add gdcmParsePixels.cxx

diff --git a/src/gdcmParsePixels.cxx b/src/gdcmParsePixels.cxx
new file mode 100644 (file)
index 0000000..c388cb5
--- /dev/null
+++ b/src/gdcmParsePixels.cxx
@@ -0,0 +1,248 @@
+// gdcmParse.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"
+
+#define str2num(str, typeNum) *((typeNum *)(str))
+
+//-----------------------------------------------------------------------------
+/**
+ * \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) {
+// DO NOT remove the printf s.
+// The ONLY purpose of this method is to PRINT the content
+   FILE *fp;
+
+   if ( !(fp=Header->OpenFile()))
+      return false;
+      
+    if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
+      Header->CloseFile();
+      return false;
+   } 
+   
+   if ( !Header->IsDicomV3()                             ||
+        Header->IsImplicitVRLittleEndianTransferSyntax() ||
+        Header->IsExplicitVRLittleEndianTransferSyntax() ||
+        Header->IsExplicitVRBigEndianTransferSyntax()    ||
+        Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { 
+        
+        printf ("gdcmFile::ParsePixelData : non JPEG/RLE File\n");
+        return false;       
+   }        
+
+   int nb;
+   std::string str_nb=Header->GetEntryByNumber(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 = Header->GetXSize() * Header->GetYSize() * Header->GetSamplesPerPixel(); 
+         
+   printf ("Checking the Dicom-encapsulated Jpeg/RLE Pixels\n");
+      
+   guint16 ItemTagGr,ItemTagEl; 
+   int ln;
+   long ftellRes;
+   char * destination = NULL;
+
+  // -------------------- for Parsing : Position on begining of Jpeg/RLE Pixels 
+
+   if( !Header->IsRLELossLessTransferSyntax()) {
+
+      // JPEG Image
+      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(Header->GetSwapCode()) {
+         ItemTagGr=Header->SwapShort(ItemTagGr); 
+         ItemTagEl=Header->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(Header->GetSwapCode()) 
+         ln=Header->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(Header->GetSwapCode()) {
+         ItemTagGr=Header->SwapShort(ItemTagGr); 
+         ItemTagEl=Header->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(Header->GetSwapCode()) 
+            ln=Header->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(Header->GetSwapCode()) {
+            ItemTagGr=Header->SwapShort(ItemTagGr); 
+            ItemTagEl=Header->SwapShort(ItemTagEl);            
+         }
+         printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+               ftellRes,ItemTagGr,ItemTagEl );
+      } 
+
+   } else {
+
+      // RLE Image
+      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(Header->GetSwapCode()) {
+         ItemTagGr=Header->SwapShort(ItemTagGr); 
+         ItemTagEl=Header->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(Header->GetSwapCode()) 
+         ln=Header->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(Header->GetSwapCode()) {
+         ItemTagGr=Header->SwapShort(ItemTagGr); 
+         ItemTagEl=Header->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(Header->GetSwapCode()) 
+            fragmentLength=Header->SwapLong(fragmentLength);    // length
+         printf("      at %x : 'fragment' length %d x(%08x)\n",
+                ftellRes, fragmentLength,fragmentLength);
+                       
+          //------------------ scanning (not reading) fragment pixels
+ 
+         fread(&nbRleSegments,4,1,fp);  // Reading : Number of RLE Segments
+         if(Header->GetSwapCode()) 
+            nbRleSegments=Header->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(Header->GetSwapCode())
+               RleSegmentOffsetTable[k]=Header->SwapLong(RleSegmentOffsetTable[k]);
+            printf("        at : %x Offset Segment %d : %d (%x)\n",
+                    ftellRes,k,RleSegmentOffsetTable[k],
+                    RleSegmentOffsetTable[k]);
+         }
+
+          if (nbRleSegments>1) { // skipping (not reading) RLE Segments
+             for(int k=1; k<=nbRleSegments-1; k++) { 
+                RleSegmentLength[k]=   RleSegmentOffsetTable[k+1]
+                                     - RleSegmentOffsetTable[k];
+                ftellRes=ftell(fp);
+                printf ("  Segment %d : Length = %d x(%x) Start at %x\n",
+                           k,RleSegmentLength[k],RleSegmentLength[k], ftellRes);
+                fseek(fp,RleSegmentLength[k],SEEK_CUR);    
+             }
+          }
+          RleSegmentLength[nbRleSegments]= fragmentLength 
+                                         - RleSegmentOffsetTable[nbRleSegments];
+          ftellRes=ftell(fp);
+          printf ("  Segment %d : Length = %d x(%x) Start at %x\n",
+                           nbRleSegments,RleSegmentLength[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(Header->GetSwapCode()) {
+            ItemTagGr=Header->SwapShort(ItemTagGr); 
+            ItemTagEl=Header->SwapShort(ItemTagEl);            
+         }
+         printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+               ftellRes,ItemTagGr,ItemTagEl );
+      } 
+   }
+   return true;            
+}
+
+//-----------------------------------------------------------------------------