X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=9351047766c5a75de5e3a692d031e20527ff8682;hb=795969b4c1adc8a26d5dfda236ef3d1e5ad1d7ca;hp=b47418923c9edb0a8c2d5f781172085faff5477e;hpb=7589d23967892c94462e22a49ec50fcd225c5c38;p=gdcm.git

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index b4741892..93510477 100644
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -2,14 +2,7 @@
 
 #include "gdcmFile.h"
 #include "gdcmUtil.h"
-
-
-// TODO : remove DEBUG
-#define DEBUG 0
-
-
-#include "iddcmjpeg.h"
-using namespace std;
+#include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess
 
 /////////////////////////////////////////////////////////////////
 /**
@@ -29,7 +22,7 @@ using namespace std;
  * @return	
  */
  
-gdcmFile::gdcmFile(string & filename) 
+gdcmFile::gdcmFile(std::string & filename) 
 	:gdcmHeader(filename.c_str())	
 {
    SetPixelDataSizeFromHeader();
@@ -46,24 +39,60 @@ gdcmFile::gdcmFile(const char * filename)
  * \brief     calcule la longueur (in bytes) A ALLOUER pour recevoir les
  *        	pixels de l'image
  *  		ou DES images dans le cas d'un multiframe
- *  		ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels	
+ *  		ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels
  *  		(dans le cas d'images compressees, elle n'a pas de sens).
  *
  * @return	longueur a allouer 
  */
 void gdcmFile::SetPixelDataSizeFromHeader(void) {
    int nb;
-   string str_nb;
+   std::string str_nb;
 
    str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
-   if (str_nb == "gdcm::Unfound" ) {
+   if (str_nb == GDCM_UNFOUND ) {
       nb = 16;
    } else {
       nb = atoi(str_nb.c_str() );
       if (nb == 12) nb =16;
    }
-   lgrTotale =  GetXSize() *  GetYSize() *  GetZSize() * (nb/8)* GetSamplesPerPixel();;
+   lgrTotale =  GetXSize() *  GetYSize() *  GetZSize() * (nb/8)* GetSamplesPerPixel();
+   std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+   if ( str_PhotometricInterpretation == "PALETTE COLOR " ) { 
+      lgrTotale*=3;
+   }
 }
+   // see PS 3.3-2003 : C.7.6.3.2.1  
+   // 
+   //   MONOCHROME1
+   //   MONOCHROME2
+   //   PALETTE COLOR
+   //   RGB
+   //   HSV  (Retired)
+   //   ARGB (Retired)
+   //   CMYK (Retired)
+   //   YBR_FULL
+   //   YBR_FULL_422 (no LUT, no Palette)
+   //   YBR_PARTIAL_422
+   //   YBR_ICT
+   //   YBR_RCT
+
+  // LUT's
+  // ex : gdcm-US-ALOKA-16.dcm
+  // 0028|1221 [OW]   [Segmented Red Palette Color Lookup Table Data]
+  // 0028|1222 [OW]   [Segmented Green Palette Color Lookup Table Data]  
+  // 0028|1223 [OW]   [Segmented Blue Palette Color Lookup Table Data]
+
+  // ex : US-PAL-8-10x-echo.dcm, 8BitsRunLengthColor.dcm
+  // 0028|1201 [OW]   [Red Palette Color Lookup Table Data]
+  // 0028|1202 [OW]   [Green Palette Color Lookup Table Data]
+  // 0028|1203 [OW]   [Blue Palette Color Lookup Table Data]
+
+  // ex  : OT-PAL-8-face.dcm
+  // 0028|1201 [US]   [Red Palette Color Lookup Table Data]
+  // 0028|1202 [US]   [Green Palette Color Lookup Table Data]
+  // 0028|1203 [US]   [Blue Palette Color Lookup Table Data]
+
+
 
 /////////////////////////////////////////////////////////////////
 /**
@@ -72,6 +101,7 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) {
  *            the pixel data represented in this file.
  * @return    The size of pixel data in bytes.
  */
+
 size_t gdcmFile::GetImageDataSize(void) {
    return (lgrTotale);
 }
@@ -82,19 +112,20 @@ size_t gdcmFile::GetImageDataSize(void) {
  * \ingroup gdcmFile
  * \brief   Read pixel data from disk (optionaly decompressing) into the
  *          caller specified memory location.
- * @param   destination Where the pixel data should be stored.
+ * @param   destination where the pixel data should be stored.
  *
  */
 bool gdcmFile::ReadPixelData(void* destination) {
+
    if ( !OpenFile())
       return false;
       
