X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=c037ba6de931a36addc304ce7cb3272daa6acfe7;hb=879f56a62d0772c95e92d0657882eb1886b4153d;hp=6e76b45c55da304592282a2c7d446550a0256004;hpb=64f79e8efbfae49231d1f469aa4fcc4acf0da70c;p=gdcm.git

diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx
index 6e76b45c..c037ba6d 100644
--- a/src/gdcmDocument.cxx
+++ b/src/gdcmDocument.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmDocument.cxx,v $
   Language:  C++
-  Date:      $Date: 2004/10/06 09:58:08 $
-  Version:   $Revision: 1.93 $
+  Date:      $Date: 2004/10/10 03:03:10 $
+  Version:   $Revision: 1.101 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -33,7 +33,7 @@
    #include <netinet/in.h>
 #endif
 
-#  include <iomanip>
+#include <iomanip>
 
 // Implicit VR Little Endian
 #define UI1_2_840_10008_1_2      "1.2.840.10008.1.2"
@@ -106,7 +106,7 @@ gdcmDocument::gdcmDocument( std::string const & filename )
    long beg = ftell(Fp);
    lgt -= beg;
    
-   (void)ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
+   ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
 
    rewind(Fp);
    
@@ -449,6 +449,22 @@ bool gdcmDocument::IsJPEG2000()
            || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) );
 }
 
+/**
+ * \brief   Determines if the Transfer Syntax corresponds to encapsulated
+ *          of encoded Pixel Data (as opposed to native).
+ * @return  True when encapsulated. False when native.
+ */
+bool gdcmDocument::IsEncapsulateTransferSyntax()
+{
+   return (   IsJPEGBaseLineProcess1TransferSyntax()
+           || IsJPEGExtendedProcess2_4TransferSyntax()
+           || IsJPEGExtendedProcess3_5TransferSyntax()
+           || IsJPEGSpectralSelectionProcess6_8TransferSyntax()
+           || IsRLELossLessTransferSyntax()
+           || IsJPEGLossless()
+           || IsJPEG2000() );
+}
+
 /**
  * \brief   Predicate for dicom version 3 file.
  * @return  True when the file is a dicom version 3.
@@ -965,12 +981,12 @@ bool gdcmDocument::SetEntryByNumber(std::string const& content,
       gdcmVRKey vr = valEntry->GetVR();
       if( vr == "US" || vr == "SS" )
       {
-         c = CountSubstring(content, "\\") + 1; // for multivaluated items
+         c = gdcmUtil::CountSubstring(content, "\\") + 1; // for multivaluated items
          l = c*2;
       }
       else if( vr == "UL" || vr == "SL" )
       {
-         c = CountSubstring(content, "\\") + 1; // for multivaluated items
+         c = gdcmUtil::CountSubstring(content, "\\") + 1; // for multivaluated items
          l = c*4;;
       }
    }
@@ -1361,14 +1377,12 @@ uint16_t gdcmDocument::UnswapShort(uint16_t a)
  * \brief   Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
  * @return  length of the parsed set. 
  */ 
-
-long gdcmDocument::ParseDES(gdcmDocEntrySet *set,
+void gdcmDocument::ParseDES(gdcmDocEntrySet *set,
                             long offset,
                             long l_max,
                             bool delim_mode)
 {
    gdcmDocEntry *newDocEntry = 0;
-   unsigned long l = 0;
    
