X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=e65e2efa9d9537086791e84b58b77ae0cb40cc32;hb=01b8a6a38ef3eb36670dada5f3abc48b09692db4;hp=0a4339b2061939fdcd89d94251ef191107417e0a;hpb=bd1e1aea88a95e4d14cd59088a7e5280703402ea;p=gdcm.git

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index 0a4339b2..e65e2efa 100644
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmFile.cxx,v $
   Language:  C++
-  Date:      $Date: 2005/10/19 12:01:51 $
-  Version:   $Revision: 1.282 $
+  Date:      $Date: 2005/10/26 06:23:37 $
+  Version:   $Revision: 1.297 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -230,16 +230,18 @@ bool File::DoTheLoadingJob( )
          // Change only made if usefull
          if ( PixelVR != oldEntry->GetVR() )
          {
-            DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel,
-                                                     PixelVR,"1","Pixel Data");
+            DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
+                                                PixelVR,"1","Pixel Data");
 
-            DataEntry *newEntry = new DataEntry(newDict);
+            DataEntry *newEntry = DataEntry::New(newDict);
+            newDict->Delete();
             newEntry->Copy(entry);
             newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
             oldEntry->SetSelfArea(false);
 
             RemoveEntry(oldEntry);
             AddEntry(newEntry);
+            newEntry->Delete();
          }
       }
    }
@@ -466,6 +468,7 @@ float File::GetXSpacing()
    if( entry )
    {
       nbValue = entry->GetValueCount();
+      // Can't use IsValueCountValid because of the complex heuristic.
       if( nbValue >= 3 )
          xspacing = (float)entry->GetValue(2);
       if( nbValue >= 2 )
@@ -479,35 +482,16 @@ float File::GetXSpacing()
    }
    else
    {
-      gdcmWarningMacro( "Unfound Pixel Spacing (0018,1164)" );
+      gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
    }
 
-/*   const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164);
-   if ( strImagerPixelSpacing != GDCM_UNFOUND )
-   {
-      if ( ( nbValues = sscanf( strImagerPixelSpacing.c_str(), 
-            "%f\\%f", &yspacing, &xspacing)) != 2 )
-      {
-         // if no values, xspacing is set to 1.0
-         if ( nbValues == 0 )
-            xspacing = 1.0;
-         // if single value is found, xspacing is defaulted to yspacing
-         if ( nbValues == 1 )
-            xspacing = yspacing;
-
-         if ( xspacing == 0.0 )
-            xspacing = 1.0;
-      }  
-      return xspacing;
-   }*/
-
    entry = GetDataEntry(0x0028,0x0030);
    if( entry )
    {
       nbValue = entry->GetValueCount();
       if( nbValue >= 3 )
          xspacing = (float)entry->GetValue(2);
-      if( nbValue >= 2 )
+      else if( nbValue >= 2 )
          xspacing = (float)entry->GetValue(1);
       else
          xspacing = (float)entry->GetValue(0);
@@ -521,41 +505,6 @@ float File::GetXSpacing()
       gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
    }
 
-/*   const std::string &strSpacing = GetEntryString(0x0028,0x0030);
-   if ( strSpacing == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
-      return 1.;
-   }
-
-   if ( ( nbValues = sscanf( strSpacing.c_str(), 
-         "%f \\%f ", &yspacing, &xspacing)) != 2 )
-   {
-      // if no values, xspacing is set to 1.0
-      if ( nbValues == 0 )
-         xspacing = 1.0;
-      // if single value is found, xspacing is defaulted to yspacing
-      if ( nbValues == 1 )
-         xspacing = yspacing;
-
-      if ( xspacing == 0.0 )
-         xspacing = 1.0;
-   return xspacing;
-
-   }*/
-
-   // to avoid troubles with David Clunie's-like images (at least one)
-/*   if ( xspacing == 0.0 && yspacing == 0.0)
-      return 1.0;
-
-   if ( xspacing == 0.0)
-   {
-      gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem");
-      // seems to be a bug in the header ...
-      nbValues = sscanf( strSpacing.c_str(), "%f \\0\\%f ", &yspacing, &xspacing);
-      gdcmAssertMacro( nbValues == 2 );
-   }
-*/
    return xspacing;
 }
 
