--- /dev/null
+#include "bruker2dicom2.h"
+#include "brukerexception.h"
+
+#include <gdcmAttribute.h>
+#include <boost/filesystem.hpp>
+#include <boost/algorithm/string.hpp>
+
+
+#ifndef PATH_MAX // If not defined yet : do it
+ #define PATH_MAX 2048
+#endif
+
+ bool Bruker2Dicom::Execute()
+ {
+
+ //--- first, Test the system----//
+ bool bigEndian = gdcm::ByteSwap<uint16_t>::SystemIsBigEndian();
+ gdcm::SwapCode sc = gdcm::SwapCode::Unknown;
+ if ( gdcm::ByteSwap<uint16_t>::SystemIsBigEndian() )
+ {
+ sc = gdcm::SwapCode::BigEndian;
+ }
+ else if ( gdcm::ByteSwap<uint16_t>::SystemIsLittleEndian() )
+ {
+ sc = gdcm::SwapCode::LittleEndian;
+ }
+ else // sc == gdcm::SwapCode::Unknown
+ {
+ return 1;
+ }
+
+ // ----- Check input directory name -----
+ if ( ! boost::filesystem::is_directory(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;
+ }
+
+ // ----- Check output directory name -----
+ if ( ! boost::filesystem::is_directory(OutputDirName) )
+ {
+ bool res=CreateDirectory(OutputDirName);
+ if (!res)
+ {
+ std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
+ throw ( BrukerHopelessException ("Output directory creation failure "));
+ }
+ }
+ else
+ {
+ if(verbose)
+ std::cout << "[" << OutputDirName << "] already exist " << std::endl;
+ }
+
+ // Deal with level 0
+ // Level 0 is the original directory
+ // who could contain "1 2 3 4 5 6" directories and "AdjStatePerStudy subject" files
+ std::string strDirNamein(InputDirName);
+ boost::filesystem::directory_iterator it(InputDirName), it_end;
+ subjectFound = false;
+ acqpFound = false;
+ for(; it != it_end; ++it)
+ {
+ if(! boost::filesystem::is_directory( (*it) ) )
+ {
+ if( (*it).filename() == "subject")
+ {
+ subjectFound = true;
+ }
+ if( (*it).filename() == "acqp")
+ {
+ acqpFound = true;
+ }
+ }
+ }
+
+ // 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;
+ 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!
+
+ switch (type)
+ {
+ case 1: {
+ std::string subject = InputDirName + VALID_FILE_SEPARATOR;
+ subject += "subject";
+ boost::algorithm::replace_all( subject, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ 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 (InputDirName, OutputDirName);
+ }
+ break;
+ }
+
+ case 2:
+ {
+ subject_name = "defaultPatName";
+ strPatientName = subject_name;
+ DealWithSingleStudyDirectory (InputDirName,OutputDirName);
+ 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::Directory::FilenamesType &dirNames,const std::string ¤tOutputDirName)
+{
+ gdcm::Directory::FilenamesType::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::Directory dirList;
+ dirList.Load(*it);
+ gdcm::Directory::FilenamesType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ gdcm::Filename file(fileNames.begin()->c_str());
+ std::string path = file.GetPath();
+ std::string subject = path +
+ VALID_FILE_SEPARATOR +
+ "subject";
+ boost::algorithm::replace_all( subject, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ 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(dirList.GetDirectories().begin()->c_str(), currentOutputDirName);
+ }
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "[" << *it << "] is NOT a directory; skipped!" << std::endl;
+ }
+ }
+}
+
+// ----------------------------------------------------------------------------------------------------------
+
+void Bruker2Dicom::DealWithSingleStudyDirectory (const std::string &dirname, const std::string &i_outputDir) //(gdcm::Directory::FilenamesType &fileNames)
+{
+ bool res;
+ // creation directory : 'nom du patient'
+ std::string output = createDirectory(subject_name.c_str(), i_outputDir);
+
+
+ if (subjectFound)
+ {
+ BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
+ 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");
+ 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");
+ subject_date = b_date.GetStringValue()[0];
+ strStudyTimeDate = subject_date;
+ cleanString(subject_date);
+
+ BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
+ subject_study_name = b_study_name.GetStringValue()[0];
+ subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
+ cleanString(subject_study_name);
+ }
+ else // Desperate trick when file 'subject' is missing
+ {
+ subject_entry = "HeadFirst"; // Why not?
+ subject_position = "Supine"; // Why not?
+ strStudyTimeDate = "06_06_06_6_June_1666"; // Why not?
+ subject_date = "6_June_1666"; // Why not?
