X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=32ef12b9af921513d04fdab8312a11780cf8b17a;hb=48c3e6379fcb2517d56c15d51e45c4c79543c16c;hp=50eeeba71a8320490354f92d6e6f44e8755fd9dd;hpb=d44cb38c3275dc302d9b523c17d346810f0e6644;p=gdcm.git

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index 50eeeba7..32ef12b9 100644
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -1,23 +1,8 @@
 // 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" // for the 'LibIDO' Jpeg LossLess
-using namespace std;
-
-#define str2num(str, typeNum) *((typeNum *)(str))
+#include "jpeg/ljpg/jpegless.h"
 
 /////////////////////////////////////////////////////////////////
 /**
@@ -37,32 +22,33 @@ 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();
 }
 
 /**
  * \ingroup   gdcmFile
  * \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	
- *  		(dans le cas d'images compressees, elle n'a pas de sens).
+ *            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
+ *          (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 ) {
       nb = 16;
@@ -70,20 +56,46 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) {
       nb = atoi(str_nb.c_str() );
       if (nb == 12) nb =16;
    }
-   lgrTotale =  GetXSize() *  GetYSize() *  GetZSize() * (nb/8)* GetSamplesPerPixel();
+   lgrTotale =  lgrTotaleRaw = GetXSize() *  GetYSize() *  GetZSize() 
+              * (nb/8)* GetSamplesPerPixel();
+   std::string str_PhotometricInterpretation = 
+                             gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+			     
+   /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
+   // pb when undealt Segmented Palette Color
    
-   string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
-   if (   str_PhotometricInterpretation == "PALETTE COLOR " 
-       || str_PhotometricInterpretation == "YBR_FULL") {   // --> some more to be added !!
+    if (HasLUT()) { 
       lgrTotale*=3;
    }
-   
-   // remaining to check :
-   //   str_PhotometricInterpretation == "YBR_FULL"
-   //   str_PhotometricInterpretation == "YBR_FULL_422" (no LUT, no Palette)
-   // -->and some more !!
 }
 
+   // 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  : 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]
+
+
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup   gdcmFile
@@ -91,127 +103,12 @@ 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);
 }
 
 
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief   Parse pixel data from disk and *prints* the result
- * \        For multi-fragment Jpeg 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)
- *
- */
-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 File\n");
-        return 0;       
-   }        
-
-   int nb;
-   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");
-      
-  // ------------------------------- for Parsing : Position on begining of Jpeg Pixels  
-      guint16 ItemTagGr,ItemTagEl; 
-      int ln;
-      long ftellRes;
-      char * destination = NULL;
-      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 );
-               
-      
-      } 
-   return 1;            
-}
-
 /////////////////////////////////////////////////////////////////
 /**
  * \ingroup gdcmFile
@@ -228,17 +125,45 @@ bool gdcmFile::ReadPixelData(void* destination) {
     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;
+      
+      unsigned short int* pdestination = (unsigned short int*)destination;    
+      for(int p=0;p<nbPixels;p+=2) {
+         fread(&b0,1,1,fp);
+         fread(&b1,1,1,fp);
+         fread(&b2,1,1,fp);      
+         //Two steps is necessary to please VC++
+         *pdestination++ =  ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+                       /* A */          /* B */            /* D */
+         *pdestination++ =  ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+                       /* F */          /* C */            /* E */
+		  
+	// Troubles expected on Big-Endian processors ?	      
+      }
+      return(true);
+   }        
 
-// ------------------------------- Uncompressed File
+   // ----------------------  Uncompressed File
     
    if ( !IsDicomV3()                             ||
         IsImplicitVRLittleEndianTransferSyntax() ||
         IsExplicitVRLittleEndianTransferSyntax() ||
         IsExplicitVRBigEndianTransferSyntax()    ||
-        IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { 
-                    
-      size_t ItemRead = fread(destination, lgrTotale, 1, fp);
+        IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
+
+      size_t ItemRead = fread(destination, GetPixelAreaLength(), 1, fp);
+      
       if ( ItemRead != 1 ) {
          CloseFile();
          return false;
@@ -247,82 +172,37 @@ bool gdcmFile::ReadPixelData(void* destination) {
          return true;
       }
    } 
+
+   // ---------------------- Run Length Encoding
+
+      if (gdcmHeader::IsRLELossLessTransferSyntax()) {
+            int res = (bool)gdcm_read_RLE_file (destination);
+            return res; 
+      }  
     
