X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmFile.cxx;h=a864ff554eb74eef882b267d643042419149b33c;hb=b950a88db3b779f409f548361bbc62882094b9fb;hp=3431c0f848bf2561d2fb2a7f37ffe2a6ea1e5677;hpb=5fbee0c35cc0f02ceea5d5a8be0c1900c63143bb;p=gdcm.git

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index 3431c0f8..a864ff55 100644
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -1,9 +1,22 @@
 // gdcmFile.cxx
 
+//This is needed when compiling in debug mode
+#ifdef _MSC_VER
+// 'type' : forcing value to bool 'true' or 'false' (performance warning)
+//#pragma warning ( disable : 4800 )
+// 'identifier' : class 'type' needs to have dll-interface to be used by
+// clients of class 'type2'
+#pragma warning ( disable : 4251 )
+// 'identifier' : identifier was truncated to 'number' characters in the
+// debug information
+#pragma warning ( disable : 4786 )
+#endif //_MSC_VER
+
 #include "gdcmFile.h"
 #include "gdcmUtil.h"
-#include "iddcmjpeg.h"
-using namespace std;
+#include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess
+
+#define str2num(str, typeNum) *((typeNum *)(str))
 
 /////////////////////////////////////////////////////////////////
 /**
@@ -23,7 +36,7 @@ using namespace std;
  * @return	
  */
  
-gdcmFile::gdcmFile(string & filename) 
+gdcmFile::gdcmFile(std::string & filename) 
 	:gdcmHeader(filename.c_str())	
 {
    SetPixelDataSizeFromHeader();
@@ -47,16 +60,27 @@ gdcmFile::gdcmFile(const char * filename)
  */
 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 " 
+       || str_PhotometricInterpretation == "YBR_FULL") {   // --> some more to be added !!
+      lgrTotale*=3;
+   }
+   
+   // remaining to check :
+   //   str_PhotometricInterpretation == "YBR_FULL"
+   //   str_PhotometricInterpretation == "YBR_FULL_422" (no LUT, no Palette)
+   // -->and some more !!
 }
 
 /////////////////////////////////////////////////////////////////
@@ -71,6 +95,236 @@ size_t gdcmFile::GetImageDataSize(void) {
 }
 