+ 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*/;
+
+ // creation directory : 'nom de la Study'
+ output = createDirectory(strStudyDescr, output);
+
+ gdcm::UIDGenerator uid;
+ strStudyUID = uid.Generate();
+ serieNumber = 0;
+ instanceNumber = 0;
+
+ // -----------------------------------------------------
+ // 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
+ // -----------------------------------------------------
+ boost::filesystem::directory_iterator it(dirname), end_iter;
+ for(; it != end_iter; ++it)
+ {
+ if(boost::filesystem::is_directory(*it))
+ {
+ std::string fname = (*it).filename() ;
+ //if (fname == "AdjResult") continue; what's the point?
+ boost::filesystem::directory_iterator it_level((*it));
+ bool bAcqp = false;
+ std::string nextLevel;
+ std::string strAcqp;
+ std::string nameAcqp;
+ for(; it_level != end_iter; ++it_level)
+ {
+ if( (*it_level).filename() == "acqp")
+ {
+ strAcqp = (*it_level).string();
+ nameAcqp = (*it_level).filename();
+ boost::algorithm::replace_all( strAcqp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ bAcqp = true;
+ }
+ else if (boost::filesystem::is_directory( (*it_level) ) && nextLevel == "")
+ {
+ nextLevel = (*it_level).string(); // Hope we found only one directory
+ }
+ else
+ {
+ // nothing
+ }
+ }
+
+ if ( bAcqp)
+ {
+ std::string acqp_scan_name;
+ std::string acqp_method;
+ std::string acqp_protocol_location;
+
+ br_acqp.LoadFile(strAcqp);
+ br_acqp.FillMap();
+ 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");
+ b_method.PrintSelf(); // why?
+ acqp_method = b_method.GetStringValue()[0];
+ cleanString(acqp_method);
+
+ BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
+ nbSlices = b_list_size.GetIntValue()[0];
+ strSerieDescr = fname
+ + "." + acqp_scan_name
+ + "." + acqp_method.c_str();
+
+
+ /*sprintf(outputDirName, "%s%c%s", i_outputDir.c_str(), VALID_FILE_SEPARATOR, strSerieDescr.c_str() );
+ std::string temp(outputDirName);
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);*/
+ output = createDirectory(strSerieDescr, output);
+ if (verbose)
+ printf ("outputDirName [%s]\n", output);
+ try {
+
+ DealWithNiveau1( (*it).string(), output);
+ }
+ catch (BrukerHopelessException &e)
+ {
+ std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
+ continue;
+ }
+ }
+ }
+ } // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
+}
+
+// =====================================================================
+
+void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName) {
+//
+// e.g. : at level 1, in B67d1.Bp1/6
+//
+// acqp fid imnd pdata pulseprogram spnam0 spnam1
+
+
+ //gdcm::Directory dirList;
+ //dirList.Load(level1Directory); // DON'T get recursively the list of files
+ //gdcm::Directory::FilenamesType fileNames;
+ //fileNames = dirList.GetFilenames();
+
+ // -----------------------------------------------------
+ // Iterate to ALL the objets(files/directories) found in the input directory
+ // -----------------------------------------------------
+ bool bmethod = false;
+ //gdcm::Directory::FilenamesType::iterator it = fileNames.begin();
+ boost::filesystem::directory_iterator it(level1Directory), it_end;
+ for(; it != it_end; it++)
+ {
+ if((*it).leaf() == "method")
+ {
+ bmethod = br_method.LoadFile((*it).string());
+ break;
+ }
+ }
+
+ // if method wasn't found or unable to load, try with imnd file
+ if(!bmethod)
+ {
+ for(; it != it_end; it++)
+ {
+ if((*it).leaf() == "imnd")
+ {
+ bmethod = br_method.LoadFile((*it).string());
+ break;
+ }
+ }
+ }
+ if(!bmethod)
+ {
+ std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
+ << level1Directory << "]; we skip it!" << std::endl;
+ }
+ // if (verbose)
+ // std::cout << "open => [" << strMethod << "] successfully" << std::endl;
+ /* a recuperer :
+ ##$PVM_Fov (dimension) // ou plutot RECO_fov !
+ */
+ /*
+ dans method (pour perfusion seulement?) :
+ ##$PVM_ObjOrderList=( 8 )
+ 0 2 4 6 1 3 5 7
+ ##$PVM_NSPacks=2
+ ##$PVM_SPackArrNSlices=( 2 )
+ 7 1
+ */
+ br_method.FillMap();
+
+ try
+ {
+ boost::filesystem::directory_iterator itDir(level1Directory), it_end;
+ for(; itDir != it_end; ++itDir)
+ {
+ if ( boost::filesystem::is_directory(*itDir) && (*itDir).leaf() == "pdata")
+ {
+ std::string output = createDirectory( (*itDir).leaf() , currentOutputDirName);
+ // will be always "pdata" ...
