X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=af62cd8f545a8856958298eca0e2e1668bb5b47c;hb=49236d643fd420ddc5787a6cab3bbc0a45729fd0;hp=70859f9dcffd1aa99cfb23a9999bec63a5c17798;hpb=f87aa828eaad96473078971c4f039e73d76b2070;p=gdcm.git

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index 70859f9d..af62cd8f 100644
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -2,14 +2,8 @@
 
 #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
+#include "jpeg/ljpg/jpegless.h"
 
 /////////////////////////////////////////////////////////////////
 /**
@@ -29,16 +23,18 @@ using namespace std;
  * @return	
  */
  
-gdcmFile::gdcmFile(string & filename) 
+gdcmFile::gdcmFile(std::string & filename) 
 	:gdcmHeader(filename.c_str())	
 {
-   SetPixelDataSizeFromHeader();
+      if (IsReadable())
+         SetPixelDataSizeFromHeader();
 }
 
 gdcmFile::gdcmFile(const char * filename) 
 	:gdcmHeader(filename)	
 {
-   SetPixelDataSizeFromHeader();
+   if (IsReadable())
+      SetPixelDataSizeFromHeader();
 }
 
 /**
@@ -46,24 +42,59 @@ 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 +103,7 @@ 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);
 }
@@ -86,15 +118,43 @@ size_t gdcmFile::GetImageDataSize(void) {
  *
  */
 bool gdcmFile::ReadPixelData(void* destination) {
+
    if ( !OpenFile())
       return false;
       
-      printf("GetPixelOffset() %d\n",GetPixelOffset() );
-      
     if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
       CloseFile();
       return false;
-   }     
+   }
+
+// -------------------------  Compacted File (12 Bits Per Pixel)
+
+   /* unpack 12 Bits pixels into 16 Bits pixels */
+   /* 2 pixels 12bit =     [0xABCDEF]           */
+   /* 2 pixels 16bit = [0x0ABD] + [0x0FCE]      */
+
+   if (GetBitsAllocated()==12) {
+      int nbPixels = GetXSize()*GetYSize();
+      unsigned char b0, b1, b2;
+      
+      for(int p=0;p<nbPixels;p+=2) {
+         fread(&b0,1,1,fp);
+         fread(&b1,1,1,fp);
+         fread(&b2,1,1,fp);      
+         *((unsigned short int*)destination)++ = 
+	            ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+                       /* A */          /* B */            /* D */
+         *((unsigned short int*)destination)++ = 
+	            ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+                       /* F */          /* C */            /* E */
+		  
+	// Troubles expected on Big-Endian processors ?	      
+      }
+      return(true);
+   }
+        
+
+// -------------------------  Uncompressed File
     
    if ( !IsDicomV3()                             ||
         IsImplicitVRLittleEndianTransferSyntax() ||
@@ -111,94 +171,120 @@ 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()) {
+// ------------------------- Run Length Encoding
+
+      if (gdcmHeader::IsRLELossLessTransferSyntax()) {
+            int res = (bool)gdcm_read_RLE_file (destination);
+            return res; 
+      }  
  
-      ClbJpeg* jpg = _IdDcmJpegRead(fp);
-      if(jpg == NULL) {
-         CloseFile();
-         return false;
-      } 
 
+    
+// ----------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 
+       
       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;
+         if (nb == 12) nb =16;  // ?? 12 should be ACR-NEMA only ?
       }
       int nBytes= nb/8;
-      int * dataJpg = jpg->DataImg;
-      int taille = GetXSize() *  GetYSize() *  GetZSize() * GetSamplesPerPixel();
-          
-      switch (nBytes) {   
-         case 1:
-         {
-            unsigned short *dest = (unsigned short *)destination;
-            for (int i=0; i<taille; i++) {
-               *((unsigned char *)dest+i) = *(dataJpg +i);    
-            }
-         }
-         break;        
+      
+      int taille = GetXSize() *  GetYSize()  * GetSamplesPerPixel();    
+      long fragmentBegining; // for ftell, fseek
+      
+      bool jpg2000 =     IsJPEG2000();
+      bool jpgLossless = IsJPEGLossless();
+       
+      bool res = true;
+      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
          
-         case 2:
-         {
-            unsigned short *dest = (unsigned short *)destination;
-            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;          
-     }
+      if (ln != 0) {
+         // What is it used for ?!?
+         char *BasicOffsetTableItemValue = (char *)malloc(ln+1);        
+         fread(BasicOffsetTableItemValue,ln,1,fp); 
+      }
       