-      printf("GetPixelOffset() %d\n",GetPixelOffset() );
-      
     if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
       CloseFile();
       return false;
    }     
+
+// -------------------------  Uncompressed File
     
    if ( !IsDicomV3()                             ||
         IsImplicitVRLittleEndianTransferSyntax() ||
@@ -111,66 +142,51 @@ bool gdcmFile::ReadPixelData(void* destination) {
          return true;
       }
    } 
-     
-  // ------------------------------- Position on begining of Jpeg Pixels
-  
-       int ln;
-      fseek(fp,4,SEEK_CUR);
-      fread(&ln,4,1,fp); 
-      if(GetSwapCode()) 
-         ln=SwapLong(ln);
-      if (DEBUG) 
-         printf ("ln %d\n",ln);
-      fseek(fp,ln,SEEK_CUR);
-      fseek(fp,4,SEEK_CUR);
-      fread(&ln,4,1,fp); 
-      if(GetSwapCode()) 
-         ln=SwapLong(ln);
-      if (DEBUG) 
-         printf ("ln image comprimée %d\n",ln);
-         
-          
-  // ------------------------------- JPEG LossLess : call to Jpeg Libido
-   
-   if (IsJPEGLossless()) {
- 
-       ClbJpeg* jpg = _IdDcmJpegRead(fp);
-      if(jpg == NULL) {
-         CloseFile();
-         return false;
-      } 
-      // Gros soucis : 
-      //  jpg->DataImg est alloue en int32 systematiquement :
-      //  il faut le copier pixel par pixel dans destination ...
-      //  ... qui est un void *
-      // --> du CAST sportif a faire ... 
-      
-     // memcpy(destination,jpg->DataImg,lgrTotale);
-     
-     // Bon ...
-     // ... y'a p't etre + ruse (?)
-          
+    
+ // ------------------------  Compressed File .
+       
       int nb;
-      string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
-      if (str_nb == "gdcm::Unfound" ) {
+      std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
+      if (str_nb == GDCM_UNFOUND ) {
          nb = 16;
       } else {
          nb = atoi(str_nb.c_str() );
          if (nb == 12) nb =16;
       }
       int nBytes= nb/8;
-      int * dataJpg = jpg->DataImg;
-      int taille = GetXSize() *  GetYSize() *  GetZSize() * GetSamplesPerPixel();
+      
+      int taille = GetXSize() *  GetYSize()  * GetSamplesPerPixel(); 
           
-      switch (nBytes) {
+                
+  // ------------------------------- JPEG LossLess : call to Jpeg Libido
+   
+   if (IsJPEGLossless() /*&& GetZSize() == 1*/) {
+   
+      int ln; //  Position on begining of Jpeg Pixels
+      fseek(fp,4,SEEK_CUR);  // skipping (fffe,e000) : Basic Offset Table Item
+      fread(&ln,4,1,fp); 
+      if(GetSwapCode()) 
+         ln=SwapLong(ln);    // Item length
+      fseek(fp,ln,SEEK_CUR); // skipping Basic Offset Table ('ln' bytes) 
+      fseek(fp,4,SEEK_CUR);  // skipping (fffe,e000) : First fragment Item Tag
+      fread(&ln,4,1,fp);     // First fragment length (just to know)
+      if(GetSwapCode()) 
+         ln=SwapLong(ln);      
+ 
+      ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
+                                         // (We use the LibIDO one :-(
+      if(jpg == NULL) {
+         CloseFile();
+         return false;
+      }      
+      int * dataJpg = jpg->DataImg;
       
+      switch (nBytes) {   
          case 1:
          {
             unsigned short *dest = (unsigned short *)destination;
             for (int i=0; i<taille; i++) {
-               if (DEBUG) 
-                  if (*(dataJpg +i) >255) printf("data %d\n",*(dataJpg +i) );
-               *((unsigned char *)dest+i) = *(dataJpg +i);    
+               *((unsigned char *)dest+i) = *(dataJpg +i);   
             }
          }
          break;        
@@ -178,60 +194,149 @@ bool gdcmFile::ReadPixelData(void* destination) {
          case 2:
          {
             unsigned short *dest = (unsigned short *)destination;
-            
-            // etonnant (?)
-            // la ligne commentee ci-dessous fait passer l'exec de 0.15 sec a 5.5 sec
-            // pour la meme image 512*512 ...
-            // optimiseur pas mis en oeuvre (?)
-            //for (int i=0; i<GetXSize() *  GetYSize() *  GetZSize(); i++) 
-            
-             for (int i=0; i<taille; i++) {           
+            for (int i=0; i<taille; i++) {           
                *((unsigned short *)dest+i) = *(dataJpg +i);    
             }
          }
-         break;
-            
-          case 4:
-          {
-            unsigned int *dest=(unsigned int *)destination;
-            for (int i=0;i<taille; i++) {
-               *((unsigned int *)dest+i) = *(dataJpg +i);    
-            }
-          }
-         break;          
+         break;       
      }
-      
       _IdDcmJpegFree (jpg);
       return true;
-   }  
+   } 
  
