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/4/method +> ##$Method=DtiEpi +> ##$PVM_DwNDiffDir=3 % 3 directions +> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b par direction +> ##$PVM_DwAoImages=1 % 1 image pour b=0 +> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b +> 1500 3000 +> +> $$ Wed Dec 2 10:14:27 2009 UTC (UT+0h) mwiart +> $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/5/method +> ##$Method=DtiStandard +> ##$PVM_DwNDiffDir=1 % 1 direction +> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b +> ##$PVM_DwAoImages=0 % 0 image pour b=0 +> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b +> 138 1600 +> + */ + + file->InsertEntryString("CREATIS HEADER", 0x0029,0x0010, "LO"); + file->InsertEntryString("CREATIS FOR BRUKER-TO-DICOM", 0x0029,0x0011, "LO"); + + BrukerFieldData brf_method = br_method.GetFieldData("Method"); + const std::vector method = brf_method.GetStringValue(); + + // std::string method = br_method.GetFieldData("Method").GetStringValue(); + file->InsertEntryString(method[0], 0x0029,0x0100, "LO"); + + std::cout << " method[" << method[0] << "]" << std::endl; + if (method[0] == "DtiEpi" || method[0] == "DtiStandard") + { + // const std::vector NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir").GetIntValue(); + BrukerFieldData brf_NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir"); + const std::vector NDiffDir = brf_NDiffDir.GetIntValue(); + + //const std::vector NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach").GetIntValue(); + BrukerFieldData brf_NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach"); + const std::vector NDiffExpEach =brf_NDiffExpEach.GetIntValue(); + +// const std::vector AoImages = br_method.GetFieldData("PVM_DwAoImages").GetIntValue(); + BrukerFieldData brf_AoImages = br_method.GetFieldData("PVM_DwAoImages"); + const std::vector AoImages = brf_AoImages.GetIntValue(); + + BrukerFieldData brf_DwBvalEach = br_method.GetFieldData("PVM_DwBvalEach"); + const std::vector DwBvalEach = brf_DwBvalEach.GetDoubleValue(); + + std::cout << "nb directions : " << NDiffDir[0] << " nb valeurs de b par direction : " << NDiffExpEach[0] + << " nb images for b=0 : " << AoImages[0] << std::endl; + + str.str(""); + str << NDiffDir[0]; + file->InsertEntryString(str.str(),0x0029,0x0101,"US"); // nb de directions + str.str(""); + str << NDiffExpEach[0]; + file->InsertEntryString(str.str(),0x0029,0x0102,"US"); // nb valeurs de b par direction + str.str(""); + str << AoImages[0]; + file->InsertEntryString(str.str(),0x0029,0x0103,"US"); // nb images pour b=0 + + str.str(""); + for (unsigned int i=0; iInsertEntryString(str.str(),0x0029,0x0104,"DS"); // Valeurs de b + } // 0020 0x1041 DS 1 Slice Location // sprintf(charImagePosition,"%f",float(imgNum)); @@ -1460,8 +1663,8 @@ std::cout << "charImageOrientation " << GDCM_NAME_SPACE::FileHelper *fileH; fileH = GDCM_NAME_SPACE::FileHelper::New(file); - fileH->SetContentType(contentType); - + fileH->SetContentType(contentType); + // cast is just to avoid warnings (*no* conversion is performed) //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float! @@ -1483,5 +1686,3 @@ std::cout << "charImageOrientation " << file->Delete(); fileH->Delete(); } - -