    while (true)
    { 
@@ -1457,29 +1471,28 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set,
          if (newDocEntry->GetGroup()   == 0x7fe0 && 
              newDocEntry->GetElement() == 0x0010 )
          {
-             if ( newDocEntry->GetReadLength()==0xffffffff ) 
+             if ( IsRLELossLessTransferSyntax() ) 
              {
-                // Broken US.3405.1.dcm
-                Parse7FE0(); // to skip the pixels 
-                             // (multipart JPEG/RLE are trouble makers)
+                long PositionOnEntry = ftell(Fp);
+                fseek(Fp, newDocEntry->GetOffset(), SEEK_SET);
+                ComputeRLEInfo();
+                fseek(Fp, PositionOnEntry, SEEK_SET);
              }
              else
              {
                 SkipToNextDocEntry(newDocEntry);
-                l = newDocEntry->GetFullLength(); 
              }
          }
          else
          {
              // to be sure we are at the beginning 
              SkipToNextDocEntry(newDocEntry);
-             l = newDocEntry->GetFullLength(); 
          }
       }
       else
       {
          // VR = "SQ"
-         l = newDocEntry->GetReadLength();            
+         unsigned long l = newDocEntry->GetReadLength();            
          if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
          {
             if ( l == 0xffffffff )
@@ -1519,9 +1532,9 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set,
 
          if ( l != 0 )
          {  // Don't try to parse zero-length sequences
-            (void)ParseSQ( newSeqEntry, 
-                           newDocEntry->GetOffset(),
-                           l, delim_mode);
+            ParseSQ( newSeqEntry, 
+                     newDocEntry->GetOffset(),
+                     l, delim_mode);
          }
          set->AddEntry( newSeqEntry );
          if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
@@ -1531,14 +1544,13 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set,
       }
       delete newDocEntry;
    }
-   return l; // Probably useless 
 }
 
 /**
  * \brief   Parses a Sequence ( SeqEntry after SeqEntry)
  * @return  parsed length for this level
  */ 
-long gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
+void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
                             long offset, long l_max, bool delim_mode)
 {
    int SQItemNumber = 0;
@@ -1583,7 +1595,7 @@ long gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
          dlm_mod = false;
       }
    
-      (void)ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+      ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
       
       seqEntry->AddEntry( itemSQ, SQItemNumber ); 
       SQItemNumber++;
@@ -1592,9 +1604,6 @@ long gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
          break;
       }
    }
-
-   int lgth = ftell(Fp) - offset;
-   return lgth;
 }
 
 /**
@@ -1776,17 +1785,19 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry )
    {
       if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" ) 
       {
-         // The following reserved two bytes (see PS 3.5-2001, section
-         // 7.1.2 Data element structure with explicit vr p27) must be
+         // The following reserved two bytes (see PS 3.5-2003, section
+         // "7.1.2 Data element structure with explicit vr", p 27) must be
          // skipped before proceeding on reading the length on 4 bytes.
          fseek(Fp, 2L, SEEK_CUR);
          uint32_t length32 = ReadInt32();
 
-         if ( vr == "OB" && length32 == 0xffffffff ) 
+         if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) 
          {
             uint32_t lengthOB;
             try 
             {
+               /// \todo rename that to FindDocEntryLengthOBOrOW since
+               ///       the above test is on both OB and OW...
                lengthOB = FindDocEntryLengthOB();
             }
             catch ( gdcmFormatUnexpected )
@@ -1941,7 +1952,7 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry )
 */
 bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr)
 {
-   char msg[100]; // for sprintf
+   std::string msg;
    bool realExplicit = true;
 
    // Assume we are reading a falsely explicit VR file i.e. we reached
@@ -1969,9 +1980,9 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr)
    {
       // We thought this was explicit VR, but we end up with an
       // implicit VR tag. Let's backtrack.   
-      sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", 
-                   entry->GetGroup(), entry->GetElement());
-      dbg.Verbose(1, "gdcmDocument::FindVR: ",msg);
+      msg = gdcmUtil::Format("Falsely explicit vr file (%04x,%04x)\n", 
+                    entry->GetGroup(), entry->GetElement());
+      dbg.Verbose(1, "gdcmDocument::FindVR: ", msg.c_str());
 
       if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000)
       {
@@ -2109,7 +2120,7 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry)
          uint16_t newInt16;
 
          tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
-         Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
+         gdcmUtil::Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
          for (unsigned int i=0; i<tokens.size(); i++) 
          {
             newInt16 = atoi(tokens[i].c_str());
@@ -2123,7 +2134,7 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry)
          uint32_t newInt32;
 
          tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
-         Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
+         gdcmUtil::Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
          for (unsigned int i=0; i<tokens.size();i++) 
          {
             newInt32 = atoi(tokens[i].c_str());
@@ -2817,33 +2828,23 @@ uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement)
 }
 