+  // ------------------------------- RLE
+
+      if (gdcmHeader::IsRLELossLessTransferSyntax()) {
+            int res = (bool)gdcm_read_RLE_file (destination);
+            return res; 
+      }
+
   // ------------------------------- JPEG Lossy : call to IJG 6b
-  
-  // TODO : faire qq chose d'intelligent pour limiter 
-  // la duplication du code JPEG <bits=8 / bits=12>
-  // TODO : eplucher icelui pour traiter *egalement* bits=16
-      int nBS;        
-      if  ((nBS = GetBitsStored()) != 12) {
-         printf("Sorry, Bits Stored = %d not yet taken into account\n",nBS);
-         return false;
+    
+      long fragmentBegining; // for ftell, fseek
+      bool b = gdcmHeader::IsJPEG2000();
+       
+      bool res;
+      guint16 ItemTagGr,ItemTagEl;
+      int ln;  //  Position on begining of Jpeg Pixels
+      
+      fread(&ItemTagGr,2,1,fp);  // Reading (fffe) : Item Tag Gr
+      fread(&ItemTagEl,2,1,fp);  // Reading (e000) : Item Tag El
+      if(GetSwapCode()) {
+         ItemTagGr=SwapShort(ItemTagGr); 
+         ItemTagEl=SwapShort(ItemTagEl);            
+      }
+      fread(&ln,4,1,fp); 
+      if(GetSwapCode()) 
+         ln=SwapLong(ln);    // Basic Offset Table Item length
+         
+      if (ln != 0) {
+         // What is it used for ?!?
+         char *BasicOffsetTableItemValue = (char *)malloc(ln+1);        
+         fread(BasicOffsetTableItemValue,ln,1,fp); 
       }
       
-      int res = gdcm_read_JPEG_file (destination);
-         if (DEBUG) 
-            printf ("res : %d\n",res);
-      return res;
+      // first Fragment initialisation
+      fread(&ItemTagGr,2,1,fp);  // Reading (fffe) : Item Tag Gr
+      fread(&ItemTagEl,2,1,fp);  // Reading (e000) : Item Tag El
+      if(GetSwapCode()) {
+         ItemTagGr=SwapShort(ItemTagGr); 
+         ItemTagEl=SwapShort(ItemTagEl);            
+      }
+              
+      // parsing fragments until Sequence Delim. Tag found
+       //unsigned short *dest = (unsigned short *)destination;
+         
+      while (  ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+         fread(&ln,4,1,fp); 
+         if(GetSwapCode()) 
+            ln=SwapLong(ln);    // Fragment Item length
+      
+         // FIXME : multi fragments 
+         fragmentBegining=ftell(fp);
+                       
  
