X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=3dc9cbefc91a74057c9a43ab26cbfcc460749ecc;hb=e290be9f28dc24bfb58f239c098b67c2a76cfbd9;hp=b41186ac00488acc07e8ebf5373c8a687ae51ab9;hpb=0194cf3ca5e4249a389cc809d3de6fae07249fa4;p=creaBruker.git

diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx
index b41186a..3dc9cbe 100644
--- a/lib/src1/bruker2dicom.cxx
+++ b/lib/src1/bruker2dicom.cxx
@@ -1,14 +1,22 @@
 #include "bruker2dicom.h"
+#include <boost/filesystem/path.hpp>
+#include <boost/filesystem/operations.hpp>
+#include "brukerexception.h"
+
+#ifndef PATH_MAX // If not defined yet : do it 
+   #define PATH_MAX 2048
+#endif 
 
 
 
 bool Bruker2Dicom::Execute()
 {
-   // ----- Begin Processing -----
+   // ----- Check input values -----
 
    bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
  
-   if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
+   //if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
+   if ( ! boost::filesystem::is_directory(InputDirName) )
    {
       std::cout << "KO : [" << InputDirName << "] is not a Directory." << std::endl;
       return 0;
@@ -23,14 +31,15 @@ bool Bruker2Dicom::Execute()
    bool res=CreateDirectory(strDirNameOut);
    if (!res) {
       std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
-      exit (0);
+      //exit (0);
+      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;
@@ -51,6 +60,7 @@ bool Bruker2Dicom::Execute()
    bool canOpen;
    std::string outputFileName;
 
+
   // BrukerDataSet br_subject;
    std::string subject;
    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
@@ -63,7 +73,8 @@ bool Bruker2Dicom::Execute()
    if (!canOpen)
    {
       std::cout << "Hopeless! no 'subject' found" << std::endl;
-      exit(0);  /// \TODO throw an exception !     
+      throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));    
+      //exit(0);  /// \TODO throw an exception !     
    }
    else
    { 
@@ -71,47 +82,44 @@ bool Bruker2Dicom::Execute()
    }
    //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);
-*/
+  // get info for 'Study Description'  
+
          BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
          std::string subject_name = b_name.GetStringValue()[0];
-	 strPatientName = subject_name;
+         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);
-	 
+         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);
-	 	  	 
+         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;
+         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);	 
+         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;
-	 	 
+
+   // subject_name is already in 'Patient Name' 
+   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();
-   
+   serieNumber = 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
    // -----------------------------------------------------
            
    GDCM_NAME_SPACE::DirListType::iterator it;
@@ -120,7 +128,7 @@ bool Bruker2Dicom::Execute()
          it != fileNames.end();
        ++it)
    {
-      if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+      if ( boost::filesystem::is_directory(*it) )
       { 
          if (verbose)
             std::cout << "[" << *it << "] is a directory" << std::endl;
@@ -156,23 +164,20 @@ bool Bruker2Dicom::Execute()
          nbSlices =  b_list_size.GetIntValue()[0];
 
          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
-                         + "-" + acqp_protocol_location
-                         + "-" + acqp_scan_name
-                         + "-" + acqp_method.c_str();
+                       /*  + "." + acqp_protocol_location */ // always the same (in each acquisition)
+                         + "." + 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"
+                   << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
                    << " ================================================================================"
                    << std::endl;
 
+
         if (verbose)
            printf ("outputDirName [%s]\n", outputDirName);   
 
@@ -194,7 +199,8 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
 
    if (!res) {
       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
-      exit (0);
+      throw ( BrukerHopelessException ("Level 1 output directory creation failure "));    
+     // exit (0);
    }
    GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
    GDCM_NAME_SPACE::DirListType fileNames;
@@ -208,10 +214,11 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
         it != fileNames.end();
       ++it)
    {
-      if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+      if ( boost::filesystem::is_regular(*it) ) 
+      //if ( ! boost::filesystem::is_directory(*it) )
       {
          if (verbose)
-            std::cout << "--- [" << *it << "] is a file" << std::endl;
+            std::cout << "--- [" << *it << "] is a file." << std::endl;
       }  
    }
 