-      _IdDcmJpegFree (jpg);
-      return true;
-   }  
- 
-  // ------------------------------- 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;
+      // 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
+      		               
+      while (  ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { 
       
-      int res = gdcm_read_JPEG_file (destination);
-         if (DEBUG) 
-            printf ("res : %d\n",res);
+                        // --- for each Fragment
+     
+         fread(&ln,4,1,fp); 
+         if(GetSwapCode()) 
+            ln=SwapLong(ln);    // Fragment Item length
+      
+         fragmentBegining=ftell(fp);   
+ 
+         if (jpg2000) {          // JPEG 2000 :    call to ???
+	 
+            res = (bool)gdcm_read_JPEG2000_file (destination);  // Not Yet written 
+
+         } // ------------------------------------- endif (JPEG2000)
+	   
+         else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
+		      
+	    JPEGLosslessDecodeImage (fp,                         // Reading Fragment pixels
+				     (unsigned short *)destination,
+				     GetPixelSize()*8* GetSamplesPerPixel(),
+                                     ln);						 	   
+	    res=1; // in order not to break the loop
+     
+         } // ------------------------------------- endif (JPEGLossless)
+                  
+         else {                   // JPEG Lossy : call to IJG 6b
+	 
+            if  (GetBitsStored() == 8) {
+            	res = (bool)gdcm_read_JPEG_file (destination);  // Reading Fragment pixels         
+            } else {
+            	res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels  
+            } 
+	 }  // ------------------------------------- endif (JPEGLossy)    
+            
+         if (!res) break;
+                  
+         destination = (char *)destination + taille * nBytes; // location in user's memory 
+                                                              // for next fragment (if any) 
+         
+         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);            
+         } 
+      
+      }     // endWhile parsing fragments until Sequence Delim. Tag found    
+    
       return res;
 }   
 
@@ -206,11 +292,13 @@ 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);
 }
 
@@ -230,7 +318,7 @@ 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"
@@ -238,45 +326,45 @@ 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) {
@@ -299,52 +387,201 @@ 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
+   } 
+
+// Just to 'see' was was actually read on disk :-(
+// Some troubles expected
+
+   // *Try* to deal with the color
+   // ----------------------------
    
-   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 i=0;i<l; i++) {
-         *(x++) = *(a++);
-         *(x++) = *(b++);
-         *(x++) = *(c++);  
+       std::string str_PhotometricInterpretation = 
+                 gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+		   
+      if ( (str_PhotometricInterpretation == "MONOCHROME1 ") 
+        || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
+         return lgrTotale; 
       }
-      a = (char *)destination;
-      x = newDest;
-      for (int i=0;i<lgrTotale; i++) {
-         *(a++) = *(x++);
+      
+   // 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 :-( 
+
+      int planConf=GetPlanarConfiguration();
+
+      // Whatever Planar Configuration is, 
+      // "PALETTE COLOR " implies that we deal with the palette. 
+      if (str_PhotometricInterpretation == "PALETTE COLOR ")
+         planConf=2;
+
+      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);
+        }
+	  
+         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
+
+            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;
+
+            // if we get a black image, let's just remove the '+1'
+            // and check again 
+            // if it works, we shall have to check the 3 Palettes
+            // to see which byte is ==0 (first one, or second one)
+	                   
+            for (int i=0;i<l; i++) {
+               j=newDest[i]*mult +1;
+               *a++ = lutR[j]; 
+               *a++ = lutG[j];
+               *a++ = lutB[j];
+            }
+
+            free(newDest);
+               
+         } 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);
-   }
+   } 
+
+            // now, it's an RGB image
+            // Lets's write it in the Header
+
+         // CreateOrReplaceIfExist ?
+	 
+   std::string spp = "3";        // Samples Per Pixel
+   gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+   std::string rgb="RGB ";       // Photometric Interpretation
+   gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+   std::string planConfig = "0"; // Planar Configuration
+   gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006);
+	 
+	 // + Drop Palette Color ? 
+	     
    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;
@@ -368,7 +605,7 @@ 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 )
@@ -409,7 +646,7 @@ 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;
 }
@@ -418,13 +655,13 @@ 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);
@@ -437,22 +674,20 @@ 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);
@@ -471,70 +706,62 @@ 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
- *
- * @param nomFichier TODO JPR
+ *        (Equivalent a IdImaWriteRawFile) 
  *
- * @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);
 }
 	
 /////////////////////////////////////////////////////////////////
@@ -549,25 +776,24 @@ 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");
@@ -578,13 +804,42 @@ 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);