- // ----------------------------- JPEG Compressed File .
+   // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 
        
       int nb;
-      string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
+      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 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);   
-            }
-         }
-         break;        
-         
-         case 2:
-         {
-            unsigned short *dest = (unsigned short *)destination;
-            for (int i=0; i<taille; i++) {           
-               *((unsigned short *)dest+i) = *(dataJpg +i);    
-            }
-         }
-         break;       
-     }
-      _IdDcmJpegFree (jpg);
-      return true;
-   }  
- 
-  // ------------------------------- JPEG Lossy : call to IJG 6b
-    
+      int taille = GetXSize() *  GetYSize()  * GetSamplesPerPixel();    
       long fragmentBegining; // for ftell, fseek
       
-      bool a=0, b=0;
-      
-      a = gdcmHeader::IsRLELossLessTransferSyntax();
-      if (!a)
-         bool b = gdcmHeader::IsJPEG2000();
+      bool jpg2000 =     IsJPEG2000();
+      bool jpgLossless = IsJPEGLossless();
        
-      bool res;
+      bool res = true;
       guint16 ItemTagGr,ItemTagEl;
-      int ln;  //  Position on begining of Jpeg Pixels
+      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
@@ -349,68 +229,46 @@ bool gdcmFile::ReadPixelData(void* destination) {
       }
               
       // parsing fragments until Sequence Delim. Tag found
-       //unsigned short *dest = (unsigned short *)destination;
-         
-      while (  ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+      		               
+      while (  ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { 
+      
+                        // --- for each Fragment
+     
          fread(&ln,4,1,fp); 
          if(GetSwapCode()) 
             ln=SwapLong(ln);    // Fragment Item length
       
-         // FIXME : multi fragments 
-         fragmentBegining=ftell(fp);
-                       
-         if (a)  
-            res = (bool)gdcm_read_RLE_file (destination);       // Reading Fragment pixels 
-         else 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);
+         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 (IsJPEGLossless())
+         } // ------------------------------------- endif (JPEGLossless)
                   
-         else
+         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;
-         
-         // 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
+                                                              // 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
@@ -422,11 +280,9 @@ bool gdcmFile::ReadPixelData(void* destination) {
             ItemTagGr=SwapShort(ItemTagGr); 
             ItemTagEl=SwapShort(ItemTagEl);            
          } 
-         
-      //(char *) destination += taille * nBytes;
-      //cout << "destination" << destination << "\n";
-      }
-                
+      
+      }     // endWhile parsing fragments until Sequence Delim. Tag found    
+    
       return res;
 }   
 
@@ -434,6 +290,9 @@ bool gdcmFile::ReadPixelData(void* destination) {
  * \ingroup gdcmFile
  * \brief   Allocates necessary memory, copies the pixel data
  *          (image[s]/volume[s]) to newly allocated zone.
+ *          Transforms YBR pixels into RGB pixels if any
+            Transforms 3 planes R, G, B into a single RGB Plane
+	    Transforms single Grey plane + 3 Palettes into a RGB Plane
  * @return  Pointer to newly allocated pixel data.
  * \        NULL if alloc fails 
  */
@@ -444,10 +303,40 @@ void * gdcmFile::GetImageData (void) {
    return(PixelData);
 }
 
+/**
+ * \ingroup gdcmFile
+ * \brief   Allocates necessary memory, copies the pixel data
+ *          (image[s]/volume[s]) to newly allocated zone.
+ *          Transforms YBR pixels into RGB pixels if any
+            Transforms 3 planes R, G, B into a single RGB Plane
+	    DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * @return  Pointer to newly allocated pixel data.
+ * \        NULL if alloc fails 
+ */
+void * gdcmFile::GetImageDataRaw (void) {
+   if (HasLUT())
+      lgrTotale /= 3;  // TODO Let gdcmHeadar user a chance 
+                       // to get the right value
+		       // Create a member lgrTotaleRaw ???
+   PixelData = (void *) malloc(lgrTotale);
+   if (PixelData)
+      GetImageDataIntoVectorRaw(PixelData, lgrTotale);
+   return(PixelData);
+}
+
 /**
  * \ingroup gdcmFile
  * \brief   Copies at most MaxSize bytes of pixel data to caller's
  *          memory space.
+ * \warning This function was designed to avoid people that want to build
+ *          a volume from an image stack to need first to get the image pixels 
+ *          and then move them to the volume area.
+ *          It's absolutely useless for any VTK user since vtk chooses 
+ *          to invert the lines of an image, that is the last line comes first
+ *          (for some axis related reasons?). Hence he will have 
+ *          to load the image line by line, starting from the end.
+ *          VTK users have to call GetImageData
+ *     
  * @param   destination Address (in caller's memory space) at which the
  *          pixel data should be copied
  * @param   MaxSize Maximum number of bytes to be copied. When MaxSize
@@ -459,8 +348,95 @@ void * gdcmFile::GetImageData (void) {
 