@@ -222,7 +229,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
         it != fileNames.end();
       ++it)
    {
-      if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+      if ( boost::filesystem::is_directory(*it) )
       {
          // will be always "pdata" ...
          if (verbose)
@@ -261,7 +268,8 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
              if (!canOpen)
              {
                 std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
-                exit(0);  /// \TODO throw an exception !
+                throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));		
+                //exit(0);  /// \TODO throw an exception !
              }
           }
           if (verbose)
@@ -297,7 +305,8 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
 
    if (!res) {
       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
-      exit (0);
+      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
@@ -318,9 +327,9 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
         it != fileNames.end();
       ++it)
    {
-      if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+      if ( ! boost::filesystem::is_directory(*it) )
       { 
-         std::cout << "--- --- [" << *it << "] is a file" << std::endl;
+         std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
       }
       
    }
@@ -329,7 +338,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
          it != fileNames.end();
        ++it)
    {
-      if ( GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+      if ( boost::filesystem::is_directory(*it) )
       { 
   
          if (verbose)
@@ -365,7 +374,7 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
              str_isa_func_name = b_isa_func_name.GetStringValue()[0];
              cleanString(str_isa_func_name);
 
-             sprintf(outputDirName, "%s%c%s-%s", currentOutputDirName.c_str(), 
+             sprintf(outputDirName, "%s%c%s.%s", currentOutputDirName.c_str(), 
                                           GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
                                           GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
              str_isa_func_name.c_str());
@@ -394,7 +403,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    if (!res)
    {
       std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
-      exit (0);
+      throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));      
+      //exit (0);
    }
 
    GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
@@ -419,21 +429,23 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );     
    
    if (verbose)
-      std::cout << "--- => [" << char_d3proc << "]" << std::endl;
+      std::cout << "d3proc: --- => [" << 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 ! 
+      throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
+      //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 !     
+      throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));      
+      //exit(0);  /// \TODO throw an exception !     
    }
  
    //-------------- end try d3proc;
@@ -448,7 +460,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
     //             "d3proc";
    if (verbose)
-      std::cout << "--- => [" << char_reco << "]" << std::endl;
+      std::cout << "reco --- => [" << char_reco << "]" << std::endl;
    std::string str_reco(char_reco);       
    canOpen = br_reco.LoadFile(str_reco);
 
@@ -463,8 +475,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
       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 !    
+         std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]"  << std::endl;	 
+         throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));  
+         //exit(0);  /// \TODO throw an exception !    
       }
    }
 
@@ -472,7 +485,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    if (!canOpen)
    {
       std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
-      exit(0);  /// \TODO throw an exception !     
+      throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));  
+      //exit(0);  /// \TODO throw an exception !     
    }
    //std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
    // br_reco.PrintSelf();
@@ -484,16 +498,19 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
    int NX = bX.GetIntValue()[0];
 
-   std::cout << "IM_SIX " << NX << std::endl;
+   if (verbose)
+      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;
+   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]; 
-   std::cout << "IM_SIZ " << nbFrames << std::endl;
+   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, ...}
  
@@ -510,7 +527,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
       std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
 
    /// \TODO probabely a more sophisticated accessor will be necessary :
-   ///  (cf : non contiguous slices, overlapping, slice thickness, space between clices, etc)
+   ///  (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
    BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
    double sliceDistance = bsliceDistance.GetDoubleValue()[0];
 
