/*=========================================================================
-
+
Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2005/06/14 13:56:41 $
- Version: $Revision: 1.65 $
+ Date: $Date: 2005/09/07 14:12:23 $
+ Version: $Revision: 1.77 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
LutRedData = 0;
LutGreenData = 0;
LutBlueData = 0;
+ RLEInfo = 0;
+ JPEGInfo = 0;
+ UserFunction = 0;
+ FileInternal = 0;
}
/// Canonical Destructor
YSize = file->GetYSize();
ZSize = file->GetZSize();
SamplesPerPixel = file->GetSamplesPerPixel();
- PixelSize = file->GetPixelSize();
+ //PixelSize = file->GetPixelSize(); Useless
PixelSign = file->IsSignedPixelData();
SwapCode = file->GetSwapCode();
std::string ts = file->GetTransferSyntax();
LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 );
if ( ! LutRedData )
{
- gdcmWarningMacro( "Unable to read Red LUT data" );
+ gdcmWarningMacro( "Unable to read Red Palette Color Lookup Table data" );
}
// //// Green round:
LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
if ( ! LutGreenData)
{
- gdcmWarningMacro( "Unable to read Green LUT data" );
+ gdcmWarningMacro( "Unable to read Green Palette Color Lookup Table data" );
}
// //// Blue round:
LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
if ( ! LutBlueData )
{
- gdcmWarningMacro( "Unable to read Blue LUT data" );
+ gdcmWarningMacro( "Unable to read Blue Palette Color Lookup Table data" );
}
}
+ FileInternal = file;
ComputeRawAndRGBSizes();
}
}
fp->seekg( PixelOffset, std::ios::beg );
- if( fp->fail() || fp->eof())
+ if ( fp->fail() || fp->eof() )
{
gdcmWarningMacro( "Unable to find PixelOffset in file." );
return false;
AllocateRaw();
//////////////////////////////////////////////////
- //// Second stage: read from disk dans decompress.
+ //// Second stage: read from disk and decompress.
if ( BitsAllocated == 12 )
{
ReadAndDecompress12BitsTo16Bits( fp);
// after the field containing the image data. In this case, these
// bad data are added to the size of the image (in the PixelDataLength
// variable). But RawSize is the right size of the image !
- if( PixelDataLength != RawSize)
+ if ( PixelDataLength != RawSize )
{
gdcmWarningMacro( "Mismatch between PixelReadConvert : "
<< PixelDataLength << " and RawSize : " << RawSize );
}
- if( PixelDataLength > RawSize)
+ if ( PixelDataLength > RawSize )
{
fp->read( (char*)Raw, RawSize);
}
{
//gdcmWarningMacro( "Sorry, MPEG not yet taken into account" );
//return false;
-// ReadMPEGFile(fp, Raw, PixelDataLength); // fp has already been seek to start of mpeg
+ // fp has already been seek to start of mpeg
+ //ReadMPEGFile(fp, Raw, PixelDataLength);
return true;
}
else
ConvertReorderEndianity();
ConvertReArrangeBits();
ConvertFixGreyLevels();
+ if (UserFunction) // user is allowed to Mirror, TopDown, Rotate,...the image
+ UserFunction( Raw, FileInternal);
ConvertHandleColor();
return true;
// The job can't be done
return false;
}
+
+ gdcmWarningMacro( "--> BuildRGBImage" );
// Build RGB Pixels
AllocateRGB();
int j;
- if( BitsAllocated <= 8)
+ if ( BitsAllocated <= 8 )
{
uint8_t *localRGB = RGB;
for (size_t i = 0; i < RawSize; ++i )
{
if ( IsJPEG2000 )
{
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEGLS );
// FIXME this is really ugly but it seems I have to load the complete
// jpeg2000 stream to use jasper:
- // I don't think we'll ever be able to deal with multiple fragments properly
+ // I don't think we'll ever be able to deal with multiple fragments properly
unsigned long inputlength = 0;
JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
{
return true;
}
+ // wow what happen, must be an error
+ return false;
}
-
- if ( IsJPEGLS )
+ else if ( IsJPEGLS )
{
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEG2000 );
// WARNING : JPEG-LS is NOT the 'classical' Jpeg Lossless :
// [JPEG-LS is the basis for new lossless/near-lossless compression
// standard for continuous-tone images intended for JPEG2000. The standard
//
// see http://datacompression.info/JPEGLS.shtml
//
+#if 0
+ std::cerr << "count:" << JPEGInfo->GetFragmentCount() << std::endl;