@@ -583,20 +532,6 @@ float File::GetYSpacing()
    {
       gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
    }
-/*   const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164);
-   if ( strImagerPixelSpacing != GDCM_UNFOUND )
-   {
-      nbValues = sscanf( strImagerPixelSpacing.c_str(), "%f", &yspacing);
-   
-   // if sscanf cannot read any float value, it won't affect yspacing
-      if ( nbValues == 0 )
-            yspacing = 1.0;
-
-      if ( yspacing == 0.0 )
-            yspacing = 1.0;
-
-      return yspacing;  
-   }*/
 
    entry = GetDataEntry(0x0028,0x0030);
    if( entry )
@@ -611,22 +546,6 @@ float File::GetYSpacing()
    {
       gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
    }
-/*   std::string strSpacing = GetEntryString(0x0028,0x0030);  
-   if ( strSpacing == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
-      return 1.;
-    }
-
-   // if sscanf cannot read any float value, it won't affect yspacing
-   nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
-
-   // if no values, yspacing is set to 1.0
-   if ( nbValues == 0 )
-      yspacing = 1.0;
-
-   if ( yspacing == 0.0 )
-      yspacing = 1.0;*/
 
    return yspacing;
 } 
@@ -688,31 +607,6 @@ float File::GetZSpacing()
       gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
 
    return zspacing;
-
-/*   const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088);
-   if ( strSpacingBSlices == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
-      const std::string &strSliceThickness = GetEntryString(0x0018,0x0050);       
-      if ( strSliceThickness == GDCM_UNFOUND )
-      {
-         gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
-         return 1.0;
-      }
-      else
-      {
-         // if no 'Spacing Between Slices' is found, 
-         // we assume slices join together
-         // (no overlapping, no interslice gap)
-         // if they don't, we're fucked up
-         return (float)atof( strSliceThickness.c_str() );
-      }
-   }
-   
-   float zsp = (float)atof( strSpacingBSlices.c_str());
-   if (zsp == 0.0) // last change not to break further computations ...
-      zsp = 1.0;
-   return zsp;*/
 }
 
 /**
@@ -736,27 +630,14 @@ float File::GetXOrigin()
    }
 
    if( entry->GetValueCount() == 3 )
-      return (float)entry->GetValue(0);
-   return 0.0f;
-
-/*   std::string strImPos = GetEntryString(0x0020,0x0032);
-   if ( strImPos == GDCM_UNFOUND )
    {
-      gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
-      strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
-      if ( strImPos == GDCM_UNFOUND )
+      if (!entry->IsValueCountValid() )
       {
-         gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
-         return 0.0;
+         gdcmErrorMacro( "Invalid Value Count" );
       }
+      return (float)entry->GetValue(0);
    }
-
-   if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
-   {
-      return 0.0;
-   }
-
-   return xImPos;*/
+   return 0.0f;
 }
 
 /**
@@ -780,28 +661,14 @@ float File::GetYOrigin()
    }
 
    if( entry->GetValueCount() == 3 )
-      return (float)entry->GetValue(1);
-   return 0.0f;
-/*   float xImPos, yImPos, zImPos;
-   std::string strImPos = GetEntryString(0x0020,0x0032);
-
-   if ( strImPos == GDCM_UNFOUND)
    {
-      gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
-      strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
-      if ( strImPos == GDCM_UNFOUND )
+      if (!entry->IsValueCountValid() )
       {
-         gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
-         return 0.;
-      }  
-   }
-
-   if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
-   {
-      return 0.;
+         gdcmErrorMacro( "Invalid Value Count" );
+      }
+      return (float)entry->GetValue(1);
    }
-
-   return yImPos;*/
+   return 0.0f;
 }
 
