X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=710129b778aaac8994e8f5d27330b037def324b2;hb=64f789199d7c134627b31cfaee6e67eb012f48bb;hp=87997d991c067abd2b43f827606ab68f7cb569da;hpb=c23d68fe2d14a4c4f4b164fdc447f38247f0efc3;p=creaBruker.git diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx index 87997d9..710129b 100644 --- a/lib/src1/bruker2dicom.cxx +++ b/lib/src1/bruker2dicom.cxx @@ -1,4 +1,6 @@ #include "bruker2dicom.h" +#include +#include #ifndef PATH_MAX // If not defined yet : do it #define PATH_MAX 2048 @@ -8,11 +10,12 @@ bool Bruker2Dicom::Execute() { - // ----- Begin Processing ----- + // ----- Check input values ----- bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(); - if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) ) + //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) ) + if ( ! boost::filesystem::is_directory(InputDirName) ) { std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl; return 0; @@ -34,7 +37,7 @@ bool Bruker2Dicom::Execute() 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; @@ -55,6 +58,7 @@ bool Bruker2Dicom::Execute() bool canOpen; std::string outputFileName; + // BrukerDataSet br_subject; std::string subject; subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+ @@ -77,11 +81,7 @@ bool Bruker2Dicom::Execute() // get info for 'Study Description' - /* - BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location"); - acqp_protocol_location = b_protocol_location.GetStringValue()[0]; - cleanString(acqp_protocol_location); -*/ + BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string"); std::string subject_name = b_name.GetStringValue()[0]; strPatientName = subject_name; @@ -104,11 +104,11 @@ bool Bruker2Dicom::Execute() 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); + subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2); cleanString(subject_date); - strStudyDescr = subject_name + "-" + subject_study_name + "-" + subject_entry + "-" + subject_position + "-" + subject_date; - + strStudyDescr = subject_name + "." + subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date; + char outputDirName[(unsigned int) PATH_MAX+2]; strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); @@ -116,6 +116,7 @@ bool Bruker2Dicom::Execute() // ----------------------------------------------------- // 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; @@ -124,7 +125,7 @@ bool Bruker2Dicom::Execute() it != fileNames.end(); ++it) { - if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_directory(*it) ) { if (verbose) std::cout << "[" << *it << "] is a directory" << std::endl; @@ -160,14 +161,20 @@ bool Bruker2Dicom::Execute() nbSlices = b_list_size.GetIntValue()[0]; strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it) - + "-" + acqp_protocol_location - + "-" + acqp_scan_name - + "-" + acqp_method.c_str(); + + "." + acqp_protocol_location + + "." + acqp_scan_name + + "." + acqp_method.c_str(); sprintf(outputDirName, "%s%c%s", 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::cout << " ================================================================================\n" << " ========================= [" << GDCM_NAME_SPACE::Util::GetName(*it).c_str() << acqp_protocol_location.c_str() @@ -176,7 +183,7 @@ bool Bruker2Dicom::Execute() << "]\n" << " ================================================================================" << std::endl; - +*/ if (verbose) printf ("outputDirName [%s]\n", outputDirName); @@ -212,10 +219,11 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr it != fileNames.end(); ++it) { - if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_regular(*it) ) + //if ( ! boost::filesystem::is_directory(*it) ) { if (verbose) - std::cout << "--- [" << *it << "] is a file" << std::endl; + std::cout << "--- [" << *it << "] is a file." << std::endl; } } @@ -226,7 +234,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr it != fileNames.end(); ++it) { - if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_directory(*it) ) { // will be always "pdata" ... if (verbose) @@ -322,9 +330,9 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr it != fileNames.end(); ++it) { - if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( ! boost::filesystem::is_directory(*it) ) { - std::cout << "--- --- [" << *it << "] is a file" << std::endl; + std::cout << "--- --- [" << *it << "] is a file.." << std::endl; } } @@ -333,7 +341,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr it != fileNames.end(); ++it) { - if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) ) + if ( boost::filesystem::is_directory(*it) ) { if (verbose) @@ -369,7 +377,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr str_isa_func_name = b_isa_func_name.GetStringValue()[0]; cleanString(str_isa_func_name); - sprintf(outputDirName, "%s%c%s-%s", currentOutputDirName.c_str(), + sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, GDCM_NAME_SPACE::Util::GetName(*it).c_str(), str_isa_func_name.c_str()); @@ -423,7 +431,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" ); if (verbose) - std::cout << "--- => [" << char_d3proc << "]" << std::endl; + std::cout << "try d3proc: --- => [" << char_d3proc << "]" << std::endl; std::string str_d3proc(char_d3proc); canOpen = br_d3proc.LoadFile(str_d3proc); @@ -452,7 +460,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr // GDCM_NAME_SPACE::GDCM_FILESEPARATOR + // "d3proc"; if (verbose) - std::cout << "--- => [" << char_reco << "]" << std::endl; + std::cout << "try reco --- => [" << char_reco << "]" << std::endl; std::string str_reco(char_reco); canOpen = br_reco.LoadFile(str_reco); @@ -514,7 +522,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl; /// \TODO probabely a more sophisticated accessor will be necessary : - /// (cf : non contiguous slices, overlapping, slice thickness, space between clices, etc) + /// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc) BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance"); double sliceDistance = bsliceDistance.GetDoubleValue()[0]; @@ -555,7 +563,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr exit (0); } - unsigned char * buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants]; + 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); @@ -569,7 +577,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr std::cout << "Single instant : do not split" << std::endl; if (mhd) { - sprintf(outputMhdFileName, "%s%cMhdData_Toutes_les_Slices.mhd", currentOutputMhdDirName, + sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName, GDCM_NAME_SPACE::GDCM_FILESEPARATOR); fp=fopen(outputMhdFileName, "w"); if (!fp) @@ -591,10 +599,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr fprintf(fp, "CenterOfRotation = 0 0 0\n" ); fprintf(fp, "ElementNumberOfChannels = 1\n" ); fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() ); - fprintf(fp, "ElementDataFile = %s\n", "../2dseq_toutes_les_Slices" ); + fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" ); fclose(fp); } - sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices", + sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR); fp=fopen(output2dseqSliceFileName, "wb"); if (!fp) @@ -610,7 +618,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr } // end if mhd if (dicom) { - sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices.dcm", + sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm", currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR); /* ----------- Write Dicom Image ---------------*/ @@ -639,7 +647,7 @@ 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]; + unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants]; k = 0; for (sliceNb=0; sliceNb Bruker2Dicom::CreateImageSet ( ) return imageSet; } - // =========================================================================================== void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,