 size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
 
+   size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
+   
+   if (!HasLUT())
+      return lgrTotale; 
+                            
+         //       from Lut R + Lut G + Lut B
+         
+   unsigned char * newDest = (unsigned char *)malloc(lgrTotale);
+   unsigned char * a       = (unsigned char *)destination;	 
+   unsigned char * lutRGBA = (unsigned char *)GetLUTRGBA();
+   if (lutRGBA) { 	    
+      int l = lgrTotale/3;
+      memmove(newDest, destination, l);// move Gray pixels to temp area	    
+      int j;	 
+      for (int i=0;i<l; i++) {         // Build RGB Pixels
+         j=newDest[i]*4;
+         *a++ = lutRGBA[j]; 
+         *a++ = lutRGBA[j+1];
+         *a++ = lutRGBA[j+2];
+      }
+      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);
+       
+               
+   } else { 
+	     // need to make RGB Pixels (?)
+             //    from grey Pixels (?!)
+             //     and Gray Lut  (!?!) 
+	     //    or Segmented xxx Palette Color Lookup Table Data and so on
+		  
+             // Well . I'll wait till I find such an image 
+		  		  
+		   // Oops! I get one (gdcm-US-ALOKA-16.dcm)
+                   // No idea how to manage it 
+		   // It seems that *no Dicom Viewer* has any idea :-(
+		   // Segmented xxx Palette Color are *more* than 65535 long ?!?
+		   
+      std::string rgb= "MONOCHROME1 ";      // Photometric Interpretation
+      gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);		   
+		   
+   }   
+    	 
+	 // TODO : Drop Palette Color out of the Header? 
+	     
+   return lgrTotale; 
+}
+
+
+
+/**
+ * \ingroup gdcmFile
+ * \brief   Copies at most MaxSize bytes of pixel data to caller's
+ *          memory space.
+ * \warning This function was designed to avoid people that want to build
+ *          a volume from an image stack to need first to get the image pixels 
+ *          and then move them to the volume area.
+ *          It's absolutely useless for any VTK user since vtk chooses 
+ *          to invert the lines of an image, that is the last line comes first
+ *          (for some axis related reasons?). Hence he will have 
+ *          to load the image line by line, starting from the end.
+ *          VTK users hace to call GetImageData
+  * \warning DOES NOT transform the Grey Plane + Palette Color (if any) 
+ *                   into a single RGB Pixels Plane
+ *          the (VTK) user will manage the palettes
+ *     
+ * @param   destination Address (in caller's memory space) at which the
+ *          pixel data should be copied
+ * @param   MaxSize Maximum number of bytes to be copied. When MaxSize
+ *          is not sufficient to hold the pixel data the copy is not
+ *          executed (i.e. no partial copy).
+ * @return  On success, the number of bytes actually copied. Zero on
+ *          failure e.g. MaxSize is lower than necessary.
+ */
+
+size_t gdcmFile::GetImageDataIntoVectorRaw (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"
@@ -492,12 +468,13 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
       highBit = nb - 1;
    } else {
       highBit = atoi(str_highBit.c_str() );
-   }
-		
-	// Signe des Pixels 
+   }		
+	// Pixel sign
+	// 0 = Unsigned
+	// 1 = Signed
    str_signe=GetPubElValByNumber(0x0028,0x0103);
    if (str_signe == GDCM_UNFOUND ) {
-      signe = 1;
+      signe = 0;  // default is unsigned
    } else {
       signe = atoi(str_signe.c_str() );
    }
@@ -505,7 +482,18 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
    // re arange bytes inside the integer
    if (nb != 8)
      SwapZone(destination, GetSwapCode(), lgrTotale, nb);
- 
+     
+   // to avoid pb with some xmedcon breakers images 
+   if (nb==16 && nbu<nb && signe==0) {
+     int l = (int)lgrTotale / (nb/8);
+     guint16 *deb = (guint16 *)destination;
+     for(int i = 0; i<l; i++) {
+        if(*deb == 0xffff) 
+	   *deb=0; 
+	   deb++;   
+         }
+    }
+
    // re arange bits inside the bytes
    if (nbu != nb){
       int l = (int)lgrTotale / (nb/8);
@@ -529,102 +517,144 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
          dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
          return (size_t)0; 
       }
-   }  
-   
-   // Try to deal with the color
-   // --------------------------
-     
-   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;
+   } 
+
+// Just to 'see' what was actually read on disk :-(
+// Some troubles expected
+//   FILE * f2;
+//   f2 = fopen("SpuriousFile.raw","wb");
+//   fwrite(destination,lgrTotale,1,f2);
+//   fclose(f2);
+
+   // Deal with the color
+   // -------------------
    