@@ -521,18 +538,22 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
       res = CreateDirectory( currentOutputMhdDirName );
       if (!res) {
          std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
-         exit (0);
+	 throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));  
+         //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;
+   if (verbose)
+         std::cout << "nbFrames " << nbFrames << std::endl;
+   if (verbose)
+         std::cout << "nbSlices " << nbSlices << std::endl;
    int k;
    int nbInstants = nbFrames/nbSlices;
-   std::cout << "nbInstants (deduced )" << nbInstants << std::endl;    
+   if (verbose)
+         std::cout << "nbInstants (deduced )" << nbInstants << std::endl;    
    int instantNb;
    int sliceNb; 
    FILE *fp;  // for MHD files
@@ -548,30 +569,41 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    if (!fp) 
    {
       std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
-      exit (0);
+      throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
+      //exit (0);
    }
    
-   unsigned char * buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];   
+   unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];   
    ///\ TODO : find a safer way to be sure to read everything!
    size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
 
    // This one will be important!
    // ---------------------------
-   imageSet = CreateImageSet ( );
+   try {
+      imageSet = CreateImageSet ( );
+   }
+   catch (BrukerInitException& e)
+   {
+      std::cout <<  "Exception " << e.what() << std::endl;
+      return;
+   }
    
+   serieNumber++;
    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 (verbose)
+          std::cout << "Single instant : do not split" << std::endl;
        if (mhd)
        {
-             sprintf(outputMhdFileName, "%s%cMhdData_Toutes_les_Slices.mhd", currentOutputMhdDirName,
+             sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
                                          GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
              fp=fopen(outputMhdFileName, "w");
              if (!fp)
              {
                 std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
-                exit(0);
+		throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
+                //exit(0);
              }
              else
              {
@@ -587,26 +619,28 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                fprintf(fp, "CenterOfRotation = 0 0 0\n" );
                fprintf(fp, "ElementNumberOfChannels = 1\n" );
                fprintf(fp, "ElementType = %s\n", mhdDataPixelType.c_str() );  
-               fprintf(fp, "ElementDataFile = %s\n", "../2dseq_toutes_les_Slices" );
+               fprintf(fp, "ElementDataFile = %s\n", "../2dseq_All_the_Slices" );
                fclose(fp);     
              }
-             sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices", 
+             sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices", 
                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
              fp=fopen(output2dseqSliceFileName, "wb");
              if (!fp)
              {
                 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 ++;
              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
        }  // end if mhd
        if (dicom)
        {
-             sprintf(output2dseqSliceFileName, "%s%c2dseq_toutes_les_Slices.dcm", 
+             sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm", 
                                        currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
               
             /* ----------- Write Dicom Image  ---------------*/
@@ -621,9 +655,9 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                day,
                strStudyUID,
                strSerieUID,
-	       strStudyDescr,
+               strStudyDescr,
                strSerieDescr,
-	       strStudyTimeDate,
+               strStudyTimeDate,
                0,// index frame number
                GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
              );
@@ -635,13 +669,13 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
           // Interleaved !
           // it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
 
-         unsigned char * pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
+         unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
 
          k = 0;
          for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
          {
-	    if (mhd)
-	    {
+            if (mhd)
+            {
                sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName, 
                                         GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k  );
                if (verbose)
@@ -650,7 +684,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                if (!fp)
                {
                    std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
-                   exit(0);
+		   throw ( BrukerHopelessException ("Hopeless! Cannot open  mhd file for writting"));
+                   //exit(0);
                }
                else
                {
@@ -679,7 +714,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                if (!fp)
                {     
                    std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
-                   exit (0);
+		   throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));		   
+                   //exit (0);
                }
                int frameSize = NX*NY*pixelSize;
                for (instantNb=0; instantNb<nbInstants; instantNb++)
@@ -692,11 +728,11 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                fclose(fp);
 // std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
             }  // end if mhd
-	    
-	    if (dicom)
-	    {
+   
+            if (dicom)
+            {
                // desperate try !
-	       /* 
+             /* 
                sprintf(output2dseqSliceFileName, "%sdummy_buffer", 
                                                  currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
                fp=fopen(output2dseqSliceFileName, "wb");
@@ -714,23 +750,23 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                             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;
+       
+               int frameSize = NX*NY*pixelSize;
                for (instantNb=0; instantNb<nbInstants; instantNb++)
                {
                   memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
@@ -752,16 +788,16 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                   day,
                   strStudyUID,
                   strSerieUID,
-		  strStudyDescr,
+                  strStudyDescr,
                   strSerieDescr,
-		  strStudyTimeDate,
+                  strStudyTimeDate,
                   sliceNb*nbInstants,
                   GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
                );
                if (verbose)
                   std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;      
 
