+#include "bruker2dicom.h"
+
+
+
+bool Bruker2Dicom::Execute()
+{
+ // ----- Begin Processing -----
+
+ bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
+
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
+ {
+ std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
+ return 0;
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
+ }
+
+ std::string strDirNameOut(OutputDirName);
+ bool res=CreateDirectory(strDirNameOut);
+ if (!res) {
+ std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
+ exit (0);
+ }
+
+ 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
+//
+
+ 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;
+ canOpen =br_subject.LoadFile(subject);
+
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! no 'subject' found" << std::endl;
+ exit(0); /// \TODO throw an exception !
+ }
+ else
+ {
+ br_subject.FillMap();
+ }
+ //br_subject.PrintSelf();
+
+ // 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;
+ 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_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_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);
+
+ 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();
+
+ // -----------------------------------------------------
+ // Iterate to ALL the objets(files/directories) found in the input directory
+ // (this is level ZERO)
+ // -----------------------------------------------------
+
+ GDCM_NAME_SPACE::DirListType::iterator it;
+
+ for (it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+ {
+ if (verbose)
+ std::cout << "[" << *it << "] is a directory" << std::endl;
+
+ //BrukerDataSet br_acqp;
+ std::string strAcqp;
+ strAcqp = (*it) +
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "acqp";
+
+ br_acqp.LoadFile(strAcqp);
+ br_acqp.FillMap();
+
+ std::string acqp_scan_name;
+ std::string acqp_method;
+ std::string acqp_protocol_location;
+
+ BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
+ acqp_protocol_location = b_protocol_location.GetStringValue()[0];
+ cleanString(acqp_protocol_location);
+
+ BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
+ acqp_scan_name = b_scan_name.GetStringValue()[0];
+ cleanString(acqp_scan_name);
+
+ BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
+ acqp_method = b_method.GetStringValue()[0];
+ cleanString(acqp_method);
+
+ BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
+ b_list_size.PrintSelf(); //JP
+
+ nbSlices = b_list_size.GetIntValue()[0];
+
+ strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
+ + "-" + 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).c_str()
+ << acqp_protocol_location.c_str()
+ << acqp_scan_name.c_str()
+ << acqp_method.c_str()
+ << "]\n"
+ << " ================================================================================"
+ << std::endl;
+
+ if (verbose)
+ printf ("outputDirName [%s]\n", outputDirName);
+
+ DealWithNiveau1(*it, outputDirName);
+ }
+ } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
+}
+
+
+// =====================================================================
+
+void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
+//
+// e.g. : at level 1, in B67d1.Bp1/6
+//
+// acqp fid imnd pdata pulseprogram spnam0 spnam1
+
+ bool res = CreateDirectory(currentOutputDirName);
+
+ if (!res) {
+ std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
+ exit (0);
+ }
+ GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
+ GDCM_NAME_SPACE::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+ // -----------------------------------------------------
+ // Iterate to ALL the objets(files/directories) found in the input directory
+ // -----------------------------------------------------
+ GDCM_NAME_SPACE::DirListType::iterator it;
+
+ for (it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+ {
+ if (verbose)
+ std::cout << "--- [" << *it << "] is a file" << std::endl;
+ }
+ }
+
+ char outputDirName[(unsigned int) PATH_MAX+2];
+ //std::string firstName;
+ bool canOpen;
+ for (it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+ {
+ // will be always "pdata" ...
+ if (verbose)
+ std::cout << "--- [" << *it << "] is a directory" << std::endl;
+
+ /* a recuperer :
+ if (FileLine.startsWith("##$ACQ_size=")) {
+ if (FileLine.startsWith("##$NI=")) {
+ if (FileLine.startsWith("##$NR=")) {
+ if (FileLine.startsWith("##$ACQ_obj_order=")) {
+ if (FileLine.startsWith("##$ACQ_word_size=")) {
+ if (FileLine.startsWith("##$BYTORDA=")) {
+ if (FileLine.startsWith("##$PULPROG=")) {
+ */
+
+ sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
+ GDCM_NAME_SPACE::Util::GetName(*it).c_str());
+ //br1.PrintSelf();
+
+ std::string strMethod;
+ //std::string firstName = *(fileNames.begin());
+
+ strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin())) +
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "method";
+ // std::cout << "---strMethod (for method)=> [" << strMethod << "]" << std::endl;
+ canOpen = br_method.LoadFile(strMethod);
+ if (!canOpen)
+ {
+ strMethod = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "imnd";
+ //std::cout << "---strMethod (for imnd) => [" << strMethod << "]" << std::endl;
+ canOpen = br_method.LoadFile(strMethod);
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
+ exit(0); /// \TODO throw an exception !