+         if (b)
+            res = (bool)gdcm_read_JPEG2000_file (destination);  // Reading Fragment pixels 
+            
+         else if (IsJPEGLossless()) {  
+                  // ------------- call to LibIDO Jpeg for each Frame/fragment
+                  
+                  // Warning : Works only if there is one fragment per frame
+                  //           (Or a single fragment for the multiframe file)
+            ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
+                                               // (We use the LibIDO one :-(
+            if(jpg == NULL) {
+               CloseFile();
+               return false;
+            }      
+            int * dataJpg = jpg->DataImg;
+            unsigned short *dest = (unsigned short *)destination;
+            switch (nBytes) {   
+               case 1:
+               {
+                  for (int i=0; i<taille; i++) {
+                     *((unsigned char *)dest+i) = *(dataJpg +i);   
+                  }
+               break;
+               }        
+         
+               case 2:
+               {
+                  for (int i=0; i<taille; i++) {        
+                     *((unsigned short *)dest+i) = *(dataJpg +i);    
+                  }
+               break;
+               }       
+           } 
+           _IdDcmJpegFree (jpg);
+     
+         } // ------------------------------------- endif (IsJPEGLossless())
+                  
+         else
+            if  (GetBitsStored() == 8) {
+            	res = (bool)gdcm_read_JPEG_file (destination);  // Reading Fragment pixels         
+            } else {
+            	res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels  
+            }       
+            
+         if (!res) break;
+         
+         // FIXME : will work only when each fragment corresponds to a Frame :-(
+         
+         destination = (char *)destination + taille * nBytes; // location in user's memory 
+                                                  // for next fragment (if any) 
+         // TODO : find a suitable file (multifragment/single Frame Jpeg file) to check
+         
+         fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start 
+         fseek(fp,ln,SEEK_CUR);               // at the begining of next fragment
+         
+         ItemTagGr = ItemTagEl =0;
+         fread(&ItemTagGr,2,1,fp);  // Reading (fffe) : Item Tag Gr
+         fread(&ItemTagEl,2,1,fp);  // Reading (e000) : Item Tag El
+         if(GetSwapCode()) {
+            ItemTagGr=SwapShort(ItemTagGr); 
+            ItemTagEl=SwapShort(ItemTagEl);            
+         } 
+         
+      //(char *) destination += taille * nBytes;
+      //std::cout << "destination" << destination << std::endl;
+      }
+                
+      return res;
 }   
 
 /**
  * \ingroup gdcmFile
  * \brief   Allocates necessary memory, copies the pixel data
  *          (image[s]/volume[s]) to newly allocated zone.
- * @return  Pointer to newly allocated pixel data. 
+ * @return  Pointer to newly allocated pixel data.
+ * \        NULL if alloc fails 
  */
 void * gdcmFile::GetImageData (void) {
    PixelData = (void *) malloc(lgrTotale);
-   GetImageDataIntoVector(PixelData, lgrTotale);
+   if (PixelData)
+      GetImageDataIntoVector(PixelData, lgrTotale);
    return(PixelData);
 }
 
@@ -251,7 +356,7 @@ void * gdcmFile::GetImageData (void) {
 size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
 
    int nb, nbu, highBit, signe;
-   string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
+   std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe;
  
    if ( lgrTotale > MaxSize ) {
       dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger"
@@ -259,45 +364,45 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
       return (size_t)0; 
    }
 	
-	(void)ReadPixelData(destination);
+   (void)ReadPixelData(destination);
 			
 	// Nombre de Bits Alloues pour le stockage d'un Pixel
-	str_nb = GetPubElValByNumber(0x0028,0x0100);
-	if (str_nb == "gdcm::Unfound" ) {
-		nb = 16;
-	} else {
-		nb = atoi(str_nb.c_str() );
-	}
+   str_nb = GetPubElValByNumber(0x0028,0x0100);
+   if (str_nb == GDCM_UNFOUND ) {
+      nb = 16;
+   } else {
+      nb = atoi(str_nb.c_str() );
+   }
 	
 	// Nombre de Bits Utilises
-	str_nbu=GetPubElValByNumber(0x0028,0x0101);
-	if (str_nbu == "gdcm::Unfound" ) {
-		nbu = nb;
-	} else {
-		nbu = atoi(str_nbu.c_str() );
-	}	
+   str_nbu=GetPubElValByNumber(0x0028,0x0101);
+   if (str_nbu == GDCM_UNFOUND ) {
+      nbu = nb;
+   } else {
+      nbu = atoi(str_nbu.c_str() );
+   }	
 	
 	// Position du Bit de Poids Fort
-	str_highBit=GetPubElValByNumber(0x0028,0x0102);
-	if (str_highBit == "gdcm::Unfound" ) {
-		highBit = nb - 1;
-	} else {
-		highBit = atoi(str_highBit.c_str() );
-	}
+   str_highBit=GetPubElValByNumber(0x0028,0x0102);
+   if (str_highBit == GDCM_UNFOUND ) {
+      highBit = nb - 1;
+   } else {
+      highBit = atoi(str_highBit.c_str() );
+   }
 		
 	// Signe des Pixels 
-	str_signe=GetPubElValByNumber(0x0028,0x0103);
-	if (str_signe == "gdcm::Unfound" ) {
-		signe = 1;
-	} else {
-		signe = atoi(str_signe.c_str() );
-	}
-
-   // On remet les Octets dans le bon ordre si besoin est
+   str_signe=GetPubElValByNumber(0x0028,0x0103);
+   if (str_signe == GDCM_UNFOUND ) {
+      signe = 1;
+   } else {
+      signe = atoi(str_signe.c_str() );
+   }
+
+   // re arange bytes inside the integer
    if (nb != 8)
      SwapZone(destination, GetSwapCode(), lgrTotale, nb);
  
