Jpeg writter is no longer confused by DataElements 7fe0|0010 inside a Sequence

[gdcm.git] / src / gdcmPixelReadConvert.cxx

diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx
index f5003106e96b8fda96cd9c278df919c0f6928059..ee0eb6cff9a46c2b42bd60fedb78dff3bb8315ed 100644 (file)
--- a/src/gdcmPixelReadConvert.cxx
+++ b/src/gdcmPixelReadConvert.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmPixelReadConvert.cxx,v $
   Language:  C++
-  Date:      $Date: 2006/01/27 10:01:34 $
-  Version:   $Revision: 1.109 $
+  Date:      $Date: 2007/08/29 08:10:14 $
+  Version:   $Revision: 1.117 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -32,7 +32,7 @@
    #include <mem.h> // for memset
 #endif 
 
-namespace gdcm
+namespace GDCM_NAME_SPACE
 {
 
 //bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght); 
@@ -85,8 +85,9 @@ bool PixelReadConvert::IsRawRGB()
 /**
  * \brief Gets various usefull informations from the file header
  * @param file gdcm::File pointer
+ * @param fileHelper gdcm::FileHelper pointer 
  */
-void PixelReadConvert::GrabInformationsFromFile( File *file, 
+void PixelReadConvert::GrabInformationsFromFile( File *file,
                                                  FileHelper *fileHelper )
 {
    // Number of Bits Allocated for storing a Pixel is defaulted to 16
@@ -97,6 +98,10 @@ void PixelReadConvert::GrabInformationsFromFile( File *file,
       BitsAllocated = 16;
    }
 
+   else if (BitsAllocated > 8 && BitsAllocated < 16 && BitsAllocated != 12)
+   {
+      BitsAllocated = 16;
+   }   
    // Number of "Bits Stored", defaulted to number of "Bits Allocated"
    // when absent from the file.
    BitsStored = file->GetBitsStored();
@@ -115,16 +120,17 @@ void PixelReadConvert::GrabInformationsFromFile( File *file,
    XSize           = file->GetXSize();
    YSize           = file->GetYSize();
    ZSize           = file->GetZSize();
+   TSize           = file->GetTSize();   
    SamplesPerPixel = file->GetSamplesPerPixel();
    //PixelSize       = file->GetPixelSize();  Useless
    PixelSign       = file->IsSignedPixelData();
    SwapCode        = file->GetSwapCode();
- 
+
    IsPrivateGETransferSyntax = IsMPEG
              = IsJPEG2000 = IsJPEGLS = IsJPEGLossy  
              = IsJPEGLossless = IsRLELossless 
              = false;
-     
+
    if (! file->IsDicomV3() )  // Should be ACR-NEMA file
    {
       IsRaw = true;
@@ -164,7 +170,7 @@ void PixelReadConvert::GrabInformationsFromFile( File *file,
             if( IsJPEG2000      = Global::GetTS()->IsJPEG2000(ts) )     break;
             if( IsMPEG          = Global::GetTS()->IsMPEG(ts) )         break;
             if( IsJPEGLS        = Global::GetTS()->IsJPEGLS(ts) )       break;
-            // DeflatedExplicitVRLittleEndian is considered as 'Unexpected' (we don't know yet haow to process !)
+            // DeflatedExplicitVRLittleEndian is considered as 'Unexpected' (we don't know yet how to process !)
             gdcmWarningMacro("Unexpected Transfer Syntax :[" << ts << "]");
             break;
          } 
@@ -270,7 +276,8 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
    unsigned int count = 0;
    unsigned int frameSize;
    unsigned int bitsAllocated = BitsAllocated;
-   if(bitsAllocated == 12)
+   //if(bitsAllocated == 12)
+   if(bitsAllocated > 8 && bitsAllocated < 16)
       bitsAllocated = 16;
    frameSize = XSize*YSize*SamplesPerPixel*bitsAllocated/8;
    