-   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
-         string spp = "3";
-         gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
-         string rgb="RGB";
-         gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
-         break;
+       std::string str_PhotometricInterpretation = 
+                 gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+		   
+      if ( (str_PhotometricInterpretation == "MONOCHROME1 ") 
+        || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
+         return lgrTotale; 
       }
       
-    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
+   // 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();  // 0028,0006
 
-            unsigned char * x = newDest;
+      // 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;
-            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];
-            }
+            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 {
          
-            // now, it's an RGB image      
-           string spp = "3";
-            gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002); 
-           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 
-         }
+         //       need to make RGB Pixels from R,G,B Planes
+	 //       (all the Frames at a time)
+
+            int l = GetXSize()*GetYSize()*GetZSize();
+
+            char * newDest = (char*) malloc(lgrTotale);
+            char * x = newDest;
+            char * a = (char *)destination;
+            char * b = a + l;
+            char * c = b + l;
+
+            for (int j=0;j<l; j++) {
+               *(x++) = *(a++);
+               *(x++) = *(b++);
+               *(x++) = *(c++);  
+            }
+           
+            memmove(destination,newDest,lgrTotale);
+            free(newDest);
+        }
+	  
          break;
-      }
+       }
+     
+       case 2:                      
+         //       Palettes were found
+	 //       Let the user deal with them !
+	  return lgrTotale;        
    } 
-    
+            // 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);
+	 
+	 // TODO : Drop Palette Color out of the Header? 
+	     
    return lgrTotale; 
 }
 
-//
-// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
-//
+
 
 /**
  * \ingroup gdcmFile
@@ -739,7 +769,7 @@ int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
  */
 
 void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
-   string content1;
+   std::string content1;
    char car[20];	
    // Assumes ElValue (0x7fe0, 0x0010) exists ...	
    sprintf(car,"%d",ImageDataSize);
@@ -766,7 +796,7 @@ void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
  * @return	
  */
 
-int gdcmFile::WriteRawData (string fileName) {
+int gdcmFile::WriteRawData (std::string fileName) {
    FILE * fp1;
    fp1 = fopen(fileName.c_str(),"wb");
    if (fp1 == NULL) {
@@ -790,7 +820,7 @@ int gdcmFile::WriteRawData (string fileName) {
  * @return int acts as a boolean
  */
 
-int gdcmFile::WriteDcmImplVR (string fileName) {
+int gdcmFile::WriteDcmImplVR (std::string fileName) {
    return WriteBase(fileName, ImplicitVR);
 }
 
@@ -803,7 +833,7 @@ int gdcmFile::WriteDcmImplVR (string fileName) {
  */
  
 int gdcmFile::WriteDcmImplVR (const char* fileName) {
-   return WriteDcmImplVR (string (fileName));
+   return WriteDcmImplVR (std::string (fileName));
 }
 	
 /////////////////////////////////////////////////////////////////
@@ -814,7 +844,7 @@ int gdcmFile::WriteDcmImplVR (const char* fileName) {
  * @return int acts as a boolean
  */
 
-int gdcmFile::WriteDcmExplVR (string fileName) {
+int gdcmFile::WriteDcmExplVR (std::string fileName) {
    return WriteBase(fileName, ExplicitVR);
 }
 	
@@ -834,7 +864,7 @@ int gdcmFile::WriteDcmExplVR (string fileName) {
  * @return int acts as a boolean	
  */
 
-int gdcmFile::WriteAcr (string fileName) {
+int gdcmFile::WriteAcr (std::string fileName) {
    return WriteBase(fileName, ACR);
 }
 
@@ -847,7 +877,7 @@ int gdcmFile::WriteAcr (string fileName) {
  *
  * @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");