+ }
+ }
+ if (verbose)
+ std::cout << "open => [" << strMethod << "] successfully" << std::endl;
+ br_method.FillMap();
+
+ /* a recuperer :
+ ##$PVM_Fov (dimension)
+ */
+ /*
+ dans method (pour perfusion seulement?) :
+ ##$PVM_ObjOrderList=( 8 )
+ 0 2 4 6 1 3 5 7
+ ##$PVM_NSPacks=2
+ ##$PVM_SPackArrNSlices=( 2 )
+ 7 1
+ */
+ DealWithNiveau2(*it,outputDirName );
+ }
+ }
+}
+
+// =====================================================================
+
+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
+//
+
+ bool res = CreateDirectory(currentOutputDirName);
+
+ if (!res) {
+ std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
+ exit (0);
+ }
+
+ GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
+
+ GDCM_NAME_SPACE::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ char outputDirName[(unsigned int) PATH_MAX+2];
+
+ // -----------------------------------------------------
+ // Iterate to ALL the objets(files/directories) found in the input directory
+ // -----------------------------------------------------
+ GDCM_NAME_SPACE::DirListType::iterator it;
+ bool canOpen;
+
+ if (verbose)
+ for (it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+ {
+ std::cout << "--- --- [" << *it << "] is a file" << std::endl;
+ }
+
+ }
+
+ for (it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+ {
+
+ 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() );
+ // MUST be 'pdata'!
+
+//
+// (interest of previous method :
+// 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;
+ 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() );
+ }
+ else
+ {
+ br_isa.FillMap();
+ BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
+
+ str_isa_func_name = b_isa_func_name.GetStringValue()[0];
+ cleanString(str_isa_func_name);
+
+ 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());
+ }
+ DealWithNiveau3(*it, outputDirName);
+ }
+ }
+}
+
+
+//
+// =====================================================================
+//
+
+void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
+
+//
+// e.g. at level 3, in
+
+ // just to be able to go on checking // JP
+ if ( GDCM_NAME_SPACE::Util::GetName(level3Directory) != "1")
+ return;
+
+ bool res = CreateDirectory(currentOutputDirName);
+
+ if (!res)
+ {
+ std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
+ exit (0);
+ }
+
+ GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
+ GDCM_NAME_SPACE::DirListType::iterator it;
+ GDCM_NAME_SPACE::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ char original2dseqName [(unsigned int) PATH_MAX+2];
+ char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
+
+ char outputMhdFileName [(unsigned int) PATH_MAX+2];
+ char output2dseqSliceFileName[(unsigned int) PATH_MAX+6]; // think about extra '.dcm'
+ char output2dseqName [(unsigned int) PATH_MAX+6];
+ char output2dseqCartoName [(unsigned int) PATH_MAX+6];
+
+ 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 << "--- => [" << char_d3proc << "]" << std::endl;
+ std::string str_d3proc(char_d3proc);
+ canOpen = br_d3proc.LoadFile(str_d3proc);
+
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! no 'd3proc' found" << std::endl;
+ exit(0); /// \TODO throw an exception !
+ }
+
+ canOpen = br_d3proc.FillMap();
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
+ exit(0); /// \TODO throw an exception !
+ }
+
+ //-------------- end try d3proc;
+
+
+ // -------------------try reco
+
+ char char_reco[(unsigned int) PATH_MAX+2];
+
+ sprintf(char_reco,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
+ //str_d3proc = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
+ // GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ // "d3proc";
+ if (verbose)
+ std::cout << "--- => [" << char_reco << "]" << std::endl;
+ std::string str_reco(char_reco);
+ canOpen = br_reco.LoadFile(str_reco);
+
+ if (!canOpen) // we try in directory ../1
+ {
+ if (verbose)
+ std::cout << "[" << str_reco << "] not found " << std::endl;
+ 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;
+ canOpen = br_reco.LoadFile(str_reco);
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl;
+ exit(0); /// \TODO throw an exception !
+ }
+ }
+
+ canOpen = br_reco.FillMap();
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
+ exit(0); /// \TODO throw an exception !