 
+/////////////////////////////////////////////////////////////////
+/**
+ * \ingroup gdcmFile
+ * \brief   Parse pixel data from disk and *prints* the result
+ * \        For multi-fragment Jpeg/Rle files checking purpose *only*
+ * \        Allows to 'see' if the file *does* conform
+ * \       (some of them do not)
+ * \        with Dicom Part 3, Annex A (PS 3.5-2003, page 58, page 85)
+ *
+ */
+bool gdcmFile::ParsePixelData(void) {
+
+   if ( !OpenFile())
+      return false;
+      
+    if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
+      CloseFile();
+      return false;
+   } 
+   
+   if ( !IsDicomV3()                             ||
+        IsImplicitVRLittleEndianTransferSyntax() ||
+        IsExplicitVRLittleEndianTransferSyntax() ||
+        IsExplicitVRBigEndianTransferSyntax()    ||
+        IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { 
+        
+        printf ("gdcmFile::ParsePixelData : non JPEG/RLE File\n");
+        return 0;       
+   }        
+
+   int nb;
+   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 taille = GetXSize() *  GetYSize() * GetZSize() * GetSamplesPerPixel();
+   int taille = GetXSize() *  GetYSize()  * GetSamplesPerPixel(); 
+         
+   printf ("Checking the Dicom-Jpeg/RLE Pixels\n");
+      
+   guint16 ItemTagGr,ItemTagEl; 
+   int ln;
+   long ftellRes;
+   char * destination = NULL;
+
+  // ------------------------------- for Parsing : Position on begining of Jpeg/RLE Pixels 
+
+   if( !IsRLELossLessTransferSyntax()) {
+
+      // JPEG Image
+
+      cout << "JPEG image" << std::endl;
+      ftellRes=ftell(fp);
+      fread(&ItemTagGr,2,1,fp);  // Reading (fffe) : Basic Offset Table Item Tag Gr
+      fread(&ItemTagEl,2,1,fp);  // Reading (e000) : Basic Offset Table Item Tag El
+      if(GetSwapCode()) {
+         ItemTagGr=SwapShort(ItemTagGr); 
+         ItemTagEl=SwapShort(ItemTagEl);            
+      }
+      printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
+                ftellRes,ItemTagGr,ItemTagEl );
+      ftellRes=ftell(fp);
+      fread(&ln,4,1,fp); 
+      if(GetSwapCode()) 
+         ln=SwapLong(ln);    // Basic Offset Table Item Lentgh
+      printf("at %x : Basic Offset Table Item Lentgh (??) %d x(%08x)\n",
+            ftellRes,ln,ln);
+      if (ln != 0) {
+         // What is it used for ??
+         char * BasicOffsetTableItemValue= (char *)malloc(ln+1);
+         fread(BasicOffsetTableItemValue,ln,1,fp); 
+         guint32 a;
+         for (int i=0;i<ln;i+=4){
+            a=str2num(&BasicOffsetTableItemValue[i],guint32);
+            printf("      x(%08x)  %d\n",a,a);
+         }              
+      }
+      
+      ftellRes=ftell(fp);
+      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);            
+      }  
+      printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+            ftellRes,ItemTagGr,ItemTagEl );
+      
+      while (  ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { // Parse fragments
+      
+         ftellRes=ftell(fp);
+         fread(&ln,4,1,fp); 
+         if(GetSwapCode()) 
+            ln=SwapLong(ln);    // length
+         printf("      at %x : fragment length %d x(%08x)\n",
+                ftellRes, ln,ln);
+
+        // destination += taille * nBytes; // location in user's memory        
+        //printf ("      Destination will be x(%x) = %d \n",
+        //     destination,destination );
+
+         // ------------------------                                     
+         fseek(fp,ln,SEEK_CUR); // skipping (not reading) fragment pixels    
+         // ------------------------              
+     
+         ftellRes=ftell(fp);
+         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);            
+         }
+         printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+               ftellRes,ItemTagGr,ItemTagEl );
+      } 
+
+   } else {
+
+      // RLE Image
+
+      cout << "RLE image" << std::endl;
+      long RleSegmentLength[15],fragmentLength;
+      guint32 nbRleSegments;
+      guint32 RleSegmentOffsetTable[15];
+      ftellRes=ftell(fp);
+      // Basic Offset Table with Item Value
+         // Item Tag
+      fread(&ItemTagGr,2,1,fp);  // Reading (fffe):Basic Offset Table Item Tag Gr
+      fread(&ItemTagEl,2,1,fp);  // Reading (e000):Basic Offset Table Item Tag El
+      if(GetSwapCode()) {
+         ItemTagGr=SwapShort(ItemTagGr); 
+         ItemTagEl=SwapShort(ItemTagEl);            
+      }
+      printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
+                ftellRes,ItemTagGr,ItemTagEl );
+         // Item Length
+      ftellRes=ftell(fp);
+      fread(&ln,4,1,fp); 
+      if(GetSwapCode()) 
+         ln=SwapLong(ln);    // Basic Offset Table Item Lentgh
+      printf("at %x : Basic Offset Table Item Lentgh (??) %d x(%08x)\n",
+            ftellRes,ln,ln);
+      if (ln != 0) {
+         // What is it used for ??
+         char * BasicOffsetTableItemValue= (char *)malloc(ln+1);
+         fread(BasicOffsetTableItemValue,ln,1,fp); 
+         guint32 a;
+         for (int i=0;i<ln;i+=4){
+            a=str2num(&BasicOffsetTableItemValue[i],guint32);
+            printf("      x(%08x)  %d\n",a,a);
+         }              
+      }
+
+      ftellRes=ftell(fp);
+      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);            
+      }  
+      printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+            ftellRes,ItemTagGr,ItemTagEl );
+
+      // while 'Sequence Delimiter Item' (fffe,e0dd) not found
+      while (  ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { 
+      // Parse fragments of the current Fragment (Frame)    
+         ftellRes=ftell(fp);
+         fread(&fragmentLength,4,1,fp); 
+         if(GetSwapCode()) 
+            fragmentLength=SwapLong(fragmentLength);    // length
+         printf("      at %x : 'fragment' length %d x(%08x)\n",
+                ftellRes, fragmentLength,fragmentLength);
+
+//         destination += taille * nBytes; // location in user's memory                 
+//         printf ("      Destination will be x(%x) = %d \n",
+//               destination,destination );
+                        
+          //------------------ scanning (not reading) fragment pixels
+ 
+         fread(&nbRleSegments,4,1,fp);  // Reading : Number of RLE Segments           
+         if(GetSwapCode()) 
+            nbRleSegments=SwapLong(nbRleSegments);
+            printf("         Nb of RLE Segments : %d\n",nbRleSegments);
+ 
+         for(int k=1; k<=15; k++) { // Reading RLE Segments Offset Table
+            ftellRes=ftell(fp);
+            fread(&RleSegmentOffsetTable[k],4,1,fp);
+            if(GetSwapCode())
+               RleSegmentOffsetTable[k]=SwapLong(RleSegmentOffsetTable[k]);
+            printf("        at : %x Offset Segment %d : %d (%x)\n",
+                      ftellRes,k,RleSegmentOffsetTable[k],RleSegmentOffsetTable[k]);
+         }
+          if (nbRleSegments>1) { 
+             for(int k=1; k<=nbRleSegments-1; k++) { // skipping (not reading) RLE Segments
+                RleSegmentLength[k]=RleSegmentOffsetTable[k+1]-RleSegmentOffsetTable[k];
+                ftellRes=ftell(fp);
+                printf ("        Segment %d : Length = %d Start at %x\n",
+                                 k,RleSegmentLength[k], ftellRes);         
+                fseek(fp,RleSegmentLength[k],SEEK_CUR);    
+             }
+          }
+          RleSegmentLength[nbRleSegments] = fragmentLength - RleSegmentOffsetTable[nbRleSegments] ; 
+                                              // TODO : Check the value
+          ftellRes=ftell(fp);
+          printf ("        Segment %d : Length = %d Start at %x\n",
+                           nbRleSegments,RleSegmentLength[nbRleSegments],ftellRes);
+
+          fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR); 
+            
+         // ------------------ end of scanning fragment pixels        
+      
+         ftellRes=ftell(fp);
+         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);            
+         }
+         printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+               ftellRes,ItemTagGr,ItemTagEl );
+      } 
+   }
+   return 1;            
+}
+
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup gdcmFile
@@ -80,6 +334,7 @@ size_t gdcmFile::GetImageDataSize(void) {
  *
  */
 bool gdcmFile::ReadPixelData(void* destination) {
+
    if ( !OpenFile())
       return false;
       
