X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=e241166e05359b664b760a5c7a0d6b6ddb05c6a7;hb=df0ba3862bc3d12cbc7d4a7c5c6af079250eac29;hp=66d2c9e0576316d90c3c3fdeab6067f48c5ec448;hpb=bc44fc75154847637a0bd24efea6338db738e4da;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 66d2c9e..e241166 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) ) { @@ -42,10 +42,10 @@ bool Bruker2Dicom::Execute() // 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(); @@ -68,25 +68,23 @@ bool Bruker2Dicom::Execute() acqpFound= true; else acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory! - - int type; + + 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); + + //int type = CheckUserDirectory(InputDirName); switch (type) { case 1: { - bool canOpen; - canOpen =br_subject.LoadFile(subject); + bool canOpen = br_subject.LoadFile(subject); if (!canOpen) { std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl; @@ -95,39 +93,97 @@ bool Bruker2Dicom::Execute() else { br_subject.FillMap(); - } - //br_subject.PrintSelf(); - - // 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 'set of studies' directory!, not yet dealt with" << std::endl; - } + + // 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; + } } } +// ---------------------------------------------------------------------------------------------------------- + +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; @@ -166,18 +222,18 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f } // 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(); @@ -189,7 +245,8 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f // (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(); @@ -201,7 +258,8 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f if (verbose) std::cout << "[" << *it << "] is a directory" << std::endl; - if((*it) == "AdjStatePerStudy") // avoid trouble with new version 'AdjStatePerStudy' directory + //if((*it) == "AdjResult") // avoid trouble with new version 'AdjResult' directory + if(GDCM_NAME_SPACE::Util::GetName(*it) == "AdjResult") continue; //BrukerDataSet br_acqp; @@ -232,13 +290,13 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f 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) @@ -246,10 +304,10 @@ void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &f + "." + 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" << " ================================================================================" @@ -330,7 +388,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string &cu 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); + std::string strOutputDirName(outputDirName); //br1.PrintSelf(); std::string strMethod; @@ -371,7 +429,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string &cu ##$PVM_NSPacks=2 ##$PVM_SPackArrNSlices=( 2 ) 7 1 - */ + */ try { DealWithNiveau2(*it, strOutputDirName); } @@ -424,7 +482,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &cu std::cout << "--- --- [" << *it << "] is a file.." << std::endl; } } - + for (it = fileNames.begin(); it != fileNames.end(); ++it) @@ -567,7 +625,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu // "d3proc"; if (verbose) std::cout << "reco: --- => [" << char_reco << "]" << std::endl; - + std::string str_reco(char_reco); canOpen = br_reco.LoadFile(str_reco); @@ -590,7 +648,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu if (verbose) std::cout << "[" << str_reco << "] successfully Loaded " << std::endl; } - + canOpen = br_reco.FillMap(); if (!canOpen) { @@ -601,7 +659,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu if (verbose) std::cout << "[" << str_reco << "] successfully Mapped" << std::endl; } - + //std::cout << "------------------------------------------------------------------------------------------------" << std::cout; // br_reco.PrintSelf(); // std::cout << "------------------------------------------------------------------------------------------------" << std::cout; @@ -652,7 +710,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu double spatResolY = spatResol.GetDoubleValue()[1]; if (verbose) std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl; - + */ /* ------ */ @@ -667,13 +725,13 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu 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; @@ -681,10 +739,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu /// \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; @@ -694,8 +752,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu { sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles"); - std::string strCurrentOutputMhdDirName(currentOutputMhdDirName); + std::string strCurrentOutputMhdDirName(currentOutputMhdDirName); res = CreateDirectory( strCurrentOutputMhdDirName ); if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; @@ -786,7 +844,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu 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" ); @@ -900,6 +958,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu 1, fp); } fclose(fp); + // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl; } // end if mhd @@ -924,7 +983,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu 1, fp); } fclose(fp); - + fp=fopen(output2dseqSliceFileName, "rb"); if (!fp) { @@ -939,7 +998,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &cu */ /* ----------- Write Dicom Image ---------------*/ - + int frameSize = NX*NY*pixelSize; for (instantNb=0; instantNb Bruker2Dicom::CreateImageSet ( ) 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()") ); @@ -1326,22 +1378,22 @@ 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(); @@ -1379,7 +1431,7 @@ 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;