+ boost::filesystem::directory_iterator itDirInside(*itDir), it_inside_end;
+ for(; itDirInside != it_end; ++it)
+ {
+ // we take the first and hope that we have only one!
+ if ( boost::filesystem::is_directory(*itDirInside))
+ {
+ output = createDirectory( (*itDirInside).leaf() , output);
+ DealWithNiveau2( (*itDirInside).string(), output);
+ }
+ }
+ }
+ }
+ }
+ catch(BrukerHopelessException &e)
+ {
+ std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
+ }
+
+}
+
+// =====================================================================
+
+void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName) {
+
+// e.g. : at level 2 in B67d1.Bp1/6/pdata
+//
+// acqp fid imnd pdata pulseprogram spnam0 spnam1
+//
+ std::string output = currentOutputDirName;
+
+ bool bisa = false;
+ boost::filesystem::directory_iterator it(level2Directory), it_end;
+ for(; it != it_end; ++it)
+ {
+ if((*it).leaf() == "isa")
+ {
+ bisa = br_isa.LoadFile((*it).string());
+ if (bisa)
+ {
+ br_isa.FillMap();
+ BrukerFieldData b_isa_func_name = br_isa.GetFieldData("ISA_func_name");
+
+ std::string str_isa_func_name = b_isa_func_name.GetStringValue()[0];
+ cleanString(str_isa_func_name);
+ output = createDirectory(str_isa_func_name, currentOutputDirName);
+
+ }
+ break;
+ }
+ }
+ try {
+ DealWithNiveau3(level2Directory, output);
+ }
+ catch (BrukerHopelessException &e)
+ {
+ std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
+ << " We skip [" << level2Directory << "]" << std::endl;
+
+ }
+ catch (BrukerInitException &e)
+ {
+ std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
+ << " We skip [" << level2Directory << "]" << std::endl;
+
+ }
+
+}
+
+//
+// =====================================================================
+//
+
+void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName){
+
+//
+// e.g. at level 3, in
+
+ // just to be able to go on checking // JP
+ gdcm::Filename file;
+
+ bool res;
+
+
+
+ gdcm::Directory dirList;
+ dirList.Load(level3Directory); // DON'T get recursively the list of files
+ gdcm::Directory::FilenamesType::iterator it;
+ gdcm::Directory::FilenamesType fileNames = dirList.GetFilenames();
+
+ char original2dseqName [(unsigned int) PATH_MAX+2];
+ char original2dseqName_XXX [(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!
+ std::string temp;
+ bool canOpen;
+
+ //-------------- try d3proc;
+
+ canOpen = br_d3proc.LoadFile(findFile( level3Directory,"d3proc"));
+
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! no 'd3proc' found" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
+ //exit(0); /// \TODO throw an exception !
+ }
+ else
+ {
+ canOpen = br_d3proc.FillMap();
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
+ }
+ }
+
+ //-------------- end try d3proc;
+
+
+ // -------------------try reco
+
+
+ std::string str_reco = level3Directory + VALID_FILE_SEPARATOR + "reco";
+ canOpen = br_reco.LoadFile(findFile( level3Directory, "reco"));
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl;
+ 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'"));
+
+ }
+ else {
+ if (verbose)
+ std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
+ }
+ }
+
+ //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];
+
+ if (verbose)
+ std::cout << "IM_SIX " << NX << std::endl;
+ BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
+ int NY = bY.GetIntValue()[0];
+
+ 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)
+ {
+ sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
+ VALID_FILE_SEPARATOR, "MhdFiles");
+ std::string temp(currentOutputMhdDirName);
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(currentOutputMhdDirName, "%s", temp);
+ std::string strCurrentOutputMhdDirName(currentOutputMhdDirName);
+ res = CreateDirectory( strCurrentOutputMhdDirName );
+ if (!res) {
+ std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
+ throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
+ //exit (0);
+ }
+
+ if (verbose)
+ std::cout << "Directory creation [" << currentOutputDirName << "]" << std::endl;
+ } // end if mhd
+
+ if (verbose)
+ std::cout << "nbFrames " << nbFrames << std::endl;
+ if (verbose)
+ std::cout << "nbSlices " << nbSlices << std::endl;
+ int k;
+ int nbInstants = nbFrames/nbSlices;
+ if (verbose)
+ std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
+ int instantNb;
+ int sliceNb;
+ FILE *fp; // for MHD files
+
+ sprintf( original2dseqName, "%s%c%s", level3Directory.c_str(),VALID_FILE_SEPARATOR, "2dseq");
+ temp = level3Directory + VALID_FILE_SEPARATOR + "2dseq" ;
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(original2dseqName, "%s", temp);
+
+/**/
+ // \TODO : tenir compte du bazar precedent
+
+ // load 2dseq in memory
+
+ fp = fopen(temp.c_str(), "rb");
+ if (!fp)
+ {
+ // try 2dseq_Angio2D ?!?