-   // On remet les Bits des Octets dans le bon ordre si besoin est
+   // re arange bits inside the bytes
    if (nbu != nb){
       int l = (int)lgrTotale / (nb/8);
       if (nb == 16) {
@@ -320,83 +425,255 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
          dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
          return (size_t)0; 
       }
-   }
+   } 
+
+// Just to 'see' was was actually read on disk :-(
+// Some troubles expected
+
+   // *Try* to deal with the color
+   // ----------------------------
+
+   // Planar configuration = 0 : Pixels are already RGB
+   // Planar configuration = 1 : 3 planes : R, G, B
+   // Planar configuration = 2 : 1 gray Plane + 3 LUT
+
+   // Well ... supposed to be !
+   // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,PhotometricInterpretation=PALETTE COLOR
+   // and heuristic has to be found :-( 
+
+      std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+   
+      if ( (str_PhotometricInterpretation == "MONOCHROME1 ") 
+        || (str_PhotometricInterpretation == "MONOCHROME2 ") 
+        || (str_PhotometricInterpretation == "RGB")) {
+         return lgrTotale; 
+      }
+      int planConf=GetPlanarConfiguration();
+ 
+      switch (planConf) {
+      case 0:                              
+         //       Pixels are already RGB
+         break;
+    
+      case 1:
+
+         {
+         if (str_PhotometricInterpretation == "YBR_FULL") { // Warning : YBR_FULL_422 acts as RGB (?!)
+
+         //       need to make RGB Pixels from Planes Y,cB,cR
+         // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+         // for code optimisation
+
+            int l = GetXSize()*GetYSize();
+            int nbFrames = GetZSize();
+
+            unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+            unsigned char *x  = newDest;
+            unsigned char * a = (unsigned char *)destination;
+            unsigned char * b = a + l;
+            unsigned char * c = b + l;
+
+            double R,G,B;
+
+            // TODO : Replace by the 'well known' 
+            //        integer computation counterpart
+            for (int i=0;i<nbFrames;i++) {
+               for (int j=0;j<l; j++) {
+                  R= 1.164 *( *a-16) + 1.596 *( *c -128) + 0.5;
+                  G= 1.164 *( *a-16) - 0.813 *( *c -128) - 0.392 *(*b -128) + 0.5;
+                  B= 1.164 *( *a-16) + 2.017 *( *b -128) + 0.5;
+
+                  if (R<0.0)   R=0.0;
+                  if (G<0.0)   G=0.0;
+                  if (B<0.0)   B=0.0;
+                  if (R>255.0) R=255.0;
+                  if (G>255.0) G=255.0;
+                  if (B>255.0) B=255.0;
+
+                  *(x++) = (unsigned char)R;
+                  *(x++) = (unsigned char)G;
+                  *(x++) = (unsigned char)B;
+                  a++; b++; c++;  
+               }
+           }
+            memmove(destination,newDest,lgrTotale);
+            free(newDest);
+
+        } else {
+         
+         //       need to make RGB Pixels from Planes R,G,B
+
+            int l = GetXSize()*GetYSize();
+            int nbFrames = GetZSize();
+
+            char * newDest = (char*) malloc(lgrTotale);
+            char *x  = newDest;
+            char * a = (char *)destination;
+            char * b = a + l;
+            char * c = b + l;
+
+               // TODO :
+               // any trick not to have to allocate temporary buffer is welcome ...
+
+            for (int i=0;i<nbFrames;i++) {
+               for (int j=0;j<l; j++) {
+                  *(x++) = *(a++);
+                  *(x++) = *(b++);
+                  *(x++) = *(c++);  
+               }
+            }
+            memmove(destination,newDest,lgrTotale);
+            free(newDest);
+        }
+
+            // now, it's an RGB image
+            // Lets's write it in the Header
+         std::string spp = "3";
+         gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+         std::string rgb="RGB";
+         gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+         break;
+       }
+     
+       case 2:                      
+         //       from Lut R + Lut G + Lut B
+       
+         // we no longer use gdcmHeader::GetLUTRGB
+         // since a lot of images have strange info 
+         // in the Lookup Table Descriptors (0028,1101),...
+         {
+         unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+         unsigned char * a = (unsigned char *)destination;
+
+         unsigned char *lutR =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1201);
+         unsigned char *lutG =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1202);
+         unsigned char *lutB =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1203);
+
+         if (lutR && lutG && lutB ) { // need to make RGB Pixels 
+                                      // from grey Pixels 
+                                      // and Lut R,Lut G,Lut B
+
+            unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+            int l = lgrTotale/3;
+            memmove(newDest, destination, l);// move Gray pixels to temp area
+
+            unsigned char * x = newDest;
+
+               int j;
+               // See PS 3.3-2003 C.11.1.1.2 p 619
+               // 
+               int mult;
+               if ( GetLUTNbits()==16 && nb==8) mult=2; // See PS 3.3 
+               else mult=1;
+       
+               for (int i=0;i<l; i++) {
+                  j=newDest[i]*mult;
+                  *a++ = lutR[j]; 
+                  *a++ = lutG[j];
+                  *a++ = lutB[j];
+               }
+
+               free(newDest);
+        
+               // now, it's an RGB image      
+           std::string spp = "3";
+           gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002); 
+           std::string rgb="RGB";
+           gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+               
+         } else { // need to make RGB Pixels (?)
+                  // from grey Pixels (?!)
+                  // and Gray Lut  (!?!) 
+               unsigned char *lutGray =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1200);
+                    // Well . I'll wait till I find such an image 
+         }
+         break;
+         }
+   } 
+    
    return lgrTotale; 
 }
 
