X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=9cc2301872833ef373a9da3bbff32c25e1550a51;hb=8f2fc8236f01d70abd3e4abe4152ea7985ab5b79;hp=6e97c5bd0f59c0afaab7a1a7971d11bc56ea328c;hpb=1d72babed2631bf4c953b43164d6088149bc3e4e;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 6e97c5b..9cc2301 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -7,8 +7,6 @@ #define PATH_MAX 2048 #endif - - bool Bruker2Dicom::Execute() { // ----- Check input directory name ----- @@ -62,7 +60,6 @@ bool Bruker2Dicom::Execute() bool canOpen; std::string outputFileName; - // BrukerDataSet br_subject; std::string subject; subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+ @@ -233,7 +230,6 @@ bool Bruker2Dicom::Execute() << " ================================================================================" << std::endl; - if (verbose) printf ("outputDirName [%s]\n", outputDirName); try { @@ -340,7 +336,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr br_method.FillMap(); /* a recuperer : - ##$PVM_Fov (dimension) + ##$PVM_Fov (dimension) // ou plutot RECO_fov ! */ /* dans method (pour perfusion seulement?) : @@ -365,7 +361,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr // ===================================================================== void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) { - + // e.g. : at level 2 in B67d1.Bp1/6/pdata // // acqp fid imnd pdata pulseprogram spnam0 spnam1 @@ -378,7 +374,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure")); //exit (0); } - + GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files GDCM_NAME_SPACE::DirListType fileNames; @@ -401,7 +397,6 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr { std::cout << "--- --- [" << *it << "] is a file.." << std::endl; } - } for (it = fileNames.begin(); @@ -413,7 +408,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr if (verbose) std::cout << "--- --- [" << *it << "] is a directory" << std::endl; - + // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), // GDCM_NAME_SPACE::GDCM_FILESEPARATOR, // GDCM_NAME_SPACE::Util::GetName(*it).c_str() ); @@ -449,7 +444,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr GDCM_NAME_SPACE::Util::GetName(*it).c_str(), str_isa_func_name.c_str()); } - try { + try { DealWithNiveau3(*it, outputDirName); } catch (BrukerHopelessException &e) @@ -463,12 +458,11 @@ 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; - } + } } } } - // // ===================================================================== // @@ -487,7 +481,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (!res) { std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl; - throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure")); + throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure")); //exit (0); } @@ -507,12 +501,12 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough! bool canOpen; - + //-------------- try d3proc; char char_d3proc[(unsigned int) PATH_MAX+2]; sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" ); - + if (verbose) std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl; std::string str_d3proc(char_d3proc); @@ -532,10 +526,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'")); //exit(0); /// \TODO throw an exception ! } - + //-------------- end try d3proc; - - + + // -------------------try reco char char_reco[(unsigned int) PATH_MAX+2]; @@ -545,8 +539,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // GDCM_NAME_SPACE::GDCM_FILESEPARATOR + // "d3proc"; if (verbose) - std::cout << "reco --- => [" << char_reco << "]" << std::endl; - std::string str_reco(char_reco); + std::cout << "reco: --- => [" << char_reco << "]" << std::endl; + + std::string str_reco(char_reco); canOpen = br_reco.LoadFile(str_reco); if (!canOpen) // we try in directory ../1 @@ -556,7 +551,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory); //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName); sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" ); - str_reco=char_reco; + //str_reco=char_reco; canOpen = br_reco.LoadFile(str_reco); if (!canOpen) { @@ -564,15 +559,22 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'")); //exit(0); /// \TODO throw an exception ! } + } else { + if (verbose) + std::cout << "[" << str_reco << "] successfully Loaded " << std::endl; } - + canOpen = br_reco.FillMap(); if (!canOpen) { std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl; throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'")); - //exit(0); /// \TODO throw an exception ! - } + //exit(0); /// \TODO throw an exception ! + } else { + if (verbose) + std::cout << "[" << str_reco << "] successfully Mapped" << std::endl; + } + //std::cout << "------------------------------------------------------------------------------------------------" << std::cout; // br_reco.PrintSelf(); // std::cout << "------------------------------------------------------------------------------------------------" << std::cout; @@ -590,37 +592,76 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr if (verbose) std::cout << "IM_SIY " << NY << std::endl; /// \todo : check if there are actually 3 dimensions or only 2 - + BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ"); int nbFrames = bZ.GetIntValue()[0]; if (verbose) std::cout << "IM_SIZ " << nbFrames << std::endl; // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...} - + BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE"); - + std::string mhdDataPixelType; int pixelSize; getImhDataType(bDPT, mhdDataPixelType, pixelSize); - + + + /* + + // See mail Denis : + // En regle generale il vaut mieux que l'on passe par RECO_* + // pour extraire les parametres de l'image + // + BrukerFieldData fov = br_method.GetFieldData("PVM_Fov"); double fovX = fov.GetDoubleValue()[0]; 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; + +*/ + +/* ------ */ +// Better we use 'get' accessors from BrukerImage class, as Denis wrote them + + BrukerFieldData fov = br_reco.GetFieldData("RECO_fov"); + double fovX = fov.GetDoubleValue()[0]; + double fovY = fov.GetDoubleValue()[1]; + if (verbose) + std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl; + + 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; +/* ------ */ /// \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; + +// ---------------------------------------------------------------------------------------- if (mhd) { @@ -644,7 +685,7 @@ 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 @@ -671,7 +712,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr //exit (0); } } - + unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants]; ///\ TODO : find a safer way to be sure to read everything! size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp); @@ -689,7 +730,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr //return; throw (e); } - + serieNumber++; strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives) @@ -745,7 +786,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr { sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR); - + /* ----------- Write Dicom Image ---------------*/ MakeDicomImage(buffer_2dseq, NX, @@ -767,7 +808,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr ); } // end if dicom } // end if nbInstants = 1 - + else // more than ONE instant { // Interleaved ! @@ -910,12 +951,12 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr } // end nbInstants == 1 delete [] buffer_2dseq; /**/ - - + + // ----------------------------------------------------- // deal with MatLab-generated Carto file. // ----------------------------------------------------- - + dealWithCarto(fileNames, NX, NY, nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance, copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName); } @@ -940,7 +981,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX GDCM_NAME_SPACE::DirListType::iterator it; char file_name_ident[500]; FILE *fp; - + // Iterate to ALL the objets(files/directories) found in the input directory for (it = fileNames.begin(); it != fileNames.end(); @@ -965,7 +1006,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX if ( loc != std::string::npos ) { - + ///\ TODO : find a safer way to be sure to read everything! unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices]; fp = fopen ( (*it).c_str(), "rb"); @@ -989,7 +1030,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" ); if (verbose) std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl; - + FILE *fp; fp=fopen(outputMhdFileName, "w"); if (!fp)