X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Fsrc1%2Fbruker2dicom.cxx;h=0473bb3ac3be310019cbbc36da201c6b931604c2;hb=c4aa711c5d7c94a0a7ace93cabc977f06a9703f9;hp=737131192fa455e3b24bcd6484f30d1331931bd0;hpb=0bc6c532e6f065b3b6664c7c6fa831b68757dea5;p=creaBruker.git

diff --git a/lib/src1/bruker2dicom.cxx b/lib/src1/bruker2dicom.cxx
index 7371311..0473bb3 100644
--- a/lib/src1/bruker2dicom.cxx
+++ b/lib/src1/bruker2dicom.cxx
@@ -3,7 +3,7 @@
 #include <boost/filesystem/operations.hpp>
 
 #ifndef PATH_MAX // If not defined yet : do it 
-	#define PATH_MAX 2048
+   #define PATH_MAX 2048
 #endif 
 
 
@@ -37,7 +37,7 @@ bool Bruker2Dicom::Execute()
    GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
    std::string strDirNameout(OutputDirName);   
 
-/*   
+/*
    if (listonly)
    {
       std::cout << "------------List of found files ------------" << std::endl;
@@ -58,6 +58,7 @@ bool Bruker2Dicom::Execute()
    bool canOpen;
    std::string outputFileName;
 
+
   // BrukerDataSet br_subject;
    std::string subject;
    subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
@@ -80,42 +81,39 @@ bool Bruker2Dicom::Execute()
 
   // get info for 'Study Description'
   
- /*
-         BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
-         acqp_protocol_location = b_protocol_location.GetStringValue()[0];
-         cleanString(acqp_protocol_location);
-*/
+
          BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
          std::string subject_name = b_name.GetStringValue()[0];
-	 strPatientName = subject_name;
+         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)
@@ -128,7 +126,6 @@ bool Bruker2Dicom::Execute()
          it != fileNames.end();
        ++it)
    {
-      if ( !boost::filesystem::is_regular(*it) ) // check twice !
       if ( boost::filesystem::is_directory(*it) )
       { 
          if (verbose)
@@ -165,29 +162,20 @@ bool Bruker2Dicom::Execute()
          nbSlices =  b_list_size.GetIntValue()[0];
 
          strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
-                         + "." + acqp_protocol_location
+                       /*  + "." + 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) << "] -> [" << strSerieDescr << "]\n"
+                   << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
                    << " ================================================================================"
                    << std::endl;
 
-/*			  
-         std::cout << " ================================================================================\n"
-	           << " ========================= [" << GDCM_NAME_SPACE::Util::GetName(*it).c_str()
-                   << acqp_protocol_location.c_str()
-                   << acqp_scan_name.c_str()
-                   << acqp_method.c_str()
-                   << "]\n"
-                   << " ================================================================================"
-                   << std::endl;
-*/
+
         if (verbose)
            printf ("outputDirName [%s]\n", outputDirName);   
 
@@ -227,7 +215,7 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
       //if ( ! boost::filesystem::is_directory(*it) )
       {
          if (verbose)
-            std::cout << "--- [" << *it << "] is a file" << std::endl;
+            std::cout << "--- [" << *it << "] is a file." << std::endl;
       }  
    }
 
@@ -238,7 +226,6 @@ void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string curr
         it != fileNames.end();
       ++it)
    {
-      if ( !boost::filesystem::is_regular(*it) ) // check twice !  
       if ( boost::filesystem::is_directory(*it) )
       {
          // will be always "pdata" ...
@@ -335,10 +322,9 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
         it != fileNames.end();
       ++it)
    {
-      if ( !boost::filesystem::is_regular(*it) ) 
-      //if ( ! boost::filesystem::is_directory(*it) )
+      if ( ! boost::filesystem::is_directory(*it) )
       { 
-         std::cout << "--- --- [" << *it << "] is a file" << std::endl;
+         std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
       }
       
    }
@@ -347,7 +333,6 @@ void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string curr
          it != fileNames.end();
        ++it)
    {
-      if ( !boost::filesystem::is_regular(*it) ) // check twice !
       if ( boost::filesystem::is_directory(*it) )
       { 
   
@@ -438,7 +423,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );     
    
    if (verbose)
-      std::cout << "--- => [" << char_d3proc << "]" << std::endl;
+      std::cout << "try d3proc: --- => [" << char_d3proc << "]" << std::endl;
    std::string str_d3proc(char_d3proc);       
    canOpen = br_d3proc.LoadFile(str_d3proc);
 
@@ -467,7 +452,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
     //             GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
     //             "d3proc";
    if (verbose)
-      std::cout << "--- => [" << char_reco << "]" << std::endl;
+      std::cout << "try reco --- => [" << char_reco << "]" << std::endl;
    std::string str_reco(char_reco);       
    canOpen = br_reco.LoadFile(str_reco);
 
@@ -529,7 +514,7 @@ 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];
 
@@ -578,6 +563,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
    // ---------------------------
    imageSet = CreateImageSet ( );
    
+   serieNumber++;
    strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
    if (nbInstants==1) // creer un seul fichier .mhd  pour toutes les Slices! (images natives)
    {
@@ -621,6 +607,7 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
                 fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);     
              }
              fclose(fp);
+             serieNumber ++;
              strSerieUID =  GDCM_NAME_SPACE::Util::CreateUniqueUID();
        }  // end if mhd
        if (dicom)
@@ -640,9 +627,9 @@ 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
              );
@@ -659,8 +646,8 @@ void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string curr
          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)
@@ -711,11 +698,11 @@ 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");
@@ -733,23 +720,23 @@ 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);
@@ -771,16 +758,16 @@ 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++;
         }
@@ -804,7 +791,7 @@ 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.
@@ -825,7 +812,7 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
       //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;
 
@@ -850,7 +837,7 @@ 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()); 
@@ -886,17 +873,17 @@ 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()));
@@ -911,9 +898,9 @@ void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX
                      day,
                      strStudyUID,
                      strSerieUID,
-		     strStudyDescr,
+                     strStudyDescr,
                      strNewSerieDescr,
-		     strStudyTimeDate,
+                     strStudyTimeDate,
                      0,
                      GDCM_NAME_SPACE::CREATED_IMAGE
                   );
@@ -921,10 +908,10 @@ 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++;
          } 
       }
@@ -940,7 +927,7 @@ bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
    
    if (verbose)
       std::cout << "Check for output directory :[" << OutputDirName << "]."
-                <<std::endl;		
+                <<std::endl;
    if ( ! boost::filesystem::is_directory(OutputDirName) )    // dirout not found
    {
       std::string strDirNameout(OutputDirName);        // to please gcc 4
@@ -1117,7 +1104,6 @@ std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
    return imageSet;
 }
 
-
 // ===========================================================================================
 
 void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels, 
@@ -1133,7 +1119,7 @@ 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 
       )