]> Creatis software - creaBruker.git/blobdiff - lib/src1/bruker2dicom.cxx
Fix 'AdjResult' dir troubles
[creaBruker.git] / lib / src1 / bruker2dicom.cxx
index 34a5ea098417e34cc633ab4088edff4a4026fc0b..961c8e7e9a2891622fe588db9b4780919e2816e8 100644 (file)
@@ -7,8 +7,6 @@
    #define PATH_MAX 2048
 #endif 
 
-
-
 bool Bruker2Dicom::Execute()
 {
    // ----- Check input directory name -----
@@ -37,69 +35,153 @@ bool Bruker2Dicom::Execute()
       throw ( BrukerHopelessException ("Output directory creation failure "));
    }
 
-   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
 //
 
+   std::string strDirNamein(InputDirName);
+   
+/* */
+   GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
+     
    GDCM_NAME_SPACE::DirListType fileNames;
    fileNames = dirList.GetFilenames();
-   bool canOpen;
-   std::string outputFileName;
 
+   std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
 
-  // 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;
-       
-   bool subjectFound;  
-   canOpen =br_subject.LoadFile(subject);  
-   if (!canOpen)
+   std::string subject =  path +
+                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+                          "subject";
+
+    std::string acqp = path +
+                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+                       "acqp";
+
+    if ( boost::filesystem::is_regular(subject) )
+       subjectFound = true;
+    else
+       subjectFound = false; // user passed only a 'serie', not a 'study 
+
+    if ( boost::filesystem::is_regular(acqp) )
+       acqpFound= true;
+    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!
+ /* */
+
+
+   // 1 : if subjectFound                       : user passed a Single Study Directory
+   // 2 : if NOT subjectFound and acqpFound     : user passed a Serie Directory
+   // 3 : if NOT subjectFound and NOT acqpFound : user passed a 'non Study Directory' (Hope it's a set of Single Study Directories)
+   
+   //int type = CheckUserDirectory(InputDirName);
+   switch (type)
    {
-      //std::cout << "Hopeless! no 'subject' found" << std::endl;
-      //throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
-       
-      std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl;
-      subjectFound = false;
-   }
-   else
-   { 
-      br_subject.FillMap();
-      subjectFound = true;   
-   }
+      case 1: {   
+         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();
+         }
    //br_subject.PrintSelf();
 
   // get info for 'Study Description'  
 
-    if (subjectFound)
-    {
-       BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
-       subject_name = b_name.GetStringValue()[0];
-       strPatientName = subject_name;
-       cleanString(subject_name);
-     }
-     else
-        subject_name ="defaultPatName";  
+         BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
+         subject_name = b_name.GetStringValue()[0];
+         strPatientName = subject_name;
+         cleanString(subject_name);
+         DealWithSingleStudyDirectory (fileNames);
+         break;
+      }
+
+      case 2: {
+           subject_name = "defaultPatName";
+          strPatientName = subject_name;
+           DealWithSingleStudyDirectory (fileNames);
+          break;
+      }
+
+      case 3: {
+         std::cout << " user passed a 'non study' directory; Hope it's a *non recursive* 'set of studies' directory! (recursive not yet dealt with)" << std::endl;
+        DealWithMultiStudyDirectory (fileNames);
+        break;
+      }
+   }
+}
+
+// ----------------------------------------------------------------------------------------------------------
+
+void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames)
+{
+   GDCM_NAME_SPACE::DirListType::iterator it;
+
+   for (it = dirNames.begin();
+         it != dirNames.end();
+       ++it)
+   {
+      if ( boost::filesystem::is_directory(*it) )
+      {
+         if (verbose)
+            std::cout << "[" << *it << "] is a directory" << std::endl;
+
+         GDCM_NAME_SPACE::DirList dirList(*it, false, true); // DON'T get recursively the list of files
+         GDCM_NAME_SPACE::DirListType fileNames;
+         fileNames = dirList.GetFilenames();
         