 /**
- * \brief   Parse pixel data from disk for multi-fragment Jpeg/Rle files
- *          No other way so 'skip' the Data
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ *        Compute the RLE extra information and store it in \ref RLEInfo
+ *        for later pixel retrieval usage.
  */
-void gdcmDocument::Parse7FE0 ()
+void gdcmDocument::ComputeRLEInfo()
 {
-   gdcmDocEntry* element = GetDocEntryByNumber(0x0002, 0x0010);
-   if ( !element )
-   {
-      // Should warn user FIXME
-      return;
-   }
-      
-   if (   IsImplicitVRLittleEndianTransferSyntax()
-       || IsExplicitVRLittleEndianTransferSyntax()
-       || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier !
-       || IsDeflatedExplicitVRLittleEndianTransferSyntax() )
+   if ( ! IsRLELossLessTransferSyntax() )
    {
       return;
    }
-
    // Encoded pixel data: for the time being we are only concerned with
    // Jpeg or RLE Pixel data encodings.
-   // As stated in ps-3.3, 8.2:
-   // "If sent in Encapsulated Format (i.e. other than the Narive Format) the
+   // As stated in PS 3.5-2003, section 8.2 p44:
+   // "If sent in Encapsulated Format (i.e. other than the Native Format) the
    //  value representation OB is used".
    // Hence we expect an OB value representation. Concerning OB VR,
-   // the section PS3.3, A.4.c (p58 and p59), states:
+   // the section PS 3.5-2003, section A.4.c p 58-59, states:
    // "For the Value Representations OB and OW, the encoding shall meet the
    //   following specifications depending on the Data element tag:"
    //   [...snip...]
@@ -2859,7 +2860,7 @@ void gdcmDocument::Parse7FE0 ()
    //          we can't rely on it for the implementation, and we will simply
    //          trash it's content (when present).
    //        - still, when present, we could add some further checks on the
-   //          lengths, but not bother with such fuses for the time being.
+   //          lengths, but we won't bother with such fuses for the time being.
    if ( itemLength != 0 )
    {
       char* basicOffsetTableItemValue = new char[itemLength + 1];
@@ -2872,89 +2873,74 @@ void gdcmDocument::Parse7FE0 ()
          std::ostringstream s;
          s << "   Read one length: ";
          s << std::hex << individualLength << std::endl;
-         dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
+         dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: ", s.str().c_str());
       }
       delete[] basicOffsetTableItemValue;
    }
 
-   if ( ! IsRLELossLessTransferSyntax() )
-   {
-      // JPEG Image
-      
-      //// We then skip (not reading them) all the fragments of images:
-      while ( (itemLength = ReadTagLength(0xfffe, 0xe000)) )
+   // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
+   // Loop on the frame[s] and store the parsed information in a
+   // gdcmRLEFramesInfo.
+   long frameLength;
+
+   // Loop on the individual frame[s] and store the information
+   // on the RLE fragments in a gdcmRLEFramesInfo.
+   // Note: - when only a single frame is present, this is a
+   //         classical image.
+   //       - when more than one frame are present, then we are in 
+   //         the case of a multi-frame image.
+   while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
+   { 
+      // Parse the RLE Header and store the corresponding RLE Segment
+      // Offset Table information on fragments of this current Frame.
+      // Note that the fragment pixels themselves are not loaded
+      // (but just skipped).
+      long frameOffset = ftell(Fp);
+
+      uint32_t nbRleSegments = ReadInt32();
+ 
+      uint32_t rleSegmentOffsetTable[15];
+      for( int k = 1; k <= 15; k++ )
       {
-         SkipBytes(itemLength);
+         rleSegmentOffsetTable[k] = ReadInt32();
       }
-   }
-   else
-   {
-      // Encapsulated RLE Compressed Images (see PS-3.3, Annex G).
-      // Loop on the frame[s] and store the parsed information in a
-      // gdcmRLEFramesInfo.
-      long frameLength;
-
-      // Loop on the individual frame[s] and store the information
-      // on the RLE fragments in a gdcmRLEFramesInfo.
-      // Note: - when only a single frame is present, this is a
-      //         classical image.
-      //       - when more than one frame are present, then we are in 
-      //         the case of a multi-frame image.
-      while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
-      { 
-         // Parse the RLE Header and store the corresponding RLE Segment
-         // Offset Table information on fragments of this current Frame.
-         // Note that the fragment pixels themselves are not loaded
-         // (but just skipped).
-         uint32_t nbRleSegments = ReadInt32();
- 
-         uint32_t rleSegmentOffsetTable[15];
-         long ftellRes;
-         for( int k = 1; k <= 15; k++ )
-         {
-            ftellRes = ftell(Fp);
-            rleSegmentOffsetTable[k] = ReadInt32();
-         }
 