@@ -289,7 +296,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
       if ( PixelDataLength != RawSize )
       {
          gdcmWarningMacro( "Mismatch between PixelReadConvert : "
-                              << PixelDataLength << " and RawSize : " << RawSize );
+                            << PixelDataLength << " and RawSize : " << RawSize );
       }
       
       //todo : is it the right patch?
@@ -317,15 +324,6 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
       if (remainingLength !=0 )
         fp->read( raw, remainingLength);
                  
-      //if ( PixelDataLength > RawSize )
-      //{
-      //   fp->read( (char*)Raw, RawSize); // Read all the frames with a single fread    
-      //}
-      //else
-      //{
-      //   fp->read( (char*)Raw, PixelDataLength); // Read all the frames with a single fread
-      //}
-
       if ( fp->fail() || fp->eof())
       {
          gdcmWarningMacro( "Reading of Raw pixel data failed." );
@@ -335,7 +333,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
    else if ( IsRLELossless )
    {
       if ( ! RLEInfo->DecompressRLEFile
-                               ( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) )
+                               ( fp, Raw, XSize, YSize, ZSize, TSize, BitsAllocated ) )
       {
          gdcmWarningMacro( "RLE decompressor failed." );
          return false;
@@ -457,7 +455,8 @@ bool PixelReadConvert::BuildRGBImage()
 void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp )
                throw ( FormatError )
 {
-   int nbPixels = XSize * YSize;
+   /// \todo Fix the 3D, 4D pb
+   int nbPixels = XSize * YSize * TSize;
    uint16_t *localDecompres = (uint16_t*)Raw;
 
    for( int p = 0; p < nbPixels; p += 2 )
@@ -593,9 +592,9 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp )
      // make sure this is the right JPEG compression
      assert( !IsJPEGLS || !IsJPEG2000 );
      // Precompute the offset localRaw will be shifted with
-     int length = XSize * YSize * SamplesPerPixel;
+     int length = XSize * YSize * ZSize * SamplesPerPixel;
      int numberBytes = BitsAllocated / 8;
-
+     
      JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length );
      return true;
    }
@@ -607,7 +606,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp )
  *         and
  *         - (0028,1101),(0028,1102),(0028,1102)
  *            xxx Palette Color Lookup Table Descriptor are found
- *          and 
+ *          and
  *         - (0028,1201),(0028,1202),(0028,1202)
  *           xxx Palette Color Lookup Table Data - are found
  * \warning does NOT deal with :
@@ -844,7 +843,7 @@ void PixelReadConvert::BuildLUTRGBA()
 void PixelReadConvert::ConvertSwapZone()
 {
    unsigned int i;
-   
+
    // If this file is 'ImplicitVR BigEndian PrivateGE Transfer Syntax', 
    // then the header is in little endian format and the pixel data is in 
    // big endian format.  When reading the header, GDCM has already established
@@ -1200,7 +1199,9 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
    // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
    // and be *very* affraid
    //
-   int l        = XSize * YSize;
+   
+   /// \todo : find an example to see how 3rd dim and 4th dim work together
+   int l        = XSize * YSize * TSize;
    int nbFrames = ZSize;
 
    uint8_t *a = copyRaw + 0;
@@ -1340,7 +1341,7 @@ void PixelReadConvert::ComputeRawAndRGBSizes()
       bitsAllocated = 16;
    }
                                                                                 
-   RawSize =  XSize * YSize * ZSize
+   RawSize =  XSize * YSize * ZSize * TSize
                      * ( bitsAllocated / 8 )
                      * SamplesPerPixel;
    if ( HasLUT )
@@ -1350,7 +1351,10 @@ void PixelReadConvert::ComputeRawAndRGBSizes()
    else
    {
       RGBSize = RawSize;
+      
    }
+   RawSize += RawSize%2;
+   RGBSize += RGBSize%2;
 }
 
 /// Allocates room for RGB Pixels