+         std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
+         std::string subject =  path +
+                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+                                "subject";
+         if (! boost::filesystem::is_regular(subject) )
+         {
+           std::cout << "no [" << subject << "] file found" << std::endl;
+           continue;
+         }
+                  
+         bool canOpen = br_subject.LoadFile(subject);
+         if (!canOpen)
+         {
+            std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl;
+            throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open"));
+         }
+         else
+         {
+            br_subject.FillMap();
+         }
+          
+         BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
+         subject_name = b_name.GetStringValue()[0];
+         strPatientName = subject_name;
+         cleanString(subject_name);     
+         
+         DealWithSingleStudyDirectory(fileNames);   
+      }
+      else
+      {
+         if (verbose)
+            std::cout << "[" << *it << "] is NOT a directory; skipped!" << std::endl; 
+      }   
+   } 
+}
+
+// ----------------------------------------------------------------------------------------------------------
+
+void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames)
+{
+     bool res;  
     // creation directory : 'nom du patient'
     std::string tempStringPatDir(OutputDirName);
     tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
@@ -108,15 +190,12 @@ bool Bruker2Dicom::Execute()
     if (!res) {
        std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
        throw ( BrukerHopelessException ("Patient directory creation failure "));
-    }    
+    }
 
-    std::string subject_entry;
-    std::string subject_position;
-    std::string subject_date;
-    std::string subject_study_name;
     if (subjectFound)
     {
+    
+ std::cout << "===================================--===========nom dir [" << tempStringPatDir << "] subjectFound, studyName : " << subject_study_name<< std::endl;
        BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
        subject_entry = b_entry.GetStringValue()[0];
        //cleanString(subject_entry);
@@ -139,6 +218,8 @@ bool Bruker2Dicom::Execute()
    }
    else  // Desperate trick when file 'subject' is missing
    {
+
+ std::cout << "==============================================nom dir [" << tempStringPatDir << "] subjectFound" << std::endl;
       subject_entry      = "HeadFirst";            // Why not?
       subject_position   = "Supine";               // Why not?
       strStudyTimeDate   = "06_06_06_6_June_1666"; // Why not?
@@ -171,6 +252,7 @@ bool Bruker2Dicom::Execute()
    // each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
    // -----------------------------------------------------
  
+   /// \TODO better use directory iterator, from boost! // JPR
    GDCM_NAME_SPACE::DirListType::iterator it;
 
    for (it = fileNames.begin();
@@ -182,6 +264,10 @@ bool Bruker2Dicom::Execute()
          if (verbose)
             std::cout << "[" << *it << "] is a directory" << std::endl;
 
+        //if((*it) == "AdjResult")  // avoid trouble with new version 'AdjResult' directory
+        if(GDCM_NAME_SPACE::Util::GetName(*it) == "AdjResult")
+           continue;
+
          //BrukerDataSet br_acqp;
          std::string strAcqp;
          strAcqp = (*it) +
@@ -224,7 +310,7 @@ bool Bruker2Dicom::Execute()
                          + "." + acqp_scan_name
                          + "." + acqp_method.c_str();
 
-         sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),                //OutputDirName.c_str(), 
+         sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(),      //OutputDirName.c_str(), 
                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
                           strSerieDescr.c_str() );
   
@@ -232,12 +318,11 @@ bool Bruker2Dicom::Execute()
                    << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
                    << " ================================================================================"
                    << std::endl;
-
-
+        std::string strOutputDirName(outputDirName);
         if (verbose)
-           printf ("outputDirName [%s]\n", outputDirName);   
+           printf ("outputDirName [%s]\n", outputDirName);
         try {
-           DealWithNiveau1(*it, outputDirName);
+           DealWithNiveau1(*it, strOutputDirName);
        }
        catch (BrukerHopelessException &e)
        {
@@ -250,7 +335,7 @@ bool Bruker2Dicom::Execute()
 
 // =====================================================================
 
-void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
+void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string &currentOutputDirName) {
 //
 // e.g. : at level 1, in B67d1.Bp1/6
 //
@@ -309,6 +394,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
          sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str());
+         std::string strOutputDirName(outputDirName);
          //br1.PrintSelf();
 
           std::string strMethod;
@@ -351,7 +437,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
           7 1  
   */    
          try {
-            DealWithNiveau2(*it, outputDirName);
+            DealWithNiveau2(*it, strOutputDirName);
         }
         catch (BrukerHopelessException &e)
         {
@@ -364,8 +450,8 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
 