@@ -87,6 +342,8 @@ bool gdcmFile::ReadPixelData(void* destination) {
       CloseFile();
       return false;
    }     
+
+// -------------------------  Uncompressed File
     
    if ( !IsDicomV3()                             ||
         IsImplicitVRLittleEndianTransferSyntax() ||
@@ -103,48 +360,52 @@ 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);
-      fseek(fp,ln,SEEK_CUR);
-      fseek(fp,4,SEEK_CUR);
-      fread(&ln,4,1,fp); 
-      if(GetSwapCode()) 
-         ln=SwapLong(ln);
-          
-  // ------------------------------- JPEG LossLess : call to Jpeg Libido
-   
-   if (IsJPEGLossless()) {
- 
-      ClbJpeg* jpg = _IdDcmJpegRead(fp);
-      if(jpg == NULL) {
-         CloseFile();
-         return false;
-      } 
-
+    
+ // ------------------------  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() * GetZSize() * GetSamplesPerPixel();
+      int taille = GetXSize() *  GetYSize()  * GetSamplesPerPixel(); 
           
+                
+  // ------------------------------- 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++) {
-               *((unsigned char *)dest+i) = *(dataJpg +i);    
+               *((unsigned char *)dest+i) = *(dataJpg +i);   
             }
          }
          break;        
@@ -156,35 +417,130 @@ bool gdcmFile::ReadPixelData(void* destination) {
                *((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); 
+      }
+      
+      // 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
       
-      bool res = (bool)gdcm_read_JPEG_file (destination);
+         // 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;
+      //cout << "destination" << destination << "\n";
+      }
+                
       return res;
 }   
 
@@ -192,11 +548,13 @@ bool gdcmFile::ReadPixelData(void* destination) {
  * \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);
 }
 