-	    } // en if dicom
+           } // en if dicom
 
         k++;
         }
@@ -785,7 +821,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
 void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices, 
                                  double fovX, double fovY, double sliceDistance,
                                  char *copyFile, std::string &currentOutputDirName, 
-				 char *outputMhdFileName, char *output2dseqCartoName)
+                                 char *outputMhdFileName, char *output2dseqCartoName)
 {
    // -----------------------------------------------------
    //  deal with MatLab-generated Carto file.
@@ -802,10 +838,11 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
         it != fileNames.end();
       ++it)
    {
-      if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(*it) )
+      if ( boost::filesystem::is_regular(*it) )
+      //if ( ! boost::filesystem::is_directory(*it) )
       {         
          if (verbose)
-            std::cout << "--- [" << *it << "] is a file" << std::endl;
+            std::cout << "--- [" << *it << "] is a file..." << std::endl;
 
          icode = 0;
 
@@ -830,7 +867,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
                          << 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()); 
@@ -866,17 +903,17 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
                      fclose(fp);
                   }
                   if (verbose)
-	             std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
+                     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;
+                     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()));
@@ -891,9 +928,9 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
                      day,
                      strStudyUID,
                      strSerieUID,
-		     strStudyDescr,
+                     strStudyDescr,
                      strNewSerieDescr,
-		     strStudyTimeDate,
+                     strStudyTimeDate,
                      0,
                      GDCM_NAME_SPACE::CREATED_IMAGE
                   );
@@ -901,10 +938,10 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
 
                delete [] buffer_carto;
                if (verbose) 
-	             std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
+                  std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
                break; // don't check for more ident on same file name!
 
-	    }
+            }
             icode++;
          } 
       }
@@ -921,14 +958,14 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
    if (verbose)
       std::cout << "Check for output directory :[" << OutputDirName << "]."
                 <<std::endl;
-   if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(OutputDirName) )    // dirout not found
+   if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
    {
-      std::string strDirNameout(OutputDirName);          // to please gcc 4
+      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 ( ! boost::filesystem::is_directory(OutputDirName) ) // be sure it worked
       {
          if (verbose) 
             std::cout << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
@@ -986,7 +1023,8 @@ void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPix
    if(bDPT.GetDataType() == "string")
    {         
          std::string brukerDataPixelType = bDPT.GetStringValue()[0];
-         std::cout << "DATTYPE " << brukerDataPixelType << std::endl;          
+	 if (verbose)
+            std::cout << "DATTYPE " << brukerDataPixelType << std::endl;          
          //std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
          
          if (brukerDataPixelType ==  "ip_short") {
@@ -1054,6 +1092,11 @@ std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
          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  ("Bruker2Dicom::CreateImageSet failure ") );
+	 }
 
          br_acqp.SetImageLoopStructure();
          br_acqp.SetBrukerImageList();
@@ -1097,7 +1140,6 @@ std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
    return imageSet;
 }
 
-
 // ===========================================================================================
 
 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, 
@@ -1113,7 +1155,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
               std::string &serieUID,
               std::string &studyDescr,
               std::string &serieDescr,
-	      std::string &strStudyTimeDate,
+              std::string &strStudyTimeDate,
               int imgNum,
               GDCM_NAME_SPACE::ImageContentType contentType 
       )
@@ -1199,7 +1241,7 @@ void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
    char charImageOrientation[256];
 
 /*
-std::cout << "try charImageOrientation  " << 
+std::cout << "charImageOrientation  " << 
                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
                               imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<