 // =====================================================================
 
-void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
-  
+void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string &currentOutputDirName) {
+
 // e.g. : at level 2 in B67d1.Bp1/6/pdata
 //
 // acqp  fid  imnd  pdata  pulseprogram  spnam0  spnam1
@@ -378,7 +464,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
       throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));       
       //exit (0);
    }
-  
+
    GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
 
    GDCM_NAME_SPACE::DirListType fileNames;
@@ -401,7 +487,6 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
       { 
          std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
       }
-      
    }
   
    for (it = fileNames.begin();
@@ -413,7 +498,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
   
          if (verbose)
             std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
+
         // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(), 
         //                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
         //                                GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
@@ -449,8 +534,9 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
              str_isa_func_name.c_str());
           }
-         try { 
-             DealWithNiveau3(*it, outputDirName);
+         std::string strOutputDirName(outputDirName);
+         try {
+             DealWithNiveau3(*it, strOutputDirName);
          }
          catch (BrukerHopelessException &e)
          {
@@ -463,17 +549,16 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
             std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); " 
                       << " We skip [" << level2Directory << "]" << std::endl;
             continue;
-         }                  
+         }          
       }
    }
 }
 
-
 //
 // =====================================================================
 //
 
-void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
+void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string &currentOutputDirName){
 
 //
 // e.g. at level 3, in
@@ -487,7 +572,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    if (!res)
    {
       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
-      throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));      
+      throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
       //exit (0);
    }
 
@@ -507,12 +592,12 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
 
    char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
    bool canOpen;
+
    //-------------- try d3proc;
    char char_d3proc[(unsigned int) PATH_MAX+2];
 
    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );     
-   
+
    if (verbose)
       std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
    std::string str_d3proc(char_d3proc);       
@@ -532,10 +617,10 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));      
       //exit(0);  /// \TODO throw an exception !     
    }
+
    //-------------- end try d3proc;
-    
+
+
  // -------------------try reco
 
    char char_reco[(unsigned int) PATH_MAX+2];
@@ -545,8 +630,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
     //             "d3proc";
    if (verbose)
-      std::cout << "reco --- => [" << char_reco << "]" << std::endl;
-   std::string str_reco(char_reco);       
+      std::cout << "reco: --- => [" << char_reco << "]" << std::endl;
+      
+   std::string str_reco(char_reco);
    canOpen = br_reco.LoadFile(str_reco);
 
    if (!canOpen) // we try in directory ../1
@@ -556,7 +642,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
       std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
       //lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
       sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
-      str_reco=char_reco;
+      //str_reco=char_reco;
       canOpen = br_reco.LoadFile(str_reco);
       if (!canOpen)
       {
@@ -564,15 +650,22 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
          throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));  
          //exit(0);  /// \TODO throw an exception !    
       }
+   } else {
+      if (verbose)
+         std::cout << "[" << str_reco << "] successfully Loaded " << std::endl;
    }
-
+   
    canOpen = br_reco.FillMap();
    if (!canOpen)
    {
       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
       throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));  
-      //exit(0);  /// \TODO throw an exception !     
-   }
+      //exit(0);  /// \TODO throw an exception !
+   } else {
+      if (verbose)
+         std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
+   }   
+   
    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
    // br_reco.PrintSelf();
    // std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
@@ -590,16 +683,16 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    if (verbose)
          std::cout << "IM_SIY " << NY << std::endl;
    /// \todo : check if there are actually 3 dimensions or only 2
-  
+
    BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
    int nbFrames = bZ.GetIntValue()[0]; 
    if (verbose)
          std::cout << "IM_SIZ " << nbFrames << std::endl;
 
         // WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
+
    BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
+
    std::string mhdDataPixelType;
    int pixelSize;
    getImhDataType(bDPT, mhdDataPixelType, pixelSize);
@@ -623,33 +716,51 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    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");
+   BrukerFieldData fov = br_reco.GetFieldData("RECO_fov");
    double fovX = fov.GetDoubleValue()[0];
    double fovY = fov.GetDoubleValue()[1];
    if (verbose)
-      std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
+      std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl;
 
