Program: gdcm
Module: $RCSfile: gdcmPixelConvert.cxx,v $
Language: C++
- Date: $Date: 2004/10/12 04:35:47 $
- Version: $Revision: 1.8 $
+ Date: $Date: 2004/10/14 22:35:02 $
+ Version: $Revision: 1.13 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
-////////////////// TEMPORARY NOT
+////////////////// TEMPORARY NOTE
// look for "fixMem" and convert that to a member of this class
// Removing the prefix fixMem and dealing with allocations should do the trick
//
// grep PIXELCONVERT everywhere and clean up !
+
#include "gdcmDebug.h"
#include "gdcmPixelConvert.h"
-// External JPEG decompression
-
-// for JPEGLosslessDecodeImage
-#include "jpeg/ljpg/jpegless.h"
-
-
-namespace gdcm
+namespace gdcm
{
-
+
#define str2num(str, typeNum) *((typeNum *)(str))
// For JPEG 2000, body in file gdcmJpeg2000.cxx
bool gdcm_read_JPEG2000_file (FILE* fp, void* image_buffer);
// For JPEG 8 Bits, body in file gdcmJpeg8.cxx
-bool gdcm_read_JPEG_file (FILE* fp, void* image_buffer);
+bool gdcm_read_JPEG_file8 (FILE* fp, void* image_buffer);
// For JPEG 12 Bits, body in file gdcmJpeg12.cxx
bool gdcm_read_JPEG_file12 (FILE* fp, void* image_buffer);
+// For JPEG 16 Bits, body in file gdcmJpeg16.cxx
+// Beware this is misleading there is no 16bits DCT algorithm, only
+// jpeg lossless compression exist in 16bits.
+bool gdcm_read_JPEG_file16 (FILE* fp, void* image_buffer);
//-----------------------------------------------------------------------------
{
RGB = 0;
RGBSize = 0;
- Uncompressed = 0;
- UncompressedSize = 0;
+ Decompressed = 0;
+ DecompressedSize = 0;
}
void PixelConvert::Squeeze()
if ( RGB ) {
delete [] RGB;
}
- if ( Uncompressed ) {
- delete [] Uncompressed;
+ if ( Decompressed ) {
+ delete [] Decompressed;
}
}
RGB = new uint8_t[RGBSize];
}
-void PixelConvert::AllocateUncompressed()
+void PixelConvert::AllocateDecompressed()
{
- if ( Uncompressed ) {
- delete [] Uncompressed;
+ if ( Decompressed ) {
+ delete [] Decompressed;
}
- Uncompressed = new uint8_t[ UncompressedSize ];
+ Decompressed = new uint8_t[ DecompressedSize ];
}
/**
* \brief Read from file a 12 bits per pixel image and uncompress it
* into a 16 bits per pixel image.
*/
-void PixelConvert::ConvertDecompress12BitsTo16Bits(
+void PixelConvert::ReadAndDecompress12BitsTo16Bits(
uint8_t* pixelZone,
- int sizeX,
- int sizeY,
FILE* filePtr)
throw ( FormatError )
{
- int nbPixels = sizeX * sizeY;
+ int nbPixels = XSize * YSize;
uint16_t* destination = (uint16_t*)pixelZone;
for( int p = 0; p < nbPixels; p += 2 )
ItemRead = fread( &b0, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- throw FormatError( "File::ConvertDecompress12BitsTo16Bits()",
- "Unfound first block" );
+ throw FormatError( "File::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound first block" );
}
ItemRead = fread( &b1, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- throw FormatError( "File::ConvertDecompress12BitsTo16Bits()",
- "Unfound second block" );
