/*========================================================================= Program: gdcm Module: $RCSfile: gdcmPixelConvert.cxx,v $ Language: C++ Date: $Date: 2004/10/13 04:05:04 $ Version: $Revision: 1.10 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ ////////////////// 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 { #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); // For JPEG 12 Bits, body in file gdcmJpeg12.cxx bool gdcm_read_JPEG_file12 (FILE* fp, void* image_buffer); //----------------------------------------------------------------------------- // Constructor / Destructor PixelConvert::PixelConvert() { RGB = 0; RGBSize = 0; Decompressed = 0; DecompressedSize = 0; } void PixelConvert::Squeeze() { if ( RGB ) { delete [] RGB; } if ( Decompressed ) { delete [] Decompressed; } } PixelConvert::~PixelConvert() { Squeeze(); } void PixelConvert::AllocateRGB() { if ( RGB ) { delete [] RGB; } RGB = new uint8_t[RGBSize]; } void PixelConvert::AllocateDecompressed() { if ( Decompressed ) { delete [] Decompressed; } 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::Decompress12BitsTo16Bits( uint8_t* pixelZone, FILE* filePtr) throw ( FormatError ) { int nbPixels = XSize * YSize; uint16_t* destination = (uint16_t*)pixelZone; for( int p = 0; p < nbPixels; p += 2 ) { uint8_t b0, b1, b2; size_t ItemRead; ItemRead = fread( &b0, 1, 1, filePtr); if ( ItemRead != 1 ) { throw FormatError( "File::Decompress12BitsTo16Bits()", "Unfound first block" ); } ItemRead = fread( &b1, 1, 1, filePtr); if ( ItemRead != 1 ) { throw FormatError( "File::Decompress12BitsTo16Bits()", "Unfound second block" ); } ItemRead = fread( &b2, 1, 1, filePtr); if ( ItemRead != 1 ) { throw FormatError( "File::Decompress12BitsTo16Bits()", "Unfound second block" ); } // Two steps are necessary to please VC++ // // 2 pixels 12bit = [0xABCDEF] // 2 pixels 16bit = [0x0ABD] + [0x0FCE] // A B D *destination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); // F C E *destination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); /// \todo JPR Troubles expected on Big-Endian processors ? } } /** * \brief Try to deal with RLE 16 Bits. * We assume the RLE has allready been parsed and loaded in * Uncompressed (through \ref ReadAndDecompressJPEGFile ). * We here need to make 16 Bits Pixels from Low Byte and * High Byte 'Planes'...(for what it may mean) * @return Boolean */ bool PixelConvert::UncompressRLE16BitsFromRLE8Bits( int NumberOfFrames, uint8_t* fixMemUncompressed ) { size_t PixelNumber = XSize * YSize; size_t fixMemUncompressedSize = XSize * YSize * NumberOfFrames; // We assumed Uncompressed contains the decoded RLE pixels but as // 8 bits per pixel. In order to convert those pixels to 16 bits // per pixel we cannot work in place within Uncompressed and hence // we copy Uncompressed in a safe place, say OldUncompressed. uint8_t* OldUncompressed = new uint8_t[ fixMemUncompressedSize * 2 ]; memmove( OldUncompressed, fixMemUncompressed, fixMemUncompressedSize * 2); uint8_t* x = fixMemUncompressed; uint8_t* a = OldUncompressed; uint8_t* b = a + PixelNumber; for ( int i = 0; i < NumberOfFrames; i++ ) { for ( unsigned int j = 0; j < PixelNumber; j++ ) { *(x++) = *(a++); *(x++) = *(b++); } } delete[] OldUncompressed; /// \todo check that operator new []didn't fail, and sometimes return false return true; } /** * \brief Implementation of the RLE decoding algorithm for uncompressing * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86] */ bool PixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone, long fragmentSize, long uncompressedSegmentSize, FILE* fp ) { int8_t count; long numberOfOutputBytes = 0; long numberOfReadBytes = 0; while( numberOfOutputBytes < uncompressedSegmentSize ) { fread( &count, 1, 1, fp ); numberOfReadBytes += 1; if ( count >= 0 ) // Note: count <= 127 comparison is always true due to limited range // of data type int8_t [since the maximum of an exact width // signed integer of width N is 2^(N-1) - 1, which for int8_t // is 127]. { fread( decodedZone, count + 1, 1, fp); numberOfReadBytes += count + 1; decodedZone += count + 1; numberOfOutputBytes += count + 1; } else { if ( ( count <= -1 ) && ( count >= -127 ) ) { int8_t newByte; fread( &newByte, 1, 1, fp); numberOfReadBytes += 1; for( int i = 0; i < -count + 1; i++ ) { decodedZone[i] = newByte; } decodedZone += -count + 1; numberOfOutputBytes += -count + 1; } } // if count = 128 output nothing if ( numberOfReadBytes > fragmentSize ) { dbg.Verbose(0, "File::gdcm_read_RLE_fragment: we read more " "bytes than the segment size."); return false; } } return true; } /** * \brief Reads from disk the Pixel Data of 'Run Length Encoded' * Dicom encapsulated file and uncompress it. * @param fp already open File Pointer * @param image_buffer destination Address (in caller's memory space) * at which the pixel data should be copied * @return Boolean */ 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 != RLEInfo->Frames.end(); ++it ) { // Loop on the fragments for( int k = 1; k <= (*it)->NumberFragments; k++ ) { fseek( fp, (*it)->Offset[k] ,SEEK_SET ); (void)PixelConvert::ReadAndUncompressRLEFragment( (uint8_t*) im, (*it)->Length[k], uncompressedSegmentSize, fp ); im += uncompressedSegmentSize; } } if ( BitsAllocated == 16 ) { // Try to deal with RLE 16 Bits (void)UncompressRLE16BitsFromRLE8Bits( ZSize, (uint8_t*) image_buffer); } return true; } /** * \brief Swap the bytes, according to swap code. * \warning not end user intended * @param im area to deal with */ void PixelConvert::SwapZone( uint8_t* im ) { unsigned int i; if( BitsAllocated == 16 ) { uint16_t* im16 = (uint16_t*)im; switch( SwapCode ) { case 0: case 12: case 1234: break; case 21: case 3412: case 2143: case 4321: for( i = 0; i < DecompressedSize / 2; i++ ) { im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); } break; default: dbg.Verbose( 0, "PixelConvert::SwapZone: SwapCode value " "(16 bits) not allowed." ); } } else if( BitsAllocated == 32 ) { uint32_t s32; uint16_t fort, faible; uint32_t* im32 = (uint32_t*)im; switch ( SwapCode ) { case 0: case 1234: break; case 4321: for( i = 0; i < DecompressedSize / 4; i++ ) { faible = im32[i] & 0x0000ffff; // 4321 fort = im32[i] >> 16; fort = ( fort >> 8 ) | ( fort << 8 ); faible = ( faible >> 8 ) | ( faible << 8); s32 = faible; im32[i] = ( s32 << 16 ) | fort; } break; case 2143: for( i = 0; i < DecompressedSize / 4; i++ ) { faible = im32[i] & 0x0000ffff; // 2143 fort = im32[i] >> 16; fort = ( fort >> 8 ) | ( fort << 8 ); faible = ( faible >> 8) | ( faible << 8); s32 = fort; im32[i] = ( s32 << 16 ) | faible; } break; case 3412: for( i = 0; i < DecompressedSize / 4; i++ ) { faible = im32[i] & 0x0000ffff; // 3412 fort = im32[i] >> 16; s32 = faible; im32[i] = ( s32 << 16 ) | fort; } break; default: 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::ReorderEndianity( uint8_t* pixelZone ) { if ( BitsAllocated != 8 ) { SwapZone( pixelZone ); } // Special kludge in order to deal with xmedcon broken images: if ( ( BitsAllocated == 16 ) && ( BitsStored < BitsAllocated ) && ( ! PixelSign ) ) { int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) ); uint16_t *deb = (uint16_t *)pixelZone; for(int i = 0; iFragments.begin(); it != JPEGInfo->Fragments.end(); ++it ) { fseek( fp, (*it)->Offset, SEEK_SET ); 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 ) ) { return false; } } else if ( BitsStored == 12) { // Reading Fragment pixels if ( ! gdcm_read_JPEG_file12 ( fp, destination ) ) { return false; } } else { // other JPEG lossy not supported dbg.Error(" File::ReadAndDecompressJPEGFile: unknown jpeg lossy " " compression "); return false; } // Advance to next free location in destination // for next fragment decompression (if any) int length = XSize * YSize * SamplesPerPixel; int numberBytes = BitsAllocated / 8; destination = (uint8_t*)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 * @return Boolean */ bool PixelConvert::ReArrangeBits( uint8_t* pixelZone ) throw ( FormatError ) { if ( BitsStored != BitsAllocated ) { int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) ); if ( BitsAllocated == 16 ) { uint16_t mask = 0xffff; mask = mask >> ( BitsAllocated - BitsStored ); uint16_t* deb = (uint16_t*)pixelZone; for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; deb++; } } else if ( BitsAllocated == 32 ) { uint32_t mask = 0xffffffff; mask = mask >> ( BitsAllocated - BitsStored ); uint32_t* deb = (uint32_t*)pixelZone; for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; deb++; } } else { dbg.Verbose(0, "PixelConvert::ReArrangeBits: weird image"); throw FormatError( "File::ReArrangeBits()", "weird image !?" ); } } 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, size_t imageDataSize ) { uint8_t* oldPixelZone = new uint8_t[ imageDataSize ]; memmove( oldPixelZone, destination, imageDataSize ); // 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, size_t imageDataSize ) { uint8_t* oldPixelZone = new uint8_t[ imageDataSize ]; memmove( oldPixelZone, destination, imageDataSize ); 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 ) { if ( !fp ) { return false; } if ( fseek(fp, PixelOffset, SEEK_SET) == -1 ) { return false; } if ( BitsAllocated == 12 ) { Decompress12BitsTo16Bits( (uint8_t*)destination, fp); return true; } //////////// Decompressed File if ( IsUncompressed ) { size_t ItemRead = fread( destination, PixelDataLength, 1, fp); if ( ItemRead != 1 ) { return false; } else { return true; } } ///////////// Run Length Encoding if ( IsRLELossless ) { return ReadAndDecompressRLEFile( destination, fp ); } ///////////// SingleFrame/Multiframe JPEG Lossless/Lossy/2000 return ReadAndDecompressJPEGFile( (uint8_t*)destination, fp ); } 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 Decompress12BitsTo16Bits() ) if ( BitsAllocated == 12 ) { bitsAllocated = 16; } DecompressedSize = XSize * YSize * ZSize * ( bitsAllocated / 8 ) * SamplesPerPixel; } } // end namespace gdcm