/*========================================================================= Program: gdcm Module: $RCSfile: gdcmPixelConvert.cxx,v $ Language: C++ Date: $Date: 2004/10/08 17:02:53 $ Version: $Revision: 1.4 $ 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 NOT // look for "fixMem" and convert that to a member of this class // Removing the prefix fixMem and dealing with allocations should do the trick #define str2num(str, typeNum) *((typeNum *)(str)) #include "gdcmDebug.h" #include "gdcmPixelConvert.h" //----------------------------------------------------------------------------- // Constructor / Destructor gdcmPixelConvert::gdcmPixelConvert() { RGB = 0; RGBSize = 0; Uncompressed = 0; UncompressedSize = 0; } void gdcmPixelConvert::Squeeze() { if ( RGB ) { delete [] RGB; } if ( Uncompressed ) { delete [] Uncompressed; } } gdcmPixelConvert::~gdcmPixelConvert() { Squeeze(); } void gdcmPixelConvert::AllocateRGB() { if ( RGB ) { delete [] RGB; } RGB = new uint8_t[RGBSize]; } void gdcmPixelConvert::AllocateUncompressed() { if ( Uncompressed ) { delete [] Uncompressed; } Uncompressed = new uint8_t[ UncompressedSize ]; } /** * \brief Read from file a 12 bits per pixel image and uncompress it * into a 16 bits per pixel image. */ void gdcmPixelConvert::ConvertDecompress12BitsTo16Bits( uint8_t* pixelZone, int sizeX, int sizeY, FILE* filePtr) throw ( gdcmFormatError ) { int nbPixels = sizeX * sizeY; 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 gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", "Unfound first block" ); } ItemRead = fread( &b1, 1, 1, filePtr); if ( ItemRead != 1 ) { throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", "Unfound second block" ); } ItemRead = fread( &b2, 1, 1, filePtr); if ( ItemRead != 1 ) { throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", "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 Read from file an uncompressed image. */ bool gdcmPixelConvert::ReadUncompressed( FILE* filePointer, size_t uncompressedSize, size_t expectedSize ) { if ( expectedSize > uncompressedSize ) { dbg.Verbose(0, "gdcmPixelConvert::ReadUncompressed: expectedSize" "is bigger than it should"); return false; } SetUncompressedSize( uncompressedSize ); AllocateUncompressed(); size_t ItemRead = fread( (void*)Uncompressed, expectedSize, 1, filePointer); if ( ItemRead != 1 ) { return false; } return true; } /** * \brief Convert a Gray plane and ( Lut R, Lut G, Lut B ) into an * RGB plane. * @return True on success. */ bool gdcmPixelConvert::ConvertGrayAndLutToRGB( uint8_t *lutRGBA ) { /// We assume Uncompressed contains the decompressed gray plane /// and build the RGB image. SetRGBSize( UncompressedSize ); AllocateRGB(); //aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa //AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA //COPY HERE THE CODE OF GetImageDataIntoVector /// \todo check that operator new []didn't fail, and sometimes return false return true; } /** * \brief Try to deal with RLE 16 Bits. * We assume the RLE has allready been parsed and loaded in * Uncompressed (through \ref ReadAndUncompressRLE8Bits ). * We here need to make 16 Bits Pixels from Low Byte and * High Byte 'Planes'...(for what it may mean) * @return Boolean */ bool gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits( int XSize, int YSize, 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 ( 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 gdcmPixelConvert::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, "gdcmFile::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 gdcmPixelConvert::gdcm_read_RLE_file( void* image_buffer, int XSize, int YSize, int ZSize, int BitsAllocated, gdcmRLEFramesInfo* RLEInfo, FILE* fp ) { uint8_t* im = (uint8_t*)image_buffer; long uncompressedSegmentSize = XSize * YSize; // Loop on the frame[s] for( gdcmRLEFramesInfo::RLEFrameList::iterator it = RLEInfo->Frames.begin(); it != RLEInfo->Frames.end(); ++it ) { // Loop on the fragments for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ ) { fseek( fp, (*it)->Offset[k] ,SEEK_SET); (void)gdcmPixelConvert::ReadAndUncompressRLEFragment( (uint8_t*) im, (*it)->Length[k], uncompressedSegmentSize, fp ); im += uncompressedSegmentSize; } } if ( BitsAllocated == 16 ) { // Try to deal with RLE 16 Bits (void)gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits( XSize, YSize, 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 * @param swap swap code * @param lgr Area Length * @param nb Pixels Bit number */ void gdcmPixelConvert::SwapZone(void* im, int swap, int lgr, int nb) { int i; if( nb == 16 ) { uint16_t* im16 = (uint16_t*)im; switch( swap ) { case 0: case 12: case 1234: break; case 21: case 3412: case 2143: case 4321: for(i=0; i < lgr/2; i++) { im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); } break; default: std::cout << "SWAP value (16 bits) not allowed :i" << swap << std::endl; } } else if( nb == 32 ) { uint32_t s32; uint16_t fort, faible; uint32_t* im32 = (uint32_t*)im; switch ( swap ) { case 0: case 1234: break; case 4321: for(i = 0; i < lgr/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 < lgr/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 < lgr/4; i++) { faible = im32[i] & 0x0000ffff; // 3412 fort = im32[i] >> 16; s32 = faible; im32[i] = ( s32 << 16 ) | fort; } break; default: std::cout << "SWAP value (32 bits) not allowed : " << swap << std::endl; } } } /** * \brief Deal with endianity i.e. re-arange bytes inside the integer */ void gdcmPixelConvert::ConvertReorderEndianity( uint8_t* pixelZone, size_t imageDataSize, int numberBitsStored, int numberBitsAllocated, int swapCode, bool signedPixel) { if ( numberBitsAllocated != 8 ) { SwapZone( pixelZone, swapCode, imageDataSize, numberBitsAllocated ); } // Special kludge in order to deal with xmedcon broken images: if ( ( numberBitsAllocated == 16 ) && ( numberBitsStored < numberBitsAllocated ) && ( ! signedPixel ) ) { int l = (int)(imageDataSize / (numberBitsAllocated/8)); uint16_t *deb = (uint16_t *)pixelZone; for(int i = 0; i