+ throw FormatError( "File::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
}
ItemRead = fread( &b2, 1, 1, filePtr);
if ( ItemRead != 1 )
{
- throw FormatError( "File::ConvertDecompress12BitsTo16Bits()",
- "Unfound second block" );
+ throw FormatError( "File::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
}
// Two steps are necessary to please VC++
* @return Boolean
*/
bool PixelConvert::UncompressRLE16BitsFromRLE8Bits(
- int XSize,
- int YSize,
int NumberOfFrames,
uint8_t* fixMemUncompressed )
{
* at which the pixel data should be copied
* @return Boolean
*/
-bool PixelConvert::ReadAndDecompressRLEFile( void* image_buffer,
- int XSize,
- int YSize,
- int ZSize,
- int BitsAllocated,
- RLEFramesInfo* RLEInfo,
- FILE* fp )
+bool PixelConvert::ReadAndDecompressRLEFile(
+ void* image_buffer,
+ FILE* fp )
{
uint8_t* im = (uint8_t*)image_buffer;
long uncompressedSegmentSize = XSize * YSize;
-
-
+
// Loop on the frame[s]
for( RLEFramesInfo::RLEFrameList::iterator
it = RLEInfo->Frames.begin();
++it )
{
// Loop on the fragments
- for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ )
+ for( int k = 1; k <= (*it)->NumberFragments; k++ )
{
fseek( fp, (*it)->Offset[k] ,SEEK_SET );
(void)PixelConvert::ReadAndUncompressRLEFragment(
if ( BitsAllocated == 16 )
{
// Try to deal with RLE 16 Bits
- (void)PixelConvert::UncompressRLE16BitsFromRLE8Bits(
- XSize,
- YSize,
- ZSize,
+ (void)UncompressRLE16BitsFromRLE8Bits( ZSize,
(uint8_t*) image_buffer);
}
* \brief Swap the bytes, according to swap code.
* \warning not end user intended
* @param im area to deal with
- * @param swap swap code
- * @param lgr Area Length
- * @param nb Pixels Bit number
*/
-void PixelConvert::SwapZone(void* im, int swap, int lgr, int nb)
+void PixelConvert::SwapZone( uint8_t* im )
{
- int i;
+ unsigned int i;
- if( nb == 16 )
+ if( BitsAllocated == 16 )
{
uint16_t* im16 = (uint16_t*)im;
- switch( swap )
+ switch( SwapCode )
{
case 0:
case 12:
case 3412:
case 2143:
case 4321:
- for(i=0; i < lgr/2; i++)
+ for( i = 0; i < DecompressedSize / 2; i++ )
{
im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
}
break;
default:
- std::cout << "SWAP value (16 bits) not allowed :i" << swap <<
- std::endl;
+ dbg.Verbose( 0, "PixelConvert::SwapZone: SwapCode value "
+ "(16 bits) not allowed." );
}
}
- else if( nb == 32 )
+ else if( BitsAllocated == 32 )
{
uint32_t s32;
uint16_t fort, faible;
uint32_t* im32 = (uint32_t*)im;
- switch ( swap )
+ switch ( SwapCode )
{
case 0:
case 1234:
break;
case 4321:
- for(i = 0; i < lgr/4; i++)
+ for( i = 0; i < DecompressedSize / 4; i++ )
{
faible = im32[i] & 0x0000ffff; // 4321
fort = im32[i] >> 16;
}
break;
case 2143:
- for(i = 0; i < lgr/4; i++)
+ for( i = 0; i < DecompressedSize / 4; i++ )
{
faible = im32[i] & 0x0000ffff; // 2143
fort = im32[i] >> 16;
}
break;
case 3412:
- for(i = 0; i < lgr/4; i++)
+ for( i = 0; i < DecompressedSize / 4; i++ )
{