@@ -216,7 +574,7 @@ 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"
@@ -224,45 +582,45 @@ 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) {
@@ -285,52 +643,113 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
          dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
          return (size_t)0; 
       }
-   }
+   }  
    
- // ---
-   string str_PlanarConfiguration = GetPubElValByNumber(0x0028,0x0006);
-   int PlanarConfiguration;
-   if (str_PlanarConfiguration == "gdcm::Unfound" ) {
-      PlanarConfiguration = 0;
-   } else {
-      PlanarConfiguration = atoi(str_PlanarConfiguration.c_str() );
-   }   
- // ---
- 
-   // TODO : replace by	 	 	 
-   // if (GetPlanarConfiguration() == 1) {
-   // after unfreeze
+   // Try to deal with the color
+   // --------------------------
+     
+   std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+   
+   if ( (str_PhotometricInterpretation == "MONOCHROME1 ") 
+     || (str_PhotometricInterpretation == "MONOCHROME2 ") 
+     || (str_PhotometricInterpretation == "RGB")) {
+      return lgrTotale; 
+   }
+     
+   switch ( GetPlanarConfiguration() ) {
+   case 0:                              
+      //       Pixels are already RGB
+      break;
    
-   if (PlanarConfiguration == 1) { // need to make RGB Pixels
-      int l = lgrTotale/3 ;
-
-      char * a = (char *)destination;
-      char * b = a + l;
-      char * c = b + l;
-      char * newDest = (char*) malloc(lgrTotale);
-      // TODO :
-      // any trick not to have to allocate temporary buffer is welcome ...
-      char *x = newDest;
-      for (int j=0;j<l; j++) {
-         *(x++) = *(a++);
-         *(x++) = *(b++);
-         *(x++) = *(c++);  
+   case 1:
+      //       need to make RGB Pixels from Planes R,G,B
+      {
+         int l = lgrTotale/3 ;
+
+         char * a = (char *)destination;
+         char * b = a + l;
+         char * c = b + l;
+         char * newDest = (char*) malloc(lgrTotale);
+         // TODO :
+         // any trick not to have to allocate temporary buffer is welcome ...
+         char *x = newDest;
+         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
+         std::string spp = "3";
+         gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+         std::string rgb="RGB";
+         gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+         break;
       }
-      a = (char *)destination;
-      x = newDest;
-      for (int i=0;i<lgrTotale; i++) {
-         *(a++) = *(x++);
+      
+    case 2:                      
+      //       from Lut R + Lut G + Lut B
+       
+      // we no longer use gdcmHeader::GetLUTRGB
+      // since a lot of images have wrong info 
+      // in the Lookup Table Descriptors (0028,1101),...
+      {
+         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;
+            unsigned char * a = (unsigned char *)destination;
+            int j;        
+            for (int i=0;i<l; i++) {
+               j=newDest[i]*2;  // Who can explain *why* we have to skip bytes
+               *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;
       }
-      free(newDest);
-   }
+   } 
+    
    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;
@@ -354,7 +773,7 @@ if(nb == 16)
          break;
  			
       default:
-         printf("valeur de SWAP (16 bits) non autorisee : %d\n", swap);
+         printf("valeur de SWAP (16 bits) not allowed : %d\n", swap);
    } 
  
 if( nb == 32 )
@@ -395,7 +814,7 @@ if( nb == 32 )
          break; 
     			        
       default:
-         printf("valeur de SWAP (32 bits) non autorisee : %d\n", swap);
+         printf(" SWAP value (32 bits) not allowed : %d\n", swap);
    } 
 return;
 }
@@ -404,13 +823,13 @@ 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);
@@ -423,22 +842,20 @@ 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 ...
- 	
+   std::string content1;
+   char car[20];	
+   // Assumes ElValue (0x7fe0, 0x0010) exists ...	
    sprintf(car,"%d",ImageDataSize);
  
    gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
@@ -457,70 +874,62 @@ 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) {
-
+int gdcmFile::WriteRawData (std::string fileName) {
    FILE * fp1;
-   fp1 = fopen(nomFichier.c_str(),"wb");
+   fp1 = fopen(fileName.c_str(),"wb");
    if (fp1 == NULL) {
-      printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str());
+      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);
 }
 	
 /////////////////////////////////////////////////////////////////
@@ -535,25 +944,24 @@ 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");
@@ -564,13 +972,42 @@ 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);