+ }
+ //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
+ // br_reco.PrintSelf();
+ // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
+
+ // -------------------end try reco
+
+
+ BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
+ int NX = bX.GetIntValue()[0];
+
+ std::cout << "IM_SIX " << NX << std::endl;
+ BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
+ int NY = bY.GetIntValue()[0];
+
+ 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];
+ 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);
+
+ 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;
+
+ /// \TODO probabely a more sophisticated accessor will be necessary :
+ /// (cf : non contiguous slices, overlapping, slice thickness, space between clices, etc)
+ BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
+ double sliceDistance = bsliceDistance.GetDoubleValue()[0];
+
+ if (mhd)
+ {
+ sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
+ res = CreateDirectory( currentOutputMhdDirName );
+ if (!res) {
+ std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
+ exit (0);
+ }
+
+ if (verbose)
+ std::cout << "Directory creation [" << currentOutputDirName << "]" << std::endl;
+ } // end if mhd
+
+ std::cout << "nbFrames " << nbFrames << std::endl;
+ std::cout << "nbSlices " << nbSlices << std::endl;
+ int k;
+ int nbInstants = nbFrames/nbSlices;
+ std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
+ int instantNb;
+ int sliceNb;
+ FILE *fp; // for MHD files
+
+ sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "2dseq");
+
+/**/
+ // \TODO : tenir compte du bazar precedent
+
+ // load 2dseq in memory
+
+ fp = fopen(original2dseqName, "rb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
+ 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);
+
+ // This one will be important!
+ // ---------------------------
+ imageSet = CreateImageSet ( );
+
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives)
+ {
+ std::cout << "Single instant : do not split" << std::endl;
+ if (mhd)
+ {
+ sprintf(outputMhdFileName, "%s%cMhdData_Toutes_les_Slices.mhd", currentOutputMhdDirName,
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
+ fp=fopen(outputMhdFileName, "w");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
+ exit(0);
+ }
+ else
+ {
+ fprintf(fp, "ObjectType = Image\n");
+ fprintf(fp, "NDims = 3\n" );
+ fprintf(fp, "BinaryData = True \n" );
+ 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, "Position = 0 0 %d\n", 0 );
+ fprintf(fp, "Offset = 0 0 0\n" );
+ 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" );
+ fclose(fp);
+ }
+ sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices",
+ currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
+ fp=fopen(output2dseqSliceFileName, "wb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
+ }
+ else
+ {
+ fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
+ }
+ fclose(fp);
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ } // end if mhd
+ if (dicom)
+ {
+ sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices.dcm",
+ currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
+
+ /* ----------- Write Dicom Image ---------------*/
+ MakeDicomImage(buffer_2dseq,
+ NX,
+ NY,
+ nbFrames,
+ pixelSize,
+ fovX/NY, fovY/NY, sliceDistance,
+ output2dseqSliceFileName,
+ strPatientName,
+ day,
+ strStudyUID,
+ strSerieUID,
+ strStudyDescr,
+ strSerieDescr,
+ strStudyTimeDate,
+ 0,// index frame number
+ GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
+ );
+ } // end if dicom
+ } // end if nbInstants = 1
+
+ else // more than ONE instant
+ {
+ // Interleaved !
+ // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
+
+ unsigned char * pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
+
+ k = 0;
+ for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
+ {
+ if (mhd)
+ {
+ sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k );
+ if (verbose)
+ std::cout << "--- Output MHD file [" << outputMhdFileName << "]" << std::endl;
+ fp=fopen(outputMhdFileName, "w");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
+ exit(0);
+ }
+ else
+ {
+ /* ----------- Write MHD Image ---------------*/
+ //if (verbose)
+ // std::cout << "Open sucessfully[" << outputMhdFileName << "] for writting" << std::endl;
+ fprintf(fp, "ObjectType = Image\n");
+ fprintf(fp, "NDims = 3\n" );
+ fprintf(fp, "BinaryData = True \n" );
+ 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, "Offset = 0 0 0\n" );
+ fprintf(fp, "CenterOfRotation = 0 0 0\n" );
+ fprintf(fp, "ElementNumberOfChannels = 1\n" );
+ fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
+ fprintf(fp, "ElementDataFile = ..%c2dseq_Slice_%d\n", GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb );
+ fclose(fp);
+ } // end write MHD
+
+ sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
+ currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,sliceNb);
+ fp=fopen(output2dseqSliceFileName, "wb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
+ exit (0);
+ }
+ int frameSize = NX*NY*pixelSize;
+ for (instantNb=0; instantNb<nbInstants; instantNb++)
+ {
+// std::cout << "------------SN " << sliceNb << " IN " << instantNb << " T " << nbSlices*instantNb + sliceNb << std::endl;
+ fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
+ frameSize,
+ 1, fp);
+ }
+ fclose(fp);
+// std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
+ } // end if mhd
+
+ if (dicom)
+ {
+ // desperate try !