faible = im32[i] & 0x0000ffff; // 3412
fort = im32[i] >> 16;
}
break;
default:
- std::cout << "SWAP value (32 bits) not allowed : " << swap <<
- std::endl;
+ dbg.Verbose( 0, "PixelConvert::SwapZone: SwapCode value "
+ "(32 bits) not allowed." );
}
}
}
-
-
/**
* \brief Deal with endianity i.e. re-arange bytes inside the integer
*/
-void PixelConvert::ConvertReorderEndianity( uint8_t* pixelZone,
- size_t imageDataSize,
- int numberBitsStored,
- int numberBitsAllocated,
- int swapCode,
- bool signedPixel)
+void PixelConvert::ReorderEndianity( uint8_t* pixelZone )
{
- if ( numberBitsAllocated != 8 )
+ if ( BitsAllocated != 8 )
{
- SwapZone( pixelZone, swapCode, imageDataSize, numberBitsAllocated );
+ SwapZone( pixelZone );
}
-
+
// Special kludge in order to deal with xmedcon broken images:
- if ( ( numberBitsAllocated == 16 )
- && ( numberBitsStored < numberBitsAllocated )
- && ( ! signedPixel ) )
+ if ( ( BitsAllocated == 16 )
+ && ( BitsStored < BitsAllocated )
+ && ( ! PixelSign ) )
{
- int l = (int)(imageDataSize / (numberBitsAllocated/8));
+ int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) );
uint16_t *deb = (uint16_t *)pixelZone;
for(int i = 0; i<l; i++)
{
* @param destination Where decompressed fragments should end up
* @return Boolean
*/
-bool PixelConvert::ReadAndDecompressJPEGFile( uint8_t* destination,
- int XSize,
- int YSize,
- int BitsAllocated,
- int BitsStored,
- int SamplesPerPixel,
- int PixelSize,
- bool isJPEG2000,
- bool isJPEGLossless,
- JPEGFragmentsInfo* JPEGInfo,
- FILE* fp )
+bool PixelConvert::ReadAndDecompressJPEGFile(
+ uint8_t* destination,
+ FILE* fp )
{
// Loop on the fragment[s]
for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
++it )
{
fseek( fp, (*it)->Offset, SEEK_SET );
-
- if ( isJPEG2000 )
+
+ if ( IsJPEG2000 )
{
if ( ! gdcm_read_JPEG2000_file( fp, destination ) )
{
return false;
}
}
- else if ( isJPEGLossless )
- {
- // JPEG LossLess : call to xmedcom Lossless JPEG
- JPEGLosslessDecodeImage( fp,
- (uint16_t*)destination,
- PixelSize * 8 * SamplesPerPixel,
- (*it)->Length );
- }
else if ( BitsStored == 8)
{
// JPEG Lossy : call to IJG 6b
- if ( ! gdcm_read_JPEG_file ( fp, destination ) )
+ if ( ! gdcm_read_JPEG_file8( fp, destination ) )
{
return false;
}
return false;
}
}
+ else if ( BitsStored == 16)
+ {
+ // Reading Fragment pixels
+ if ( ! gdcm_read_JPEG_file16 ( fp, destination ) )
+ {
+ return false;
+ }
+ //assert( IsJPEGLossless );
+ }
else
{
// other JPEG lossy not supported
- dbg.Error(" File::ReadPixelData : unknown jpeg lossy "
+ dbg.Error(" File::ReadAndDecompressJPEGFile: unknown jpeg lossy "
" compression ");
return false;
}
// for next fragment decompression (if any)
int length = XSize * YSize * SamplesPerPixel;
int numberBytes = BitsAllocated / 8;
-
- destination = (uint8_t*)destination + length * numberBytes;
-
+
+ destination += length * numberBytes;
}
return true;
}
/**
* \brief Re-arrange the bits within the bytes.