+ unsigned long inputlength = 0;
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ inputlength += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ gdcmAssertMacro( inputlength != 0);
+ uint8_t *inputdata = new uint8_t[inputlength];
+ char *pinputdata = (char*)inputdata;
+ jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
+ fp->read(pinputdata, jpegfrag->GetLength());
+ pinputdata += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+
+ //fp->read((char*)Raw, PixelDataLength);
+
+ std::ofstream out("/tmp/jpegls.jpg");
+ out.write((char*)inputdata, inputlength);
+ out.close();
+ delete[] inputdata;
+#endif
gdcmWarningMacro( "Sorry, JPEG-LS not yet taken into account" );
fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg);
return false;
}
else
- {
+ {
+ // 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 numberBytes = BitsAllocated / 8;
JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length );
return true;
- }
+ }
}
/**
nbRead = sscanf( LutRedDescriptor.c_str(),
"%d\\%d\\%d",
&lengthR, &debR, &nbitsR );
- if( nbRead != 3 )
+ if ( nbRead != 3 )
{
gdcmWarningMacro( "Wrong Red LUT descriptor" );
}
nbRead = sscanf( LutGreenDescriptor.c_str(),
"%d\\%d\\%d",
&lengthG, &debG, &nbitsG );
- if( nbRead != 3 )
+ if ( nbRead != 3 )
{
gdcmWarningMacro( "Wrong Green LUT descriptor" );
}
nbRead = sscanf( LutRedDescriptor.c_str(),
"%d\\%d\\%d",
&lengthB, &debB, &nbitsB );
- if( nbRead != 3 )
+ if ( nbRead != 3 )
{
gdcmWarningMacro( "Wrong Blue LUT descriptor" );
}
if ( !lengthR ) // if = 2^16, this shall be 0 see : CP-143
lengthR=65536;
- if( !lengthG ) // if = 2^16, this shall be 0
+ if ( !lengthG ) // if = 2^16, this shall be 0
lengthG=65536;
if ( !lengthB ) // if = 2^16, this shall be 0
lengthB=65536;
// -------------------------------------------------------------
- if ( BitsAllocated <= 8)
+ if ( BitsAllocated <= 8 )
{
// forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
if ( !LutRGBA )
return;
-
+ LutItemNumber = 256;
+ LutItemSize = 8;
memset( LutRGBA, 0, 1024 );
int mult;
//take "Subscript of the first Lut Value" (debR,debG,debB) into account!
+ //FIXME : +1 : to get 'low value' byte
+ // Trouble expected on Big Endian Processors ?
+ // 16 BIts Per Pixel Palette Color to be swapped?
+
a = LutRGBA + 0 + debR;
for( i=0; i < lengthR; ++i )
{
- *a = LutRedData[i*mult+1];
+ *a = LutRedData[i*mult+1];
a += 4;
}
*a = LutBlueData[i*mult+1];
a += 4;
}
-
+
a = LutRGBA + 3 ;
for(i=0; i < 256; ++i)
{
return;
memset( LutRGBA, 0, 65536*4*2 ); // 16 bits = 2 bytes ;-)
+ LutItemNumber = 65536;
+ LutItemSize = 16;
+
int i;
uint16_t *a16;
a16 = (uint16_t*)LutRGBA + 0 + debR;
for( i=0; i < lengthR; ++i )
{
- *a16 = ((uint16_t*)LutRedData)[i+1];
+ *a16 = ((uint16_t*)LutRedData)[i];
a16 += 4;
}
a16 = (uint16_t*)LutRGBA + 1 + debG;
for( i=0; i < lengthG; ++i)
{
- *a16 = ((uint16_t*)LutGreenData)[i+1];
+ *a16 = ((uint16_t*)LutGreenData)[i];
a16 += 4;
}
a16 = (uint16_t*)LutRGBA + 2 + debB;
for(i=0; i < lengthB; ++i)
{
- *a16 = ((uint16_t*)LutBlueData)[i+1];
+ *a16 = ((uint16_t*)LutBlueData)[i];
a16 += 4;
}
*a16 = 1; // Alpha component
a16 += 4;
}
-/*
+/* Just to 'see' the LUT, at debug time
+
a16=(uint16_t*)LutRGBA;
for (int j=0;j<65536;j++)
{
{
unsigned int i;
- if( BitsAllocated == 16 )
+ if ( BitsAllocated == 16 )
{
uint16_t *im16 = (uint16_t*)Raw;
switch( SwapCode )
gdcmWarningMacro("SwapCode value (16 bits) not allowed.");
}
}
- else if( BitsAllocated == 32 )
+ else if ( BitsAllocated == 32 )
{
uint32_t s32;
uint16_t high;
uint16_t *deb = (uint16_t *)Raw;
for(int i = 0; i<l; i++)
{
- if( *deb == 0xffff )
+ if ( *deb == 0xffff )
{
*deb = 0;
}
*/
bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
{
+
if ( BitsStored != BitsAllocated )
{
int l = (int)( RawSize / ( BitsAllocated / 8 ) );
if ( BitsAllocated == 16 )
{
- uint16_t mask = 0xffff;
- mask = mask >> ( BitsAllocated - BitsStored );
+ // pmask : to mask the 'unused bits' (may contain overlays)
+ uint16_t pmask = 0xffff;
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+
uint16_t *deb = (uint16_t*)Raw;
- for(int i = 0; i<l; i++)
+
+ if ( !PixelSign ) // Pixels are unsigned