+ /*
+ sprintf(output2dseqSliceFileName, "%sdummy_buffer",
+ currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
+ fp=fopen(output2dseqSliceFileName, "wb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
+ exit (0);
+ }
+ int frameSize = NX*NY*pixelSize;
+ for (instantNb=0; instantNb<nbInstants; instantNb++)
+ {
+// std::cout << "------------SN " << sliceNb << " IN " << instantNb << " T " << nbSlices*instantNb + sliceNb << std::endl;
+ fwrite( buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize,
+ frameSize,
+ 1, fp);
+ }
+ fclose(fp);
+
+ fp=fopen(output2dseqSliceFileName, "rb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
+ exit (0);
+ }
+ fread( pixelsForCurrentSlice,
+ frameSize*nbInstants,
+ 1, fp);
+ fclose(fp);
+ // end of desperate try !
+ */
+
+ /* ----------- Write Dicom Image ---------------*/
+
+ int frameSize = NX*NY*pixelSize;
+ for (instantNb=0; instantNb<nbInstants; instantNb++)
+ {
+ memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
+ }
+
+ int indOfFirsImageWithinImageSet = nbSlices*instantNb;
+ sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d.dcm",
+ currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR, sliceNb);
+
+ MakeDicomImage(
+ pixelsForCurrentSlice,
+ NX,
+ NY,
+ nbInstants,
+ pixelSize,
+ fovX/NY, fovY/NY, sliceDistance,
+ output2dseqSliceFileName,
+ strPatientName,
+ day,
+ strStudyUID,
+ strSerieUID,
+ strStudyDescr,
+ strSerieDescr,
+ strStudyTimeDate,
+ sliceNb*nbInstants,
+ GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
+ );
+ if (verbose)
+ std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
+
+ } // en if dicom
+
+ k++;
+ }
+ delete [] pixelsForCurrentSlice;
+ } // end nbInstants == 1
+ delete [] buffer_2dseq;
+/**/
+
+
+ // -----------------------------------------------------
+ // deal with MatLab-generated Carto file.
+ // -----------------------------------------------------
+
+ dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance,
+ copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
+}
+
+
+// ===========================================================================================
+
+void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
+ double fovX, double fovY, double sliceDistance,
+ char *copyFile, std::string ¤tOutputDirName,
+ char *outputMhdFileName, char *output2dseqCartoName)
+{
+ // -----------------------------------------------------
+ // 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;
+ 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();
+ ++it)
+ {
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+ {
+ if (verbose)
+ std::cout << "--- [" << *it << "] is a file" << std::endl;
+
+ icode = 0;
+
+ while (code[icode][0] != 0)
+ {
+ sprintf(file_name_ident, "2dseq_%s",code[icode]); // e.g "2dseq_ADC"
+ std::string::size_type loc = (*it).rfind(file_name_ident);
+
+ 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");
+ if (!fp){
+ std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
+
+ }
+ fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
+
+ 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());
+ if (mhd)
+ {
+ // Copy the data file in the new directory
+ sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
+ 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" );
+ if (verbose)
+ std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
+
+ FILE *fp;
+ fp=fopen(outputMhdFileName, "w");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
+ }
+ else
+ {
+ fprintf(fp, "ObjectType = Image\n");
+ fprintf(fp, "NDims = 3\n" );
+ 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, "Position = 0 0 0\n" );
+ fprintf(fp, "Offset = 0 0 0\n" );
+ fprintf(fp, "CenterOfRotation = 0 0 0\n" );
+ fprintf(fp, "ElementNumberOfChannels = 1\n" );
+ fprintf(fp, "ElementType = %s\n", "MET_DOUBLE" );
+ fprintf(fp, "ElementDataFile = %s\n", lastFileName.c_str() );
+
+ fclose(fp);
+ }
+ if (verbose)
+ std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
+ } // end if mhd
+
+ // ----------- Write Dicom Image ---------------
+
+ if (dicom)
+ {
+ sprintf(output2dseqCartoName, "%s%c%s%s",
+ currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
+ if (verbose)
+ std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
+
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
+ std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
+ MakeDicomImage(buffer_carto,
+ NX,
+ NY,
+ nbSlices,
+ 8, // pixelSize
+ fovX/NY, fovY/NY, sliceDistance,
+ output2dseqCartoName,
+ strPatientName,
+ day,
+ strStudyUID,
+ strSerieUID,
+ strStudyDescr,
+ strNewSerieDescr,
+ strStudyTimeDate,
+ 0,
+ GDCM_NAME_SPACE::CREATED_IMAGE
+ );
+ } // end if dicom
+
+ delete [] buffer_carto;
+ 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
+}
+
+
+// ==========================================================================================================
+
+bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
+{
+ std::string systemCommand;
+
+ if (verbose)
+ std::cout << "Check for output directory :[" << OutputDirName << "]."
+ <<std::endl;
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(OutputDirName) ) // dirout not found
+ {
+ std::string strDirNameout(OutputDirName); // to please gcc 4
+ systemCommand = "mkdir " + strDirNameout; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(OutputDirName) ) // be sure it worked
+ {
+ if (verbose)
+ std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
+ return 0;
+ /// \todo : THROW AN EXCEPTION
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Directory [" << OutputDirName << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
+ }
+
+ return 1;
+
+}
+
+
+// ===========================================================================================
+
+/// \TODO move cleanString to 'crea' ?
+
+void Bruker2Dicom::cleanString(std::string &s)
+{
+ int l = s.size();
+ if (s[l-1] == 0x0A || s[l-1] == 0x0D ) // CR or NL
+ {
+ l--;
+ s = s.substr(0, l);
+ }
+ if (s[l-1] == ' ' ) // blank space
+ {
+ l--;
+ s = s.substr(0, l);
+ }
+
+ if (s[0] == '<')
+ s= s.substr(1,l-2);
+ std::string repChar("_");
+ GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
+}
+
+
+
+// ===========================================================================================
+
+
+void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
+{
+ if(bDPT.GetDataType() == "string")
+ {
+ std::string brukerDataPixelType = bDPT.GetStringValue()[0];
+ std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
+ //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
+
+ if (brukerDataPixelType == "ip_short") {
+ mhdDataPixelType = "MET_USHORT";
+ pixelSize = 2;
+ }
+ if (brukerDataPixelType == "ip_int") {
+ mhdDataPixelType = "MET_UINT";
+ pixelSize = 4;
+ }
+ if (brukerDataPixelType == "ip_char") {
+ mhdDataPixelType = "MET_UCHAR";
+ pixelSize = 1;
+ }
+ /// \TODO : finish the list
+ /*
+ case 0 : fp << "ElementType = MET_CHAR" << std::endl;
+ break;
+ case 1 : fp << "ElementType = MET_UCHAR" << std::endl;
+ break;
+ case 2 : fp << "ElementType = MET_SHORT" << std::endl;
+ break;
+ case 3 : fp << "ElementType = MET_USHORT" << std::endl;
+ break;
+ case 4 : fp << "ElementType = MET_INT" << std::endl;
+ break;
+ case 5 : fp << "ElementType = MET_UINT" << std::endl;
+ break;
+ case 6 : fp << "ElementType = MET_FLOAT" << std::endl;
+ break;
+ case 7 : fp << "ElementType = MET_DOUBLE" << std::endl;
+ */
+ }
+ else
+ {
+ int brukerDataPixelType = bDPT.GetIntValue()[0];
+ std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
+ //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
+
+// Cross your fingers !!!
+
+// pb : found values : 2, 3, 5
+
+ if (brukerDataPixelType == 2) {
+ mhdDataPixelType = "MET_USHORT";
+ pixelSize = 2;
+ }
+ if (brukerDataPixelType == 3) {
+ mhdDataPixelType = "MET_USHORT";
+ pixelSize = 2;
+ }
+ if (brukerDataPixelType == 1) {
+ mhdDataPixelType = "MET_UCHAR";
+ pixelSize = 1;
+ }
+ }
+}
+
+// ===========================================================================================
+
+std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
+{
+ std::vector<BrukerImage> imageSet;
+ br_acqp.SetLoopStructure();
+ std::vector<int> tempVect = br_acqp.GetLoopStructure() ;
+ std::map<std::string, BrukerFieldData> map = br_acqp.GetBrukerHeaderMap();
+ bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect);
+
+ br_acqp.SetImageLoopStructure();
+ br_acqp.SetBrukerImageList();
+ std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
+
+ BrukerImage image(br_acqp,br_reco);
+ image.Init(br_acqp,br_reco,1);
+
+ for(int i=0;i<brukerImageList.size();i++)
+ {
+ image.Init(br_acqp,br_reco,i);
+ imageSet.push_back(image);
+ }
+
+ // Just for checking
+ /*
+
+ std::vector<std::vector <double> > imageOrientation;
+ std::vector <double> imagePosition;
+ for(int i=0;i<brukerImageList.size();i++)
+ {
+ // fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
+
+ imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
+ std::cout << "Position " << imagePosition[0] << " "
+ << imagePosition[1] << " " << imagePosition[2] ;
+ 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 << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition();
+ std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition();
+
+ std::cout << "\t [";
+ for (int i3=0; i3<imageSet[i].getLoopStamp().size();i3++)
+ std::cout << " " << imageSet[i].getLoopStamp()[i3];
+ std::cout << "]" << std::endl;
+ }
+*/
+ return imageSet;
+}
+
+
+// ===========================================================================================
+
+void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
+ int X,
+ int Y,
+ int nbFrames,
+ int pixelSize,
+ double spacingX, double spacingY, double sliceDistance,
+ std::string dcmImageName,
+ const std::string &patientName,
+ const char *day,
+ std::string &studyUID,
+ std::string &serieUID,
+ std::string &studyDescr,
+ std::string &serieDescr,
+ std::string &strStudyTimeDate,
+ int imgNum,
+ GDCM_NAME_SPACE::ImageContentType contentType
+ )
+{
+ std::ostringstream str;
+
+ GDCM_NAME_SPACE::File *file;
+ file = GDCM_NAME_SPACE::File::New();
+
+ // Set the image size
+ str.str("");
+ str << X;
+ file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
+ str.str("");
+ str << Y;
+ file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
+
+ if (nbFrames != 1)
+ {
+ str.str("");
+ str << nbFrames;
+ file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
+ }
+
+ // Set the pixel type
+ // //8, 16, 32, 64 (for double ?)
+ str.str("");
+ str << pixelSize*8;
+ file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
+
+ file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
+
+ str.str("");
+ str << pixelSize*8-1;
+ file->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
+
+ // 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
+
+// 0028 0030 DS 2 Pixel Spacing
+ 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");
+
+ // 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" , 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
+ file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
+ file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI"); // [SOP Class UID]
+
+ // if (strlen(patientName) != 0)
+ file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
+
+ file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
+ file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
+
+// 0008 0020 DA 1 Study Date
+// 0008 0030 TM 1 Study Time
+
+/// \TODO split into 2 strings!
+ file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
+ file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),0x0008,0x0030, "TM");
+
+ file->InsertEntryString(studyDescr,0x0008,0x1030, "LO"); // Study Description
+ file->InsertEntryString(serieDescr,0x0008,0x103e, "LO"); // Series Description
+
+//0008|0060 [CS] [Modality]
+ file->InsertEntryString("MR",0x0008,0x0060, "CS");
+
+// 0020 0037 DS 6 Image Orientation (Patient)
+ char charImageOrientation[256];
+
+/*
+std::cout << "try charImageOrientation " <<
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0] << " " <<
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1] << " " <<
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] << std::endl ;
+*/
+ sprintf(charImageOrientation,"%f\\%f\\%f \\ %f\\%f\\%f",
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0],
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1],
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2],
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
+ imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
+
+ file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
+
+
+// 0020 0032 DS 3 Image Position (Patient)
+
+ char charImagePosition[256];
+ sprintf(charImagePosition,"%f\\%f\\%f",
+ 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)
+
+
+
+// 0020 0x1041 DS 1 Slice Location
+// sprintf(charImagePosition,"%f",float(imgNum));
+// file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
+/*
+ // Set Rescale Intercept
+ str.str("");
+ str << div;
+ file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
+
+ // Set Rescale Slope
+ str.str("");
+ str << mini;
+ file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
+*/
+
+ GDCM_NAME_SPACE::FileHelper *fileH;
+ fileH = GDCM_NAME_SPACE::FileHelper::New(file);
+ 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!
+
+//std::cout << "-------------------------------- X*Y*nbFrames*pixelSize " << X << " " << Y << " " << nbFrames << " " << pixelSize << std::endl;
+
+ fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
+ fileH->SetWriteModeToRaw();
+ fileH->SetWriteTypeToDcmExplVR();
+ if( !fileH->Write(dcmImageName))
+ std::cout << "Failed for [" << dcmImageName << "]\n"
+ << " File is unwrittable" << std::endl;
+
+ if (verbose)
+ file->Print();
+
+ file->Delete();
+ fileH->Delete();
+}
+
+