- * @param fp already open File Pointer
- * @param destination Where decompressed fragments should end up
+ * @param pixelZone zone
* @return Boolean
*/
-bool PixelConvert::ConvertReArrangeBits(
- uint8_t* pixelZone,
- size_t imageDataSize,
- int numberBitsStored,
- int numberBitsAllocated,
- int highBitPosition )
+bool PixelConvert::ReArrangeBits( uint8_t* pixelZone )
throw ( FormatError )
{
- if ( numberBitsStored != numberBitsAllocated )
+ if ( BitsStored != BitsAllocated )
{
- int l = (int)(imageDataSize / (numberBitsAllocated/8));
- if ( numberBitsAllocated == 16 )
+ int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) );
+ if ( BitsAllocated == 16 )
{
uint16_t mask = 0xffff;
- mask = mask >> ( numberBitsAllocated - numberBitsStored );
+ mask = mask >> ( BitsAllocated - BitsStored );
uint16_t* deb = (uint16_t*)pixelZone;
for(int i = 0; i<l; i++)
{
- *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
deb++;
}
}
- else if ( numberBitsAllocated == 32 )
+ else if ( BitsAllocated == 32 )
{
uint32_t mask = 0xffffffff;
- mask = mask >> ( numberBitsAllocated - numberBitsStored );
+ mask = mask >> ( BitsAllocated - BitsStored );
uint32_t* deb = (uint32_t*)pixelZone;
for(int i = 0; i<l; i++)
{
- *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask;
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
deb++;
}
}
else
{
- dbg.Verbose(0, "PixelConvert::ConvertReArrangeBits: weird image");
- throw FormatError( "File::ConvertReArrangeBits()",
+ dbg.Verbose(0, "PixelConvert::ReArrangeBits: weird image");
+ throw FormatError( "File::ReArrangeBits()",
"weird image !?" );
}
}
- return true; //???
+ return true;
+}
+
+/**
+ * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelConvert::ConvertYcBcRPlanesToRGBPixels( uint8_t* destination )
+{
+ uint8_t* oldPixelZone = new uint8_t[ DecompressedSize ];
+ memmove( oldPixelZone, destination, DecompressedSize );
+
+ // to see the tricks about YBR_FULL, YBR_FULL_422,
+ // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
+ // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
+ // and be *very* affraid
+ //
+ int l = XSize * YSize;
+ int nbFrames = ZSize;
+
+ uint8_t* a = oldPixelZone;
+ uint8_t* b = oldPixelZone + l;
+ uint8_t* c = oldPixelZone + l + l;
+ double R, G, B;
+
+ /// \todo : Replace by the 'well known' integer computation
+ /// counterpart. Refer to
+ /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ /// for code optimisation.
+
+ for ( int i = 0; i < nbFrames; i++ )
+ {
+ for ( int j = 0; j < l; j++ )
+ {
+ R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
+ G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
+ B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
+
+ if (R < 0.0) R = 0.0;
+ if (G < 0.0) G = 0.0;
+ if (B < 0.0) B = 0.0;
+ if (R > 255.0) R = 255.0;
+ if (G > 255.0) G = 255.0;
+ if (B > 255.0) B = 255.0;
+
+ *(destination++) = (uint8_t)R;
+ *(destination++) = (uint8_t)G;
+ *(destination++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
+ }
+ }
+ delete[] oldPixelZone;
+}
+
+/**
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelConvert::ConvertRGBPlanesToRGBPixels( uint8_t* destination )
+{
+ uint8_t* oldPixelZone = new uint8_t[ DecompressedSize ];
+ memmove( oldPixelZone, destination, DecompressedSize );
+
+ int l = XSize * YSize * ZSize;
+
+ uint8_t* a = oldPixelZone;
+ uint8_t* b = oldPixelZone + l;
+ uint8_t* c = oldPixelZone + l + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(destination++) = *(a++);
+ *(destination++) = *(b++);
+ *(destination++) = *(c++);
+ }
+ delete[] oldPixelZone;
+}
+
+bool PixelConvert::ReadAndDecompressPixelData( void* destination, FILE* fp )
+{
+ //////////////////////////////////////////////////
+ //// First stage: get our hands on the Pixel Data.
+ if ( !fp )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "unavailable file pointer." );
+ return false;
+ }
+
+ if ( fseek(fp, PixelOffset, SEEK_SET) == -1 )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "unable to find PixelOffset in file." );
+ return false;
+ }
+
+ //////////////////////////////////////////////////
+ //// Second stage: read from disk dans uncompress.