+ temp = original2dseqName_XXX;
+ sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
+ sprintf(original2dseqName_XXX, "%s", temp);
+ fp = fopen(original2dseqName_XXX, "rb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << original2dseqName << "] nor [" << original2dseqName_XXX << "] for reading" << std::endl;
+ fclose(fp);
+ throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
+ //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!
+ // ---------------------------
+ try {
+ imageSet = CreateImageSet ( );
+ }
+ catch (BrukerInitException& e)
+ {
+ if (verbose)
+ std::cout << "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
+ << "catched in DealWithNiveau3" << std::endl;
+ //return;
+ throw (e);
+ }
+
+ serieNumber++;
+ gdcm::UIDGenerator uid;
+ strSerieUID = uid.Generate();
+
+ if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives)
+ {
+ if (verbose)
+ std::cout << "Single instant : do not split" << std::endl;
+ if (mhd)
+ {
+ sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
+ VALID_FILE_SEPARATOR);
+ temp = currentOutputDirName + VALID_FILE_SEPARATOR + "MhdFiles" + VALID_FILE_SEPARATOR +"MhdData_All_the_Slices.mhd";
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(outputMhdFileName,"%s", temp);
+ fp=fopen(temp.c_str(), "w");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
+ //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, "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" );
+ fprintf(fp, "ElementNumberOfChannels = 1\n" );
+ fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );
+ fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
+ fclose(fp);
+ }
+ sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices",
+ currentOutputDirName.c_str(), VALID_FILE_SEPARATOR);
+ temp = currentOutputDirName + VALID_FILE_SEPARATOR + "2dseq_All_the_Slices";
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(output2dseqSliceFileName,"%s",temp);
+ fp=fopen(temp.c_str(), "wb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
+ }
+ else
+ {
+ fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
+ }
+ fclose(fp);
+ serieNumber ++;
+ gdcm::UIDGenerator uid;
+ strSerieUID = uid.Generate();
+
+ } // end if mhd
+ if (dicom)
+ {
+ sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
+ VALID_FILE_SEPARATOR);
+ temp = currentOutputDirName + VALID_FILE_SEPARATOR + "2dseq_All_the_Slices.dcm";
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(output2dseqSliceFileName, "%s", temp);
+
+ /* ----------- Write Dicom Image ---------------*/
+ MakeDicomImage(buffer_2dseq,
+ NX,
+ NY,
+ nbFrames,
+ pixelSize,
+ //fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
+ temp.c_str(),
+ subject_name,
+ day,
+ strStudyUID,
+ strSerieUID,
+ strStudyDescr,
+ strSerieDescr,
+ strStudyTimeDate,
+ 0,// index frame number
+ 4 //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,
+ VALID_FILE_SEPARATOR, k );
+ temp = outputMhdFileName;
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(outputMhdFileName, "%s", temp);
+ 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;
+ throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
+ //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 ); //
+ fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 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", VALID_FILE_SEPARATOR, sliceNb );
+ fclose(fp);
+ } // end write MHD
+
+ sprintf(output2dseqSliceFileName, "%s%c2dseq_Slice_%d",
+ currentOutputDirName.c_str(), VALID_FILE_SEPARATOR,sliceNb);
+ temp = output2dseqSliceFileName;
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(output2dseqSliceFileName, "%s", temp);
+ fp=fopen(output2dseqSliceFileName, "wb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
+ //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(), VALID_FILE_SEPARATOR, sliceNb);
+ temp= output2dseqSliceFileName;
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(output2dseqSliceFileName, "%s", temp);
+
+ MakeDicomImage(
+ pixelsForCurrentSlice,
+ NX,
+ NY,
+ nbInstants,
+ pixelSize,
+ spatResolX, spatResolY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
+ output2dseqSliceFileName,
+ subject_name,
+ day,
+ strStudyUID,
+ strSerieUID,
+ strStudyDescr,
+ strSerieDescr,
+ strStudyTimeDate,
+ sliceNb*nbInstants,
+ 4 //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,*/ spatResolX, spatResolY, sliceDistance,
+ copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
+}
+
+// ===========================================================================================
+
+void Bruker2Dicom::dealWithCarto(gdcm::Directory::FilenamesType &fileNames, int NX, int NY, int nbSlices,
+ /*double fovX, double fovY, */
+ double spatResolX, double spatResolY, double sliceDistance,
+ char *copyFile, std::string ¤tOutputDirName,
+ char *outputMhdFileName, char *output2dseqCartoName)
+{
+ // -----------------------------------------------------
+ // deal with MatLab-generated Carto file.
+ // -----------------------------------------------------
+
+ const char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with ""
+ const char *separator[] = { "_", ".", "-", "" }; // add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
+ int icode;
+ int iseparator;
+ gdcm::Directory::FilenamesType::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 ( boost::filesystem::is_regular(*it) )
+ //if ( ! boost::filesystem::is_directory(*it) )
+ {
+ if (verbose)
+ std::cout << "--- [" << *it << "] is a file..." << std::endl;
+
+ icode = 0;
+ while (code[icode][0] != 0)
+ {
+ iseparator = 0;
+ while (separator[iseparator][0] != 0)
+ {
+ sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g "2dseq_ADC"
+ //if (verbose)
+ // std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
+ 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;
+ throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
+ }
+ fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
+
+ // ?!? sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
+ std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
+ << NX*NY*sizeof(double)*nbSlices << std::endl;
+ gdcm::Filename file ( (*it).c_str());
+ std::string lastFileName = file.GetName();
+ if (mhd)
+ {
+ // Copy the data file in the new directory
+ sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
+ currentOutputDirName.c_str(), VALID_FILE_SEPARATOR, lastFileName.c_str());
+ std::string temp(copyFile);
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(copyFile, "%s", temp);
+
+ system(copyFile);
+ sprintf(outputMhdFileName, "%s%c%s%s",
+ currentOutputDirName.c_str(),VALID_FILE_SEPARATOR, lastFileName.c_str(), ".mhd" );
+ temp = outputMhdFileName;
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(outputMhdFileName, "%s", temp);
+
+ 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, "HeaderSize = %d\n", 0 );
+ fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 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(), VALID_FILE_SEPARATOR, lastFileName.c_str(), ".dcm" );
+
+ std::string temp(output2dseqCartoName);
+ boost::algorithm::replace_all( temp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ sprintf(output2dseqCartoName,"%s", temp);
+
+ if (verbose)
+ std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
+ gdcm::UIDGenerator uid;
+ strSerieUID = uid.Generate();
+
+ gdcm::Filename file( (*it).c_str() );
+ std::string strNewSerieDescr(strSerieDescr+ "_" + file.GetName());
+ MakeDicomImage(buffer_carto,
+ NX,
+ NY,
+ nbSlices,
+ 8, // pixelSize
+ //fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
+ output2dseqCartoName,
+ subject_name,
+ day,
+ strStudyUID,
+ strSerieUID,
+ strStudyDescr,
+ strNewSerieDescr,
+ strStudyTimeDate,
+ 0,
+ 3// 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!
+
+ } // end deal with _ADC, -adc, etc
+ iseparator ++;
+ } // end iterate speparators
+ icode++;
+ } // end iterate code
+ } // end boost::filesystem::is_regular(*it)
+ } // end iterate on all objects (files, dir, etc)
+} // end method
+
+// ==========================================================================================================
+
+int Bruker2Dicom::CheckUserDirectory(std::string &userDirName)
+{
+ gdcm::Directory dirList;
+ dirList.Load(userDirName); // DON'T get recursively the list of files
+
+ gdcm::Directory::FilenamesType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ gdcm::Filename file( fileNames.begin()->c_str());
+ std::string path = file.GetPath();
+
+ std::string subject = path +
+ VALID_FILE_SEPARATOR +
+ "subject";
+ boost::algorithm::replace_all( subject, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ std::string acqp = path +
+ VALID_FILE_SEPARATOR +
+ "acqp";
+ boost::algorithm::replace_all( acqp, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ if ( boost::filesystem::is_regular(subject) )
+ subjectFound = true; // user passed a 'study
+ else
+ subjectFound = false; // user didnt' pass a 'study
+
+ if ( boost::filesystem::is_regular(acqp) )
+ acqpFound= true; // user passes a 'serie', not a 'study'
+ 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!
+
+ return type;
+}
+
+// ==========================================================================================================
+
+bool Bruker2Dicom::CreateDirectory(const std::string &OutputDirName)
+{
+ std::string systemCommand;
+
+ if (verbose)
+ std::cout << "Check for output directory :[" << OutputDirName << "]."
+ <<std::endl;
+ boost::filesystem::directory_entry ent(OutputDirName);
+ if ( ! boost::filesystem::is_directory(ent) ) // dirout not found
+ {
+ systemCommand = "mkdir " + OutputDirName; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ // if ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
+ // {
+ // if (verbose)
+ // std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
+ // //return 0;
+ //throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
+ // }
+ // 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("_");
+ ////boost::algorithm::replace_all(
+ //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];
+ if (verbose)
+ 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];
+ if (verbose)
+ 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);
+
+ if (result == false)
+ {
+ throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
+ }
+
+ 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] << " ";CreateImageSet
+
+ //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,
+ int contentType
+ )
+{
+ std::ostringstream str;
+
+ gdcm::File file;
+ gdcm::DataSet ds;
+ ds.Clear();
+
+
+ // Set the image size
+ // columns
+ {
+ gdcm::Attribute<0x0028,0x0011, gdcm::VR::US> at;
+ at.SetValue(X);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // rows
+ {
+ gdcm::Attribute<0x0028,0x0010, gdcm::VR::US> at;
+ at.SetValue(Y);
+ ds.Replace(at.GetAsDataElement());
+ }
+
+ //file.SetDataSet( createDataSet(str.str(),0x0028,0x0011,"US"));
+ // 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)
+ {
+ gdcm::Attribute<0x0028,0x0008, gdcm::VR::IS> at;
+ at.SetValue(nbFrames);
+ ds.Replace(at.GetAsDataElement());
+ // file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
+ }
+
+ // Set the pixel type
+ // Bits allocated
+ {
+ gdcm::Attribute<0x0028,0x0100, gdcm::VR::US> at;
+ at.SetValue(pixelSize*8);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // Bits stored
+ {
+ gdcm::Attribute<0x0028,0x0101, gdcm::VR::US> at;
+ at.SetValue(pixelSize*8);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // High Bit
+ {
+ gdcm::Attribute<0x0028,0x0102, gdcm::VR::US> at;
+ at.SetValue(pixelSize*8 -1);
+ ds.Replace(at.GetAsDataElement());
+ }
+
+ // pixel representation
+ {
+ gdcm::Attribute<0x0028,0x0103, gdcm::VR::US> at;
+ at.SetValue(1);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // sample per pixel
+ {
+ gdcm::Attribute<0x0028,0x0002, gdcm::VR::US> at;
+ at.SetValue(1);
+ ds.Replace(at.GetAsDataElement());
+ }
+
+ // pixel spacing
+ {
+ char temp[256];
+ sprintf(temp,"%d%s%d",spacingX, "\\", spacingY);
+ std::string st;
+ st = temp;
+ gdcm::Attribute<0x0028,0x0030, gdcm::VR::DS> at;
+ // at.SetValue(st);
+ ds.Replace(at.GetAsDataElement());
+ }
+ //Slice Thickness
+ {
+ gdcm::Attribute<0x0018,0x00500, gdcm::VR::DS> at;
+
+ at.SetValue(sliceDistance);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // Series Number
+ {
+ gdcm::Attribute<0x0020,0x0011, gdcm::VR::IS> at;
+ at.SetValue(serieNumber);
+ ds.Replace(at.GetAsDataElement());
+ }
+ //Instance Number
+ {
+ gdcm::Attribute<0x0020,0x00131,gdcm::VR::IS> at;
+ at.SetValue(++instanceNumber);
+ ds.Replace(at.GetAsDataElement());
+
+ }
+ // [Media Storage SOP Class UID]
+ {
+ /*
+ str.str("");
+ str << "1.2.840.10008.5.1.4.1.1.4";
+ gdcm::Tag tag(0x0002, 0x0002);
+ tag.Write(str);
+ at.SetValue(str);
+ ds.Replace(at.GetAsDataElement());*/
+ }
+ // [SOP Class UID]
+ {
+ /* gdcm::Attribute<0x0008, 0x0162gdcm::VR::UI> at;
+ at.SetValue("1.2.840.10008.5.1.4.1.1.4");
+ ds.Replace(at.GetAsDataElement());*/
+ }
+ // Patient Name
+ {
+ gdcm::Attribute<0x0010,0x0010, gdcm::VR::PN> at;
+ at.SetValue(patientName);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // Patient's ID