 /**
@@ -818,97 +685,62 @@ float File::GetZOrigin()
    if( entry )
    {
       if( entry->GetValueCount() == 3 )
-         return (float)entry->GetValue(0);
+      {
+         if (!entry->IsValueCountValid() )
+         {
+            gdcmErrorMacro( "Invalid Value Count" );
+         }
+         return (float)entry->GetValue(2);
+      }
       gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
       return 0.0f;
    }
-/*   float xImPos, yImPos, zImPos; 
-   std::string strImPos = GetEntryString(0x0020,0x0032);
-
-   if ( strImPos != GDCM_UNFOUND )
-   {
-      if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3)
-      {
-         gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
-         return 0.;  // bug in the element 0x0020,0x0032
-      }
-      else
-      {
-         return zImPos;
-      }
-   }*/
 
    entry = GetDataEntry(0x0020,0x0030);
    if( entry )
    {
       if( entry->GetValueCount() == 3 )
-         return (float)entry->GetValue(0);
+      {
+         if (!entry->IsValueCountValid() )
+         {
+            gdcmErrorMacro( "Invalid Value Count" );
+         }
+         return (float)entry->GetValue(2);
+      }
       gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
       return 0.0f;
    }
-/*   strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
-   if ( strImPos != GDCM_UNFOUND )
-   {
-      if ( sscanf( strImPos.c_str(), 
-          "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 )
-      {
-         gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
-         return 0.;  // bug in the element 0x0020,0x0032
-      }
-      else
-      {
-         return zImPos;
-      }
-   }*/
 
    // for *very* old ACR-NEMA images
    entry = GetDataEntry(0x0020,0x1041);
    if( entry )
    {
       if( entry->GetValueCount() == 1 )
-         return (float)entry->GetValue(0);
-      gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
-      return 0.0f;
-   }
-/*   std::string strSliceLocation = GetEntryString(0x0020,0x1041);
-   if ( strSliceLocation != GDCM_UNFOUND )
-   {
-      if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1)
-      {
-         gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
-         return 0.;  // bug in the element 0x0020,0x1041
-      }
-      else
       {
-         return zImPos;
+         if (!entry->IsValueCountValid() )
+         {
+            gdcmErrorMacro( "Invalid Value Count" );
+         }
+         return (float)entry->GetValue(0); // VM=1 !
       }
+      gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
+      return 0.0f;
    }
-   gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/
 
    entry = GetDataEntry(0x0020,0x0050);
    if( entry )
    {
-      gdcmWarningMacro( "Unfound Location (0020,0050)");
       if( entry->GetValueCount() == 1 )
+      {
+         if (!entry->IsValueCountValid() )
+         {
+            gdcmErrorMacro( "Invalid Value Count" );
+         }
          return (float)entry->GetValue(0);
+      }
       gdcmWarningMacro( "Wrong Location (0020,0050)");
       return 0.0f;
    }
-/*   std::string strLocation = GetEntryString(0x0020,0x0050);
-   if ( strLocation != GDCM_UNFOUND )
-   {
-      if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 )
-      {
-         gdcmWarningMacro( "Wrong Location (0020,0050)");
-         return 0.;  // bug in the element 0x0020,0x0050
-      }
-      else
-      {
-         return zImPos;
-      }
-   }
-   gdcmWarningMacro( "Unfound Location (0020,0050)");*/
-
    return 0.; // Hopeless
 }
 
@@ -952,8 +784,6 @@ bool File::GetImageOrientationPatient( float iop[6] )
    return true;
 }
 
-
-
 /**
  * \brief   Retrieve the number of Bits Stored (actually used)
  *          (as opposed to number of Bits Allocated)
@@ -969,15 +799,6 @@ int File::GetBitsStored()
       return 0;
    }
    return (int)entry->GetValue(0);
-
-/*   std::string strSize = GetEntryString( 0x0028, 0x0101 );
-   if ( strSize == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
-      return 0;  // It's supposed to be mandatory
-                 // the caller will have to check
-   }
-   return atoi( strSize.c_str() );*/
 }
 
 /**
@@ -995,15 +816,6 @@ int File::GetBitsAllocated()
       return 0;
    }
    return (int)entry->GetValue(0);
-
-/*   std::string strSize = GetEntryString(0x0028,0x0100);
-   if ( strSize == GDCM_UNFOUND  )
-   {
-      gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
-      return 0; // It's supposed to be mandatory
-                // the caller will have to check
-   }
-   return atoi( strSize.c_str() );*/
 }
 
 /**
@@ -1021,14 +833,6 @@ int File::GetHighBitPosition()
       return 0;
    }
    return (int)entry->GetValue(0);
-
-/*   std::string strSize = GetEntryString( 0x0028, 0x0102 );
-   if ( strSize == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
-      return 0;
-   }
-   return atoi( strSize.c_str() );*/
 }
 
 /**
@@ -1047,15 +851,6 @@ int File::GetSamplesPerPixel()
                 // but sometimes it's missing : *we* assume Gray pixels
    }
    return (int)entry->GetValue(0);
-
-/*   const std::string &strSize = GetEntryString(0x0028,0x0002);
-   if ( strSize == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro( "(0028,0002) is supposed to be mandatory");
-      return 1; // Well, it's supposed to be mandatory ...
-                // but sometimes it's missing : *we* assume Gray pixels
-   }
-   return atoi( strSize.c_str() );*/
 }
 
 /**
@@ -1072,14 +867,6 @@ int File::GetPlanarConfiguration()
       return 0;
    }
    return (int)entry->GetValue(0);
-
-/*   std::string strSize = GetEntryString(0x0028,0x0006);
-   if ( strSize == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
-      return 0;
-   }
-   return atoi( strSize.c_str() );*/
 }
 
 /**
@@ -1162,44 +949,6 @@ std::string File::GetPixelType()
    {
       sign = "U";
    }
-
-/*   std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
-   if ( bitsAlloc == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro( "Missing  Bits Allocated (0028,0100)");
-      bitsAlloc = "16"; // default and arbitrary value, not to polute the output
-   }
-
-   if ( bitsAlloc == "64" )
-   {
-      return "FD";
-   }
-   else if ( bitsAlloc == "12" )
-   {
-      // It will be unpacked
-      bitsAlloc = "16";
-   }
-   else if ( bitsAlloc == "24" )
-   {
-      // (in order no to be messed up by old RGB images)
-      bitsAlloc = "8";
-   }
-
-   std::string sign = GetEntryString(0x0028, 0x0103);//"Pixel Representation"
-
-   if (sign == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
-      sign = "U"; // default and arbitrary value, not to polute the output
-   }
-   else if ( sign == "0" )
-   {
-      sign = "U";
-   }
-   else
-   {
-      sign = "S";
-   }*/
    return bitsAlloc + sign;
 }
 
@@ -1220,18 +969,6 @@ bool File::IsSignedPixelData()
       return false;
    }
    return entry->GetValue(0) != 0;
-/*   std::string strSign = GetEntryString( 0x0028, 0x0103 );
-   if ( strSign == GDCM_UNFOUND )
-   {
-      gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
-      return false;
-   }
-   int sign = atoi( strSign.c_str() );
-   if ( sign == 0 ) 
-   {
-      return false;
-   }
-   return true;*/
 }
 
 /**
@@ -1405,19 +1142,6 @@ float File::GetRescaleIntercept()
    }
    return (float)entry->GetValue(0);
 
-/*   float resInter = 0.;
-   /// 0028 1052 DS IMG Rescale Intercept
-   const std::string &strRescInter = GetEntryString(0x0028,0x1052);
-   if ( strRescInter != GDCM_UNFOUND )
-   {
-      if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 )
-      {
-         // bug in the element 0x0028,0x1052
-         gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
-      }
-   }
-
-   return resInter;*/
 }
 
 /**
@@ -1434,19 +1158,6 @@ float File::GetRescaleSlope()
       return 1.0f;
    }
    return (float)entry->GetValue(0);
-/*   float resSlope = 1.;
-   //0028 1053 DS IMG Rescale Slope
-   std::string strRescSlope = GetEntryString(0x0028,0x1053);
-   if ( strRescSlope != GDCM_UNFOUND )
-   {
-      if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 )
-      {
-         // bug in the element 0x0028,0x1053
-         gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
-      }
-   }
-
-   return resSlope;*/
 }
 
 /**
@@ -1763,10 +1474,10 @@ bool File::Write(std::string fileName, FileType writetype)
 
    // Derma?.dcm does not have it...let's remove it  FIXME FIXME
    if( writetype != JPEG )
-     {
+   {
      int i_lgPix = GetEntryLength(GrPixel, NumPixel);
      if (i_lgPix != -2)
-       {
+     {
        // no (GrPixel, NumPixel) element
        std::string s_lgPix = Util::Format("%d", i_lgPix+12);
        s_lgPix = Util::DicomString( s_lgPix.c_str() );
@@ -1966,7 +1677,7 @@ void File::ComputeJPEGFragmentInfo()
 
 /**
  * \brief   Assuming the internal file pointer \ref Document::Fp 
- *          is placed at the beginning of a tag check whether this
+ *          is placed at the beginning of a tag, check whether this
  *          tag is (TestGroup, TestElem).
  * \warning On success the internal file pointer \ref Document::Fp
  *          is modified to point after the tag.
@@ -2001,15 +1712,17 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
       return false;
    }
    if ( itemTagGroup != testGroup || itemTagElem != testElem )
-   {
-      gdcmErrorMacro( "Wrong Item Tag found:"
-       << "   We should have found tag ("
-       << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
-       << "   but instead we encountered tag ("
-       << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
-       << "  at address: " << "  0x(" << std::hex 
-       << (unsigned int)currentPosition  << std::dec << ")" 
-       ) ;
+   { 
+       // in order not to pollute output we don't warn on 'delimitors'
+      if (itemTagGroup != 0xfffe ||  testGroup != 0xfffe )
+         gdcmErrorMacro( "Wrong Item Tag found:"
+          << "   We should have found tag ("
+          << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
+          << "   but instead we encountered tag ("
+          << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
+          << "  at address: " << "  0x(" << std::hex 
+          << (unsigned int)currentPosition  << std::dec << ")" 
+          ) ;
       Fp->seekg(positionOnEntry, std::ios::beg);
 
       return false;
@@ -2036,7 +1749,9 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
 
    if ( !ReadTag(testGroup, testElem) )
    {
-      gdcmErrorMacro( "ReadTag did not succeed for ("
+      // Avoid polutting output
+      if ( testGroup != 0xfffe ) 
+         gdcmErrorMacro( "ReadTag did not succeed for ("
                     << DictEntry::TranslateToKey(testGroup,testElem) 
                     << ")..." );
       return 0;
@@ -2093,27 +1808,12 @@ void File::ReadEncapsulatedBasicOffsetTable()
 // These are the deprecated method that one day should be removed (after the next release)
 
 #ifndef GDCM_LEGACY_REMOVE
-/**
- * \brief  Constructor (DEPRECATED : temporaryly kept not to break the API)
- * @param  filename name of the file whose header we want to analyze
- * @deprecated do not use any longer
- */
-File::File( std::string const &filename )
-     :Document( )
-{    
-   RLEInfo  = new RLEFramesInfo;
-   JPEGInfo = new JPEGFragmentsInfo;
-
-   SetFileName( filename );
-   Load( ); // gdcm::Document is first Loaded, then the 'File part'
-}
-
-/**
- * \brief   Loader. (DEPRECATED :  temporaryly kept not to break the API)
- * @param   fileName file to be open for parsing
- * @return false if file cannot be open or no swap info was found,
+/*
+ * \ brief   Loader. (DEPRECATED :  temporaryly kept not to break the API)
+ * @ param   fileName file to be open for parsing
+ * @ return false if file cannot be open or no swap info was found,
  *         or no tag was found.
- * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
+ * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
  */
 bool File::Load( std::string const &fileName ) 
 {