+ if ( BitsAllocated == 12 )
+ {
+ ReadAndDecompress12BitsTo16Bits( (uint8_t*)destination, fp);
+ }
+ else if ( IsUncompressed )
+ {
+ size_t ItemRead = fread( destination, PixelDataLength, 1, fp);
+ if ( ItemRead != 1 )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "reading of uncompressed pixel data failed." );
+ return false;
+ }
+ }
+ else if ( IsRLELossless )
+ {
+ if ( ! ReadAndDecompressRLEFile( destination, fp ) )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "RLE decompressor failed." );
+ return false;
+ }
+ }
+ else
+ {
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( (uint8_t*)destination, fp ) )
+ {
+ dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: "
+ "JPEG decompressor failed." );
+ return false;
+ }
+ }
+
+ ////////////////////////////////////////////
+ //// Third stage: twigle the bytes and bits.
+ ReorderEndianity( (uint8_t*) destination );
+ ReArrangeBits( (uint8_t*) destination );
+
+ return true;
+}
+
+bool PixelConvert::HandleColor( uint8_t* destination )
+{
+ //////////////////////////////////
+ // Deal with the color decoding i.e. handle:
+ // - R, G, B planes (as opposed to RGB pixels)
+ // - YBR (various) encodings.
+ // - LUT[s] (or "PALETTE COLOR").
+ //
+ // The classification in the color decoding schema is based on the blending
+ // of two Dicom tags values:
+ // * "Photometric Interpretation" for which we have the cases:
+ // - [Photo A] MONOCHROME[1|2] pictures,
+ // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB),
+ // - [Photo C] YBR_* (with the above exception of YBR_FULL_422)
+ // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s].
+ // * "Planar Configuration" for which we have the cases:
+ // - [Planar 0] 0 then Pixels are already RGB
+ // - [Planar 1] 1 then we have 3 planes : R, G, B,
+ // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs
+ //
+ // Now in theory, one could expect some coherence when blending the above
+ // cases. For example we should not encounter files belonging at the
+ // time to case [Planar 0] and case [Photo D].
+ // Alas, this was only theory ! Because in practice some odd (read ill
+ // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:
+ // - "Planar Configuration" = 0,
+ // - "Photometric Interpretation" = "PALETTE COLOR".
+ // Hence gdcm shall use the folowing "heuristic" in order to be tolerant
+ // towards Dicom-non-conformance files:
+ // << whatever the "Planar Configuration" value might be, a
+ // "Photometric Interpretation" set to "PALETTE COLOR" forces
+ // a LUT intervention >>
+ //
+ // Now we are left with the following handling of the cases:
+ // - [Planar 0] OR [Photo A] no color decoding (since respectively
+ // Pixels are already RGB and monochrome pictures have no color :),
+ // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels()
+ // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
+ // - [Planar 2] OR [Photo D] requires LUT intervention.
+
+ if ( IsMonochrome
+ || ( PlanarConfiguration == 2 )
+ || IsPaletteColor )
+ {
+ // [Planar 2] OR [Photo D]: LUT intervention done outside
+ return false;
+ }
+
+ if ( PlanarConfiguration == 1 )
+ {
+ if ( IsYBRFull )
+ {
+ // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ ConvertYcBcRPlanesToRGBPixels( (uint8_t*)destination );
+ }
+ else
+ {
+ // [Planar 1] AND [Photo C]
+ ConvertRGBPlanesToRGBPixels( (uint8_t*)destination );
+ }
+ }
+
+ // When planarConf is 0, pixels are allready in RGB
+ return true;
}
+
+void PixelConvert::ComputeDecompressedImageDataSize()
+{
+ int bitsAllocated;
+ // Number of "Bits Allocated" is fixed to 16 when it's 12, since
+ // in this case we will expand the image to 16 bits (see
+ // \ref ReadAndDecompress12BitsTo16Bits() )
+ if ( BitsAllocated == 12 )
+ {
+ bitsAllocated = 16;
+ }
+
+ DecompressedSize = XSize * YSize * ZSize
+ * ( bitsAllocated / 8 )
+ * SamplesPerPixel;
+}
+
} // 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