-         // Deduce from both the RLE Header and the frameLength the
-         // fragment length, and again store this infor in a
-         // gdcmRLEFramesInfo.
-         long rleSegmentLength[15];
-         // skipping (not reading) RLE Segments
-         if ( nbRleSegments > 1)
+      // Deduce from both the RLE Header and the frameLength the
+      // fragment length, and again store this info in a
+      // gdcmRLEFramesInfo.
+      long rleSegmentLength[15];
+      // skipping (not reading) RLE Segments
+      if ( nbRleSegments > 1)
+      {
+         for(unsigned int k = 1; k <= nbRleSegments-1; k++)
          {
-            for(unsigned int k = 1; k <= nbRleSegments-1; k++)
-            {
-                rleSegmentLength[k] =  rleSegmentOffsetTable[k+1]
-                                     - rleSegmentOffsetTable[k];
-                ftellRes = ftell(Fp);
-                SkipBytes(rleSegmentLength[k]);
-             }
+             rleSegmentLength[k] =  rleSegmentOffsetTable[k+1]
+                                  - rleSegmentOffsetTable[k];
+             SkipBytes(rleSegmentLength[k]);
           }
+       }
 
-          rleSegmentLength[nbRleSegments] = frameLength 
-                                         - rleSegmentOffsetTable[nbRleSegments];
-          ftellRes = ftell(Fp);
-          SkipBytes(rleSegmentLength[nbRleSegments]);
-
-          // Store the collected info
-          gdcmRLEFrame* newFrameInfo = new gdcmRLEFrame;
-          newFrameInfo->NumberFragments = nbRleSegments;
-          for( unsigned int k = 1; k <= nbRleSegments; k++ )
-          {
-             newFrameInfo->Offset[k] = rleSegmentOffsetTable[k];
-             newFrameInfo->Length[k] = rleSegmentLength[k];
-          }
-          RLEInfo.Frames.push_back( newFrameInfo );
-      }
+       rleSegmentLength[nbRleSegments] = frameLength 
+                                      - rleSegmentOffsetTable[nbRleSegments];
+       SkipBytes(rleSegmentLength[nbRleSegments]);
 
-      // Make sure that at the end of the item we encounter a 'Sequence
-      // Delimiter Item':
-      if ( !ReadTag(0xfffe, 0xe0dd) )
-      {
-         dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item");
-         dbg.Verbose(0, "    at end of RLE item sequence");
-      }
+       // Store the collected info
+       gdcmRLEFrame* newFrameInfo = new gdcmRLEFrame;
+       newFrameInfo->NumberFragments = nbRleSegments;
+       for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
+       {
+          newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk];
+          newFrameInfo->Length[uk] = rleSegmentLength[uk];
+       }
+       RLEInfo.Frames.push_back( newFrameInfo );
+   }
+
+   // Make sure that at the end of the item we encounter a 'Sequence
+   // Delimiter Item':
+   if ( !ReadTag(0xfffe, 0xe0dd) )
+   {
+      dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: no sequence delimiter ");
+      dbg.Verbose(0, "    item at end of RLE item sequence");
    }
 }