Comments

[gdcm.git] / src / gdcmFile.cxx

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index 2cc7443f9acffc925463e4c90bd9b2c525df6a99..25831770ad62730f51fdce21eb33cbe0bb920647 100644 (file)
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmFile.cxx,v $
   Language:  C++
-  Date:      $Date: 2007/08/22 16:14:04 $
-  Version:   $Revision: 1.334 $
+  Date:      $Date: 2009/05/19 15:08:36 $
+  Version:   $Revision: 1.344 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -491,7 +491,7 @@ bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing)
         }
       else
         {
-        if( mediastoragesopclassuid == sopclassuid )
+        if ( mediastoragesopclassuid == sopclassuid )
           {
           sopclassuid_used = mediastoragesopclassuid;
           }
@@ -502,7 +502,7 @@ bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing)
           return false;
           }
         }
-      // ok we have now the correc SOP Class UID
+      // ok we have now the correct SOP Class UID
       if( sopclassuid_used == "Enhanced MR Image Storage" )
         {
         SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230);
@@ -568,8 +568,6 @@ int File::GetTSize()
    }      
 }
 
-
-
 /**
   * \brief gets the info from 0018,1164 : ImagerPixelSpacing
   *                      then 0028,0030 : Pixel Spacing
@@ -1455,6 +1453,13 @@ bool File::IsPaletteColor()
    {
       return true;
    }
+   
+   // MONOCHROME + [Enhanced CT Image Storage] actually have Palettes
+   std::string sopClassUid = GetEntryString( 0x0008, 0x0016 );
+   if (Util::DicomStringEqual( sopClassUid, "1.2.840.10008.5.1.4.1.1.2.1"))
+   {
+      return true;
+   }   
    if ( PhotometricInterp == GDCM_UNFOUND )
    {
       gdcmDebugMacro( "Not found : Palette color (0028,0004)");
@@ -1469,7 +1474,7 @@ bool File::IsPaletteColor()
  */
 bool File::IsYBRFull()
 {
-   std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
+   std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );   
    if (   PhotometricInterp == "YBR_FULL" )
    {
       return true;
@@ -1508,7 +1513,13 @@ bool File::HasLUT()
       return false;
    }
    // Red Palette Color Lookup Table Data
-   if ( !GetDocEntry(0x0028,0x1201) )
+   bool segmented;
+   segmented = GetDocEntry(0x0028,0x1221) && 
+     GetDocEntry(0x0028,0x1222) && 
+     GetDocEntry(0x0028,0x1223);
+   if( segmented ) return true;
+
+   if( !GetDocEntry(0x0028,0x1201) )
    {
       return false;
    }
@@ -1902,12 +1913,13 @@ bool File::AnonymizeFile()
             gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
             continue;
          }
-
+/*
          if ( dynamic_cast<DataEntry *>(d) )
          {
             gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
             continue;
          }
+*/
          else
             SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
       }
@@ -1978,6 +1990,7 @@ bool File::AnonymizeFile()
  */
 bool File::Write(std::string fileName, FileType writetype)
 {
+      gdcmDebugMacro(" File::Write ");
    std::ofstream *fp = new std::ofstream(fileName.c_str(), 
                                          std::ios::out | std::ios::binary);
    if (*fp == NULL)
@@ -1996,10 +2009,10 @@ bool File::Write(std::string fileName, FileType writetype)
    }
 
    /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
-   if( writetype != JPEG )
+   if( writetype != JPEG && writetype != JPEG2000)
    {
       int i_lgPix = GetEntryLength(GrPixel, NumPixel);
-      if (i_lgPix != -2)
+      if (i_lgPix != -2)  /// \todo wtf "-2" ?!?
       {
          // no (GrPixel, NumPixel) element
          std::string s_lgPix = Util::Format("%d", i_lgPix+12);
@@ -2007,7 +2020,7 @@ bool File::Write(std::string fileName, FileType writetype)
          InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL");
       }
    }
-   Document::WriteContent(fp, writetype);
+   Document::WriteContent(fp, writetype,false,false);
 
    fp->close();
    delete fp;
@@ -2023,7 +2036,7 @@ bool File::Write(std::string fileName, FileType writetype)
 // Private
 /**
  * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
- *        Compute the RLE extra information and store it in \ref RLEInfo
+ *        Compute the RLE extra information and store it in RLEInfo
  *        for later pixel retrieval usage.
  */
 void File::ComputeRLEInfo()
@@ -2135,7 +2148,7 @@ void File::ComputeRLEInfo()
 /**
  * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
  *        Compute the jpeg extra information (fragment[s] offset[s] and
- *        length) and store it[them] in \ref JPEGInfo for later pixel
+ *        length) and store it[them] in JPEGInfo for later pixel
  *        retrieval usage.
  */
 void File::ComputeJPEGFragmentInfo()
@@ -2198,14 +2211,14 @@ void File::ComputeJPEGFragmentInfo()
 }
 
 /**
- * \brief   Assuming the internal file pointer \ref Document::Fp 
+ * \brief   Assuming the internal file pointer Document::Fp 
  *          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
+ * \warning On success the internal file pointer Document::Fp
  *          is modified to point after the tag.
  *          On failure (i.e. when the tag wasn't the expected tag
  *          (TestGroup, TestElem) the internal file pointer
- *          \ref Document::Fp is restored to its original position.
+ *          Document::Fp is restored to its original position.
  * @param   testGroup The expected group   of the tag.
  * @param   testElem  The expected Element of the tag.
  * @return  True on success, false otherwise.
@@ -2226,8 +2239,9 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
    }
    catch ( FormatError )
    {
-      gdcmErrorMacro( "Can not read tag for "
-       << "   We should have found tag ("
+      gdcmErrorMacro( "Can not read tag at 0x(" 
+       << std::hex << positionOnEntry
+       << ").  We should have found tag ("
        << DictEntry::TranslateToKey(testGroup,testElem) << ")"
        ) ;
 
@@ -2253,14 +2267,14 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
 }
 
 /**
- * \brief   Assuming the internal file pointer \ref Document::Fp 
+ * \brief   Assuming the internal file pointer Document::Fp 
  *          is placed at the beginning of a tag (TestGroup, TestElement),
  *          read the length associated to the Tag.
- * \warning On success the internal file pointer \ref Document::Fp
+ * \warning On success the internal file pointer Document::Fp
  *          is modified to point after the tag and its length.
  *          On failure (i.e. when the tag wasn't the expected tag
  *          (TestGroup, TestElement) the internal file pointer
- *          \ref Document::Fp is restored to its original position.
+ *          Document::Fp is restored to its original position.
  * @param   testGroup The expected Group   of the tag.
  * @param   testElem  The expected Element of the tag.
  * @return  On success returns the length associated to the tag. On failure