-
 //
 // Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
 //
 
+/**
+ * \ingroup gdcmFile
+ * \brief   Swap the bytes, according to swap code.
+ * \warning not end user intended
+ * @param   im area to deal with
+ * @param   swap swap code
+ * @param   lgr Area Length
+ * @param   nb Pixels Bit number 
+ */
+
 void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
 guint32 s32;
 guint16 fort,faible;
 int i;
 
-if(nb == 16)
-    
-	switch(swap) {
-		case 0:
-		case 12:
- 		case 1234:
-			break;
+if(nb == 16)  
+   switch(swap) {
+      case 0:
+      case 12:
+      case 1234:
+         break;
 		
- 		case 21:
- 		case 3412:
- 		case 2143:
- 		case 4321:
-
- 			for(i=0;i<lgr;i++)
-  				((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
-                            			| ((((unsigned short int*)im)[i])<<8);
- 			break;
+      case 21:
+      case 3412:
+      case 2143:
+      case 4321:
+
+         for(i=0;i<lgr;i++)
+            ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
+                                        | ((((unsigned short int*)im)[i])<<8);
+         break;
  			
- 		default:
- 			printf("valeur de SWAP (16 bits) non autorisee : %d\n", swap);
-	} 
+      default:
+         printf("valeur de SWAP (16 bits) not allowed : %d\n", swap);
+   } 
  
 if( nb == 32 )
+   switch (swap) {
+      case 0:
+      case 1234:
+         break;
 
-	switch (swap) {
-    		case 0:
-     		case 1234:
-    			 break;
-
-    		case 4321:
-    			 for(i=0;i<lgr;i++) {
-        			faible=  ((unsigned long int*)im)[i]&0x0000ffff;    /* 4321 */
-       				fort  =((unsigned long int*)im)[i]>>16;
-        			fort=  (fort>>8)   | (fort<<8);
-        			faible=(faible>>8) | (faible<<8);
-        			s32=faible;
-        			((unsigned long int*)im)[i]=(s32<<16)|fort;
-       			}
-    			break;
-
-    		case 2143:
-    			for(i=0;i<lgr;i++) {
-       				faible=  ((unsigned long int*)im)[i]&0x0000ffff;    /* 2143 */
-       				fort=((unsigned long int*)im)[i]>>16;
-       				fort=  (fort>>8)   | (fort<<8);
-       				faible=(faible>>8) | (faible<<8);
-       				s32=fort; 
-       				((unsigned long int*)im)[i]=(s32<<16)|faible;
-      			}
-    			break;
+      case 4321:
+         for(i=0;i<lgr;i++) {
+            faible=  ((unsigned long int*)im)[i]&0x0000ffff;    /* 4321 */
+            fort  =((unsigned long int*)im)[i]>>16;
+            fort=  (fort>>8)   | (fort<<8);
+            faible=(faible>>8) | (faible<<8);
+            s32=faible;
+            ((unsigned long int*)im)[i]=(s32<<16)|fort;
+         }
+         break;
+
+      case 2143:
+         for(i=0;i<lgr;i++) {
+            faible=  ((unsigned long int*)im)[i]&0x0000ffff;    /* 2143 */
+            fort=((unsigned long int*)im)[i]>>16;
+            fort=  (fort>>8)   | (fort<<8);
+            faible=(faible>>8) | (faible<<8);
+            s32=fort; 
+            ((unsigned long int*)im)[i]=(s32<<16)|faible;
+         }
+         break;
   