+ {
+ gdcm::Attribute<0x0010,0x0020, gdcm::VR::LO> at;
+ at.SetValue(patientName);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // study UID
+ {
+ gdcm::Attribute< 0x0020, 0x000d, gdcm::VR::UI> at;
+ at.SetValue(studyUID);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // serieUID
+ {
+ gdcm::Attribute< 0x0020, 0x000e, gdcm::VR::UI> at;
+ at.SetValue(serieUID);
+ ds.Replace(at.GetAsDataElement());
+ }
+ {
+ gdcm::Attribute< 0x0008,0x0020, gdcm::VR::DA> at;
+ at.SetValue(strStudyTimeDate.substr(10,11).c_str());
+ ds.Replace(at.GetAsDataElement());
+ }
+ {
+ gdcm::Attribute< 0x0008,0x0030, gdcm::VR::TM> at;
+ at.SetValue(strStudyTimeDate.substr(1,8).c_str());
+ ds.Replace(at.GetAsDataElement());
+ }
+ // Study Description
+ {
+ gdcm::Attribute< 0x0008,0x1030, gdcm::VR::LO> at;
+ at.SetValue(studyDescr);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // Series Description
+ {
+ gdcm::Attribute< 0x0008,0x103e, gdcm::VR::LO> at;
+ at.SetValue(serieDescr);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // Modalirty
+ {
+ gdcm::Attribute< 0x0008,0x0060, gdcm::VR::CS> at;
+ at.SetValue("MR");
+ ds.Replace(at.GetAsDataElement());
+ }
+
+
+ // //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");
+
+// 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" , 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(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
+//
+///// \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 << "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 ;
+*/
+
+ {
+ gdcm::Attribute< 0x0020,0x0037, gdcm::VR::DS> at;
+ at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0], 0);
+ at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1], 1);
+ at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2], 2);
+ at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0], 3);
+ at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1], 4);
+ at.SetValue( imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2], 4);
+ ds.Replace(at.GetAsDataElement());
+ }
+// file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
+
+ 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 0032 DS 3 Image Position (Patient)
+ {
+ gdcm::Attribute< 0x0020,0x0032,gdcm::VR::DS> at;
+ at.SetValue( imageSet[imgNum].getTranslationVectorRPS2XYZ()[0], 0);
+ at.SetValue( imageSet[imgNum].getTranslationVectorRPS2XYZ()[1], 1);
+ at.SetValue(imageSet[imgNum].getTranslationVectorRPS2XYZ()[2], 2);
+ ds.Replace(at.GetAsDataElement());
+ }
+
+
+ // 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
+>
+ */
+ {
+ gdcm::Attribute< 0x0029,0x0010, gdcm::VR::LO> at;
+ at.SetValue( "CREATIS HEADER");
+ ds.Replace(at.GetAsDataElement());
+ }
+ {
+ gdcm::Attribute< 0x0029,0x0011, gdcm::VR::LO> at;
+ at.SetValue( "CREATIS FOR BRUKER-TO-DICOM");
+ ds.Replace(at.GetAsDataElement());
+ }
+
+ // 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<std::string> method = brf_method.GetStringValue();
+
+ // std::string method = br_method.GetFieldData("Method").GetStringValue();
+ //{
+ // gdcm::Attribute< 0x0029,0x0100, gdcm::VR::LO> at;
+ // at.SetValue(method[0]);
+ // ds.Replace(at.GetAsDataElement());
+ //}
+ //file->InsertEntryString(method[0], 0x0029,0x0100, "LO");
+
+ std::cout << " method[" << method[0] << "]" << std::endl;
+ if (method[0] == "DtiEpi" || method[0] == "DtiStandard")
+ {
+ // const std::vector<int> NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir").GetIntValue();
+ BrukerFieldData brf_NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir");
+ const std::vector<int> NDiffDir = brf_NDiffDir.GetIntValue();
+
+ //const std::vector<int> NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach").GetIntValue();
+ BrukerFieldData brf_NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach");
+ const std::vector<int> NDiffExpEach =brf_NDiffExpEach.GetIntValue();
+
+// const std::vector<int> AoImages = br_method.GetFieldData("PVM_DwAoImages").GetIntValue();
+ BrukerFieldData brf_AoImages = br_method.GetFieldData("PVM_DwAoImages");
+ const std::vector<int> AoImages = brf_AoImages.GetIntValue();
+
+ BrukerFieldData brf_DwBvalEach = br_method.GetFieldData("PVM_DwBvalEach");
+ const std::vector<double> 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];
+ {
+ gdcm::Attribute< 0x0029,0x0101, gdcm::VR::US> at;
+ at.SetValue( NDiffDir[0]);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // file->InsertEntryString(str.str(),0x0029,0x0101,"US"); // directions
+ str.str("");
+ str << NDiffExpEach[0];
+ {
+ gdcm::Attribute< 0x0029,0x0102, gdcm::VR::US> at;
+ at.SetValue( NDiffExpEach[0]);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // file->InsertEntryString(str.str(),0x0029,0x0102,"US"); // valeurs de b par direction
+ str.str("");
+ str << AoImages[0];
+ {
+ gdcm::Attribute< 0x0029,0x0103, gdcm::VR::US> at;
+ at.SetValue( AoImages[0]);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // file->InsertEntryString(str.str(),0x0029,0x0103,"US"); // image pour b=0
+
+ {
+ gdcm::Attribute< 0x0029,0x0104,gdcm::VR::DS> at;
+ for (unsigned int i=0; i<NDiffExpEach[0]; i++)
+ at.SetValue( DwBvalEach[i], i);
+ ds.Replace(at.GetAsDataElement());
+ }
+ // file->InsertEntryString(str.str(),0x0029,0x0104,"DS"); // Valeurs de b
+ }
+ file.SetDataSet(ds);
+
+// 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");
+*/
+ // dcmImageName = "c:\\toto.dcm";
+ boost::algorithm::replace_all( dcmImageName, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ FILE *fil=fopen("c:\\toto", "a");
+ fclose(fil);
+
+ gdcm::ImageWriter writer;
+ writer.SetFileName(dcmImageName.c_str());
+ writer.SetFile(file);
+ gdcm::DataElement pixeldata( gdcm::Tag(0x7fe0,0x0010) );
+ pixeldata.SetByteValue( (char*)tabPixels ,X*Y*nbFrames*pixelSize );
+ gdcm::Image im;
+ im.SetDataElement(pixeldata);
+ writer.SetImage(im);
+
+// 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;
+// file->Delete();
+// fileH->Delete();
+// throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
+// }
+// //if (verbose)
+// // file->Print();
+//
+// file->Delete();
+// fileH->Delete();
+}
+
+//////////////////////////////////////////////////////////////////////
+// Generic repertory creation //
+//////////////////////////////////////////////////////////////////////
+const std::string Bruker2Dicom::createDirectory(const std::string &i_name, const std::string &i_dir)
+{
+
+ // creation directory : 'nom du patient'
+ std::string tempString(i_dir);
+ tempString = tempString + VALID_FILE_SEPARATOR + i_name;
+ boost::algorithm::replace_all( tempString, INVALID_FILE_SEPARATOR , VALID_FILE_SEPARATOR);
+ if (!CreateDirectory(tempString))
+ {
+ std::cout << "[" << tempString << "] Directory creation failure " << std::endl;
+ throw ( BrukerHopelessException ("Patient directory creation failure "));
+ }
+ return tempString.c_str();
+}
+
+ std::string Bruker2Dicom::findFile(const std::string &i_dir, const std::string i_name)
+{
+ bool bres = false;
+ std::string file;
+ boost::filesystem::directory_iterator it(i_dir), it_end;
+ for(; it != it_end; ++it)
+ {
+ if((*it).leaf() == i_name)
+ {
+ file = (*it).string();
+ bres = true;
+ break;
+ }
+ }
+
+ if(!bres)
+ {
+ boost::filesystem::path pth (i_dir);
+ boost::filesystem::directory_iterator itless(pth.branch_path()), it_end;
+ for(; itless != it_end; ++itless)
+ {
+ if((*itless).leaf() == i_name)
+ {
+ file = (*itless).string();
+ bres = true;
+ break;
+ }
+ }
+ }
+ return file.c_str();
+}
+
+
+//const gdcm::DataSet Bruker2Dicom::createDataSet(const std::string &i_val,
+// const uint16_t &i_gr, const uint16_t &i_el,
+// const gdcm::VR &i_vr)
+//
+//{
+// gdcm::Attribute<i_gr, i_el> at;
+// at.SetValue(i_val.c_str());
+//
+//
+// gdcm::DataElement de;
+// de.Clear();
+// de.SetVR(i_vr);
+// de.SetTag( gdcm::Tag(i_gr, i_el) );
+//
+// gdcm::DataSet ds;
+// ds.Clear();
+// ds.Replace(at.GetAsDataElement());
+// return ds;
+//}
git://git.creatis.insa-lyon.fr / creaBruker.git / commitdiff