-   BrukerFieldData spatResol = br_reco.GetFieldData("PVM_SpatResol");
-   double spatResolX = spatResol.GetDoubleValue()[0];
-   double spatResolY = spatResol.GetDoubleValue()[1];
+   BrukerFieldData size = br_reco.GetFieldData("RECO_size");
+   double sizeX = size.GetDoubleValue()[0];
+   double sizeY = size.GetDoubleValue()[1];
+   
    if (verbose)
-      std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
+      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(),
                                GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
-      res = CreateDirectory( currentOutputMhdDirName );
+
+      std::string strCurrentOutputMhdDirName(currentOutputMhdDirName);
+      res = CreateDirectory( strCurrentOutputMhdDirName );
       if (!res) {
          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
         throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));  
@@ -667,7 +778,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    int k;
    int nbInstants = nbFrames/nbSlices;
    if (verbose)
-         std::cout << "nbInstants (deduced )" << nbInstants << std::endl;    
+         std::cout << "nbInstants (deduced)" << nbInstants << std::endl;    
    int instantNb;
    int sliceNb; 
    FILE *fp;  // for MHD files
@@ -739,7 +850,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
                fprintf(fp, "HeaderSize = %d\n", 0);
                //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
-              fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
+               fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
                fprintf(fp, "Position = 0 0 %d\n", 0 );
                fprintf(fp, "Offset = 0 0 0\n" );
                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
@@ -853,6 +964,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                             1, fp);
                }
                fclose(fp);
+              
 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
             }  // end if mhd
    
@@ -956,8 +1068,8 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
    //  deal with MatLab-generated Carto file.
    // -----------------------------------------------------
    
-   char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" };  // add more carto file name identifiers if necessary; end with ""
-   char *separator[] =  { "_", ".", "-", "" }; //  add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
+   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_NAME_SPACE::DirListType::iterator it;
@@ -1087,9 +1199,47 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
 } // end method
 
 
+// ==========================================================================================================
+
+int Bruker2Dicom::CheckUserDirectory(std::string &userDirName)
+{
+   GDCM_NAME_SPACE::DirList dirList(userDirName, false, true); // DON'T get recursively the list of files
+     
+   GDCM_NAME_SPACE::DirListType fileNames;
+   fileNames = dirList.GetFilenames();
+
+   std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
+
+   std::string subject =  path +
+                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+                          "subject";
+
+    std::string acqp = path +
+                       GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+                       "acqp";
+
+    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(std::string OutputDirName)
+bool Bruker2Dicom::CreateDirectory(std::string &OutputDirName)
 {
    std::string systemCommand;
    
@@ -1098,8 +1248,7 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
                 <<std::endl;
    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
    {
-      std::string strDirNameout(OutputDirName);        // to please gcc 4
-      systemCommand = "mkdir " + strDirNameout;        // create it!
+      systemCommand = "mkdir " + OutputDirName;        // create it!      
       if (verbose)
          std::cout << systemCommand << std::endl;
       system (systemCommand.c_str());
@@ -1121,9 +1270,7 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
        if (verbose)
             std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
    }
-   
    return 1;
-
 }
 
 
@@ -1151,11 +1298,8 @@ void Bruker2Dicom::cleanString(std::string &s)
    GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
 }
 
-
-
 // ===========================================================================================
 
-
 void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
 { 
    if(bDPT.GetDataType() == "string")
@@ -1358,13 +1502,11 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
    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
@@ -1373,6 +1515,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
 
   // 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");
@@ -1412,7 +1555,6 @@ std::cout << "charImageOrientation  " <<
     
    file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
 
-
 // 0020 0032 DS 3 Image Position (Patient) 
 
    char charImagePosition[256];   
@@ -1422,8 +1564,6 @@ std::cout << "charImageOrientation  " <<
                              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));
@@ -1465,5 +1605,3 @@ std::cout << "charImageOrientation  " <<
    file->Delete();
    fileH->Delete();  
 }
-
-