-    		case 3412:
-    			for(i=0;i<lgr;i++) {
-      				faible=  ((unsigned long int*)im)[i]&0x0000ffff;    /* 3412 */
-       				fort=((unsigned long int*)im)[i]>>16;                  
-       				s32=faible; 
-       				((unsigned long int*)im)[i]=(s32<<16)|fort;
-      			}                 
-    			break; 
+      case 3412:
+         for(i=0;i<lgr;i++) {
+            faible=  ((unsigned long int*)im)[i]&0x0000ffff;    /* 3412 */
+            fort=((unsigned long int*)im)[i]>>16;                  
+            s32=faible; 
+            ((unsigned long int*)im)[i]=(s32<<16)|fort;
+         }                 
+         break; 
     			        
-   		default:
-   			printf("valeur de SWAP (32 bits) non autorisee : %d\n", swap);
-	} 
+      default:
+         printf(" SWAP value (32 bits) not allowed : %d\n", swap);
+   } 
 return;
 }
 
@@ -404,20 +681,18 @@ return;
 /**
  * \ingroup   gdcmFile
  * \brief TODO JPR
- * \warning doit-etre etre publique ?  FIXME JPR
+ * \warning doit-etre etre publique ?  
  * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions
  *
- * @param inData TODO JPR
- * @param ExpectedSize TODO JPR
+ * @param inData 
+ * @param ExpectedSize 
  *
- * @return TODO JPR	
+ * @return integer acts as a boolean	
  */
 int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
    SetImageDataSize(ExpectedSize);
    PixelData = inData;
    lgrTotale = ExpectedSize;
-   
-   
    return(1);
 }
 
@@ -425,31 +700,29 @@ int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup   gdcmFile
- * \brief TODO JPR
- * \
- * \warning WARNING doit-etre etre publique ? FIXME JPR
+ * \brief Sets the Pixel Area size in the Header
+ *        --> not-for-rats function
+ * 
+ * \warning WARNING doit-etre etre publique ? 
  * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
  *
- * @param ImageDataSize TODO JPR
- *
+ * @param ImageDataSize new Pixel Area Size
+ *        warning : nothing else is checked
  */
 
 void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
-
- 	string content1;
- 	char car[20];
- 	
- 	// suppose que le ElValue (0x7fe0, 0x0010) existe ...
- 	
- 	sprintf(car,"%d",ImageDataSize);
+   std::string content1;
+   char car[20];	
+   // Assumes ElValue (0x7fe0, 0x0010) exists ...	
+   sprintf(car,"%d",ImageDataSize);
  
- 	gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
- 	a->SetLength(ImageDataSize);
+   gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
+   a->SetLength(ImageDataSize);
  		
- 	ImageDataSize+=8;
- 	sprintf(car,"%d",ImageDataSize);
- 	content1=car;	
- 	SetPubElValByNumber(content1, 0x7fe0, 0x0000);
+   ImageDataSize+=8;
+   sprintf(car,"%d",ImageDataSize);
+   content1=car;	
+   SetPubElValByNumber(content1, 0x7fe0, 0x0000);
 }
 
 
@@ -459,70 +732,62 @@ void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
  * \brief Ecrit sur disque les pixels d'UNE image
  *        Aucun test n'est fait sur l'"Endiannerie" du processeur.
  *        Ca sera à l'utilisateur d'appeler son Reader correctement
- *        (Equivalent a IdImaWriteRawFile) FIXME JPR
+ *        (Equivalent a IdImaWriteRawFile) 
  *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR	
+ * @param fileName 
+ * @return	
  */
 
-int gdcmFile::WriteRawData (string nomFichier) {
-
-	FILE * fp1;
-	fp1 = fopen(nomFichier.c_str(),"wb");
-	if (fp1 == NULL) {
-		printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str());
-		return (0);
-	} 
-	
-	fwrite (PixelData,lgrTotale, 1, fp1);
-	fclose (fp1);
-	return(1);
+int gdcmFile::WriteRawData (std::string fileName) {
+   FILE * fp1;
+   fp1 = fopen(fileName.c_str(),"wb");
+   if (fp1 == NULL) {
+      printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str());
+      return (0);
+   } 	
+   fwrite (PixelData,lgrTotale, 1, fp1);
+   fclose (fp1);
+   return(1);
 }
 
-
-
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup   gdcmFile
  * \brief Ecrit sur disque UNE image Dicom
  *        Aucun test n'est fait sur l'"Endiannerie" du processeur.
  *         Ca fonctionnera correctement (?) sur processeur Intel
- *         (Equivalent a IdDcmWrite) FIXME JPR 
- *
- * @param nomFichier TODO JPR
+ *         (Equivalent a IdDcmWrite) 
  *
- * @return	TODO JPR
+ * @param fileName 
+ * @return int acts as a boolean
  */
 
-int gdcmFile::WriteDcmImplVR (string nomFichier) {
-   return WriteBase(nomFichier, ImplicitVR);
+int gdcmFile::WriteDcmImplVR (std::string fileName) {
+   return WriteBase(fileName, ImplicitVR);
 }
 
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup   gdcmFile
- *
- * @param  nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \brief  
+ * @param  fileName 
+ * @return int acts as a boolean
  */
  
-int gdcmFile::WriteDcmImplVR (const char* nomFichier) {
-   return WriteDcmImplVR (string (nomFichier));
+int gdcmFile::WriteDcmImplVR (const char* fileName) {
+   return WriteDcmImplVR (std::string (fileName));
 }
 	
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup   gdcmFile
- *
- * @param  nomFichier TODO JPR
- *
- * @return TODO JPR
+ * \brief  
+ * @param  fileName
+ * @return int acts as a boolean
  */
 
-int gdcmFile::WriteDcmExplVR (string nomFichier) {
-   return WriteBase(nomFichier, ExplicitVR);
+int gdcmFile::WriteDcmExplVR (std::string fileName) {
+   return WriteBase(fileName, ExplicitVR);
 }
 	
 /////////////////////////////////////////////////////////////////
@@ -537,25 +802,24 @@ int gdcmFile::WriteDcmExplVR (string nomFichier) {
  *        Ca fonctionnera correctement (?) sur processeur Intel
  *        (Equivalent a IdDcmWrite) 
  *
- * @param nomFichier TODO JPR
- *
- * @return TODO JPR	
+ * @param fileName
+ * @return int acts as a boolean	
  */
 
-int gdcmFile::WriteAcr (string nomFichier) {
-   return WriteBase(nomFichier, ACR);
+int gdcmFile::WriteAcr (std::string fileName) {
+   return WriteBase(fileName, ACR);
 }
 
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup   gdcmFile
  *
- * @param  FileName TODO JPR
- * @param  type TODO JPR
+ * @param  FileName
+ * @param  type 
  *
- * @return TODO JPR
+ * @return int acts as a boolean
  */
-int gdcmFile::WriteBase (string FileName, FileType type) {
+int gdcmFile::WriteBase (std::string FileName, FileType type) {
 
    FILE * fp1;
    fp1 = fopen(FileName.c_str(),"wb");
@@ -566,13 +830,42 @@ int gdcmFile::WriteBase (string FileName, FileType type) {
 
    if ( (type == ImplicitVR) || (type == ExplicitVR) ) {
       char * filePreamble;
-      // Ecriture Dicom File Preamble
+      // writing Dicom File Preamble
       filePreamble=(char*)calloc(128,1);
       fwrite(filePreamble,128,1,fp1);
       fwrite("DICM",4,1,fp1);
    }
 
+   // --------------------------------------------------------------
+   // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+   //
+   // if recognition code tells us we dealt with a LibIDO image
+   // we reproduce on disk the switch between lineNumber and columnNumber
+   // just before writting ...
+
+   std::string rows, columns; 
+   if ( filetype == ACR_LIBIDO){
+         rows    = GetPubElValByNumber(0x0028, 0x0010);
+         columns = GetPubElValByNumber(0x0028, 0x0011);
+         SetPubElValByNumber(columns,  0x0028, 0x0010);
+         SetPubElValByNumber(rows   ,  0x0028, 0x0011);
+   }	
+   // ----------------- End of Special Patch ----------------
+
    gdcmHeader::Write(fp1, type);
+
+   // --------------------------------------------------------------
+   // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+   // 
+   // ...and we restore the Header to be Dicom Compliant again 
+   // just after writting
+
+   if (filetype == ACR_LIBIDO){
+         SetPubElValByNumber(rows   , 0x0028, 0x0010);
+         SetPubElValByNumber(columns, 0x0028, 0x0011);
+   }	
+   // ----------------- End of Special Patch ----------------
+
    fwrite(PixelData, lgrTotale, 1, fp1);
    fclose (fp1);
    return(1);