{
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
- deb++;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
+ deb++;
+ }
+ }
+ else // Pixels are signed
+ {
+ // smask : to check the 'sign' when BitsStored != BitsAllocated
+ uint16_t smask = 0x0001;
+ smask = smask << ( 16 - (BitsAllocated - BitsStored + 1) );
+ // nmask : to propagate sign bit on negative values
+ int16_t nmask = (int16_t)0x8000;
+ nmask = nmask >> ( BitsAllocated - BitsStored - 1 );
+
+ for(int i = 0; i<l; i++)
+ {
+ *deb = *deb >> (BitsStored - HighBitPosition - 1);
+ if ( *deb & smask )
+ {
+ *deb = *deb | nmask;
+ }
+ else
+ {
+ *deb = *deb & pmask;
+ }
+ deb++;
+ }
}
}
else if ( BitsAllocated == 32 )
{
- uint32_t mask = 0xffffffff;
- mask = mask >> ( BitsAllocated - BitsStored );
+ // pmask : to mask the 'unused bits' (may contain overlays)
+ uint32_t pmask = 0xffffffff;
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+
uint32_t *deb = (uint32_t*)Raw;
- for(int i = 0; i<l; i++)
+
+ if ( !PixelSign )
{
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
- deb++;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
+ deb++;
+ }
+ }
+ else
+ {
+ // smask : to check the 'sign' when BitsStored != BitsAllocated
+ uint32_t smask = 0x00000001;
+ smask = smask >> ( 32 - (BitsAllocated - BitsStored +1 ));
+ // nmask : to propagate sign bit on negative values
+ int32_t nmask = 0x80000000;
+ nmask = nmask >> ( BitsAllocated - BitsStored -1 );
+
+ for(int i = 0; i<l; i++)
+ {
+ *deb = *deb >> (BitsStored - HighBitPosition - 1);
+ if ( *deb & smask )
+ *deb = *deb | nmask;
+ else
+ *deb = *deb & pmask;
+ deb++;
+ }
}
}
else
{
- gdcmWarningMacro("Weird image");
+ gdcmWarningMacro("Weird image (BitsAllocated !=8, 12, 16, 32)");
throw FormatError( "Weird image !?" );
}
}
*/
void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
{
+ gdcmWarningMacro("--> ConvertRGBPlanesToRGBPixels");
+
uint8_t *localRaw = Raw;
uint8_t *copyRaw = new uint8_t[ RawSize ];
memmove( copyRaw, localRaw, RawSize );
*/
void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
{
+ // Remarks for YBR newbees :
+ // YBR_FULL works very much like RGB, i.e. three samples per pixel,
+ // just the color space is YCbCr instead of RGB. This is particularly useful
+ // for doppler ultrasound where most of the image is grayscale
+ // (i.e. only populates the Y components) and Cb and Cr are mostly zero,
+ // except for the few patches of color on the image.
+ // On such images, RLE achieves a compression ratio that is much better
+ // than the compression ratio on an equivalent RGB image.
+
+ gdcmWarningMacro("--> ConvertYcBcRPlanesToRGBPixels");
+
uint8_t *localRaw = Raw;
uint8_t *copyRaw = new uint8_t[ RawSize ];
memmove( copyRaw, localRaw, RawSize );
// - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
// - [Planar 2] OR [Photo D] requires LUT intervention.
+ gdcmWarningMacro("--> ConvertHandleColor"
+ << "Planar Configuration " << PlanarConfiguration );
+
if ( ! IsRawRGB() )
{
// [Planar 2] OR [Photo D]: LUT intervention done outside
+ gdcmWarningMacro("--> RawRGB : LUT intervention done outside");
return;
}
if ( IsYBRFull )
{
// [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ gdcmWarningMacro("--> YBRFull");
ConvertYcBcRPlanesToRGBPixels();
}
else
{
// [Planar 1] AND [Photo C]
+ gdcmWarningMacro("--> YBRFull");
ConvertRGBPlanesToRGBPixels();
}
return;
}
// When planarConf is 0, and RLELossless (forbidden by Dicom norm)
- // pixels need to be RGB-fied anyway
+ // pixels need to be RGB-fyied anyway
+
if (IsRLELossless)
- {
+ {
+ gdcmWarningMacro("--> RLE Lossless");
ConvertRGBPlanesToRGBPixels();
}
+
// In *normal *case, when planarConf is 0, pixels are already in RGB
}
//-----------------------------------------------------------------------------
} // end namespace gdcm
-
-// NOTES on File internal calls
-// User
-// ---> GetImageData
-// ---> GetImageDataIntoVector
-// |---> GetImageDataIntoVectorRaw
-// | lut intervention
-// User
-// ---> GetImageDataRaw
-// ---> GetImageDataIntoVectorRaw
-
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff