X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelConvert.cxx;h=d3d6b7aa980d70c5d77f1e980cacd173415f7171;hb=e5e7b1bd7ee84e8f9dc7da5d1d42b598fac68399;hp=789a600a7c699a905e8d1c9e075f40551857b75a;hpb=67845c7dc1241480f5c5fcfa0cfc2e86918dad1e;p=gdcm.git diff --git a/src/gdcmPixelConvert.cxx b/src/gdcmPixelConvert.cxx index 789a600a..d3d6b7aa 100644 --- a/src/gdcmPixelConvert.cxx +++ b/src/gdcmPixelConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelConvert.cxx,v $ Language: C++ - Date: $Date: 2004/10/08 16:27:20 $ - Version: $Revision: 1.3 $ + Date: $Date: 2004/11/25 10:24:34 $ + Version: $Revision: 1.33 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,206 +16,203 @@ =========================================================================*/ -////////////////// 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 -#define str2num(str, typeNum) *((typeNum *)(str)) +// +// grep PIXELCONVERT everywhere and clean up ! #include "gdcmDebug.h" #include "gdcmPixelConvert.h" +#include +#include + +namespace gdcm +{ +#define str2num(str, typeNum) *((typeNum *)(str)) + +// For JPEG 2000, body in file gdcmJpeg2000.cxx +bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer); + +// For JPEG 8 Bits, body in file gdcmJpeg8.cxx +bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer); + +// For JPEG 12 Bits, body in file gdcmJpeg12.cxx +bool gdcm_read_JPEG_file12 (std::ifstream* 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 (std::ifstream* fp, void* image_buffer); //----------------------------------------------------------------------------- // Constructor / Destructor -gdcmPixelConvert::gdcmPixelConvert() +PixelConvert::PixelConvert() { RGB = 0; RGBSize = 0; - Uncompressed = 0; - UncompressedSize = 0; + Decompressed = 0; + DecompressedSize = 0; + LutRGBA = 0; + LutRedData = 0; + LutGreenData = 0; + LutBlueData =0; } -void gdcmPixelConvert::Squeeze() +void PixelConvert::Squeeze() { - if ( RGB ) { + if ( RGB ) + { delete [] RGB; } - if ( Uncompressed ) { - delete [] Uncompressed; + RGB = 0; + + if ( Decompressed ) + { + delete [] Decompressed; } + Decompressed = 0; + + if ( LutRGBA ) + { + delete [] LutRGBA; + } + LutRGBA = 0; } -gdcmPixelConvert::~gdcmPixelConvert() +PixelConvert::~PixelConvert() { Squeeze(); } -void gdcmPixelConvert::AllocateRGB() +void PixelConvert::AllocateRGB() { if ( RGB ) { delete [] RGB; } - RGB = new uint8_t[RGBSize]; + RGB = new uint8_t[ RGBSize ]; } -void gdcmPixelConvert::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 + * \brief Read from file a 12 bits per pixel image and decompress it * into a 16 bits per pixel image. */ -bool gdcmPixelConvert::ReadAndUncompress12Bits( FILE* filePointer, - size_t uncompressedSize, - size_t PixelNumber ) +void PixelConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp ) + throw ( FormatError ) { - SetUncompressedSize( uncompressedSize ); - AllocateUncompressed(); + int nbPixels = XSize * YSize; + uint16_t* localDecompres = (uint16_t*)Decompressed; - uint16_t* pdestination = (uint16_t*)Uncompressed; - - for(int p = 0; p < PixelNumber; p += 2 ) + for( int p = 0; p < nbPixels; p += 2 ) { - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] uint8_t b0, b1, b2; - size_t ItemRead; - ItemRead = fread( &b0, 1, 1, filePointer); - if ( ItemRead != 1 ) + + fp->read( (char*)&b0, 1); + if ( fp->fail() || fp->eof() )//Fp->gcount() == 1 { - return false; + throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound first block" ); } - ItemRead = fread( &b1, 1, 1, filePointer); - if ( ItemRead != 1 ) + + fp->read( (char*)&b1, 1 ); + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 { - return false; + throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); } - ItemRead = fread( &b2, 1, 1, filePointer); - if ( ItemRead != 1 ) + + fp->read( (char*)&b2, 1 ); + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 { - return false; + throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); } - - //Two steps are necessary to please VC++ - *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // A B D - *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - // F C E - - /// \todo JPR Troubles expected on Big-Endian processors ? - } - return true; -} -/** - * \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(); + // Two steps are necessary to please VC++ + // + // 2 pixels 12bit = [0xABCDEF] + // 2 pixels 16bit = [0x0ABD] + [0x0FCE] + // A B D + *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); + // F C E + *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); -//aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa -//AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -//COPY HERE THE CODE OF GetImageDataIntoVector - - /// \todo check that operator new []didn't fail, and sometimes return false - return true; + /// \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 ReadAndUncompressRLE8Bits ). + * Decompressed (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 gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits( - int XSize, - int YSize, - int NumberOfFrames, - uint8_t* fixMemUncompressed ) +bool PixelConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) { size_t PixelNumber = XSize * YSize; - size_t fixMemUncompressedSize = XSize * YSize * NumberOfFrames; + size_t decompressedSize = XSize * YSize * NumberOfFrames; - // We assumed Uncompressed contains the decoded RLE pixels but as + // We assumed Decompressed 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. + // per pixel we cannot work in place within Decompressed and hence + // we copy it in a safe place, say copyDecompressed. - uint8_t* OldUncompressed = new uint8_t[ fixMemUncompressedSize * 2 ]; - memmove( OldUncompressed, fixMemUncompressed, fixMemUncompressedSize * 2); + uint8_t* copyDecompressed = new uint8_t[ decompressedSize * 2 ]; + memmove( copyDecompressed, Decompressed, decompressedSize * 2 ); - uint8_t* x = fixMemUncompressed; - uint8_t* a = OldUncompressed; + uint8_t* x = Decompressed; + uint8_t* a = copyDecompressed; uint8_t* b = a + PixelNumber; for ( int i = 0; i < NumberOfFrames; i++ ) { - for ( int j = 0; j < PixelNumber; j++ ) + for ( unsigned int j = 0; j < PixelNumber; j++ ) { - *(x++) = *(a++); *(x++) = *(b++); + *(x++) = *(a++); } } - delete[] OldUncompressed; + delete[] copyDecompressed; /// \todo check that operator new []didn't fail, and sometimes return false return true; } /** - * \brief Implementation of the RLE decoding algorithm for uncompressing + * \brief Implementation of the RLE decoding algorithm for decompressing * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86] + * @param subDecompressed Sub region of \ref Decompressed where the de + * decoded fragment should be placed. + * @param fragmentSize The length of the binary fragment as found on the disk. + * @param decompressedSegmentSize The expected length of the fragment ONCE + * decompressed. + * @param fp File Pointer: on entry the position should be the one of + * the fragment to be decoded. */ -bool gdcmPixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone, - long fragmentSize, - long uncompressedSegmentSize, - FILE* fp ) +bool PixelConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed, + long fragmentSize, + long decompressedSegmentSize, + std::ifstream* fp ) { int8_t count; long numberOfOutputBytes = 0; long numberOfReadBytes = 0; - - while( numberOfOutputBytes < uncompressedSegmentSize ) + + while( numberOfOutputBytes < decompressedSegmentSize ) { - fread( &count, 1, 1, fp ); + fp->read( (char*)&count, 1 ); numberOfReadBytes += 1; if ( count >= 0 ) // Note: count <= 127 comparison is always true due to limited range @@ -223,9 +220,9 @@ bool gdcmPixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone, // 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; + fp->read( (char*)subDecompressed, count + 1); + numberOfReadBytes += count + 1; + subDecompressed += count + 1; numberOfOutputBytes += count + 1; } else @@ -233,13 +230,13 @@ bool gdcmPixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone, if ( ( count <= -1 ) && ( count >= -127 ) ) { int8_t newByte; - fread( &newByte, 1, 1, fp); + fp->read( (char*)&newByte, 1); numberOfReadBytes += 1; for( int i = 0; i < -count + 1; i++ ) { - decodedZone[i] = newByte; + subDecompressed[i] = newByte; } - decodedZone += -count + 1; + subDecompressed += -count + 1; numberOfOutputBytes += -count + 1; } } @@ -247,8 +244,8 @@ bool gdcmPixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone, if ( numberOfReadBytes > fragmentSize ) { - dbg.Verbose(0, "gdcmFile::gdcm_read_RLE_fragment: we read more " - "bytes than the segment size."); + dbg.Verbose(0, "PixelConvert::ReadAndDecompressRLEFragment: we " + "read more bytes than the segment size."); return false; } } @@ -257,26 +254,18 @@ bool gdcmPixelConvert::ReadAndUncompressRLEFragment( uint8_t* decodedZone, /** * \brief Reads from disk the Pixel Data of 'Run Length Encoded' - * Dicom encapsulated file and uncompress it. + * Dicom encapsulated file and decompress 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 ) +bool PixelConvert::ReadAndDecompressRLEFile( std::ifstream* fp ) { - uint8_t* im = (uint8_t*)image_buffer; - long uncompressedSegmentSize = XSize * YSize; - - + uint8_t* subDecompressed = Decompressed; + long decompressedSegmentSize = XSize * YSize; + // Loop on the frame[s] - for( gdcmRLEFramesInfo::RLEFrameList::iterator + for( RLEFramesInfo::RLEFrameList::iterator it = RLEInfo->Frames.begin(); it != RLEInfo->Frames.end(); ++it ) @@ -284,24 +273,878 @@ bool gdcmPixelConvert::gdcm_read_RLE_file( void* image_buffer, // 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; + fp->seekg( (*it)->Offset[k] , std::ios_base::beg ); + (void)ReadAndDecompressRLEFragment( subDecompressed, + (*it)->Length[k], + decompressedSegmentSize, + fp ); + subDecompressed += decompressedSegmentSize; } } - + if ( BitsAllocated == 16 ) { // Try to deal with RLE 16 Bits - (void)gdcmPixelConvert::UncompressRLE16BitsFromRLE8Bits( - XSize, - YSize, - ZSize, - (uint8_t*) image_buffer); + (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); + } + + return true; +} + +/** + * \brief Swap the bytes, according to \ref SwapCode. + */ +void PixelConvert::ConvertSwapZone() +{ + unsigned int i; + + if( BitsAllocated == 16 ) + { + uint16_t* im16 = (uint16_t*)Decompressed; + 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::ConvertSwapZone: SwapCode value " + "(16 bits) not allowed." ); + } + } + else if( BitsAllocated == 32 ) + { + uint32_t s32; + uint16_t high; + uint16_t low; + uint32_t* im32 = (uint32_t*)Decompressed; + switch ( SwapCode ) + { + case 0: + case 1234: + break; + case 4321: + for( i = 0; i < DecompressedSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 4321 + high = im32[i] >> 16; + high = ( high >> 8 ) | ( high << 8 ); + low = ( low >> 8 ) | ( low << 8 ); + s32 = low; + im32[i] = ( s32 << 16 ) | high; + } + break; + case 2143: + for( i = 0; i < DecompressedSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 2143 + high = im32[i] >> 16; + high = ( high >> 8 ) | ( high << 8 ); + low = ( low >> 8 ) | ( low << 8 ); + s32 = high; + im32[i] = ( s32 << 16 ) | low; + } + break; + case 3412: + for( i = 0; i < DecompressedSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 3412 + high = im32[i] >> 16; + s32 = low; + im32[i] = ( s32 << 16 ) | high; + } + break; + default: + dbg.Verbose( 0, "PixelConvert::ConvertSwapZone: SwapCode value " + "(32 bits) not allowed." ); + } + } +} + +/** + * \brief Deal with endianity i.e. re-arange bytes inside the integer + */ +void PixelConvert::ConvertReorderEndianity() +{ + if ( BitsAllocated != 8 ) + { + ConvertSwapZone(); + } + + // 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 *)Decompressed; + for(int i = 0; iFragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + fp->seekg( (*it)->Offset, std::ios_base::beg); + + if ( IsJPEG2000 ) + { + if ( ! gdcm_read_JPEG2000_file( fp,localDecompressed ) ) + { + return false; + } + } + else if ( BitsStored == 8) + { + // JPEG Lossy : call to IJG 6b + if ( ! gdcm_read_JPEG_file8( fp, localDecompressed ) ) + { + return false; + } + } + else if ( BitsStored <= 12) + { + // Reading Fragment pixels + if ( ! gdcm_read_JPEG_file12 ( fp, localDecompressed ) ) + { + return false; + } + } + else if ( BitsStored <= 16) + { + // Reading Fragment pixels + if ( ! gdcm_read_JPEG_file16 ( fp, localDecompressed ) ) + { + return false; + } + //assert( IsJPEGLossless ); + } + else + { + // other JPEG lossy not supported + dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown " + "jpeg lossy compression "); + return false; + } + + // Advance to next free location in Decompressed + // for next fragment decompression (if any) + int length = XSize * YSize * SamplesPerPixel; + int numberBytes = BitsAllocated / 8; + + localDecompressed += length * numberBytes; + } + return true; +} + +/** + * \brief Re-arrange the bits within the bytes. + * @return Boolean + */ +bool PixelConvert::ConvertReArrangeBits() 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*)Decompressed; + 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*)Decompressed; + for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; + deb++; + } + } + else + { + dbg.Verbose(0, "PixelConvert::ConvertReArrangeBits: weird image"); + throw FormatError( "PixelConvert::ConvertReArrangeBits()", + "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* localDecompressed = Decompressed; + uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ]; + memmove( copyDecompressed, localDecompressed, 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 = copyDecompressed; + uint8_t* b = copyDecompressed + l; + uint8_t* c = copyDecompressed + 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; + + *(localDecompressed++) = (uint8_t)R; + *(localDecompressed++) = (uint8_t)G; + *(localDecompressed++) = (uint8_t)B; + a++; + b++; + c++; + } + } + delete[] copyDecompressed; +} + +/** + * \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* localDecompressed = Decompressed; + uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ]; + memmove( copyDecompressed, localDecompressed, DecompressedSize ); + + int l = XSize * YSize * ZSize; + + uint8_t* a = copyDecompressed; + uint8_t* b = copyDecompressed + l; + uint8_t* c = copyDecompressed + l + l; + + for (int j = 0; j < l; j++) + { + *(localDecompressed++) = *(a++); + *(localDecompressed++) = *(b++); + *(localDecompressed++) = *(c++); + } + delete[] copyDecompressed; +} + +bool PixelConvert::ReadAndDecompressPixelData( std::ifstream* fp ) +{ + // ComputeDecompressedAndRGBSizes is already made by + // ::GrabInformationsFromHeader. So, the structure sizes are + // correct + Squeeze(); + + ////////////////////////////////////////////////// + //// First stage: get our hands on the Pixel Data. + if ( !fp ) + { + dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: " + "unavailable file pointer." ); + return false; + } + + fp->seekg( PixelOffset, std::ios_base::beg ); + if( fp->fail() || fp->eof()) //Fp->gcount() == 1 + { + dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: " + "unable to find PixelOffset in file." ); + return false; + } + + AllocateDecompressed(); + + ////////////////////////////////////////////////// + //// Second stage: read from disk dans decompress. + if ( BitsAllocated == 12 ) + { + ReadAndDecompress12BitsTo16Bits( fp); + } + else if ( IsDecompressed ) + { + // This problem can be found when some obvious informations are found + // after the field containing the image datas. In this case, these + // bad datas are added to the size of the image (in the PixelDataLength + // variable). But DecompressedSize is the right size of the image ! + if( PixelDataLength != DecompressedSize) + { + dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: " + "Mismatch between PixelConvert and DecompressedSize." ); + } + if( PixelDataLength > DecompressedSize) + { + fp->read( (char*)Decompressed, DecompressedSize); + } + else + { + fp->read( (char*)Decompressed, PixelDataLength); + } + + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + { + dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: " + "reading of decompressed pixel data failed." ); + return false; + } + } + else if ( IsRLELossless ) + { + if ( ! ReadAndDecompressRLEFile( fp ) ) + { + dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: " + "RLE decompressor failed." ); + return false; + } + } + else + { + // Default case concerns JPEG family + if ( ! ReadAndDecompressJPEGFile( fp ) ) + { + dbg.Verbose( 0, "PixelConvert::ReadAndDecompressPixelData: " + "JPEG decompressor failed." ); + return false; + } + } + + //////////////////////////////////////////// + //// Third stage: twigle the bytes and bits. + ConvertReorderEndianity(); + ConvertReArrangeBits(); + ConvertHandleColor(); + + return true; +} + +void PixelConvert::ConvertHandleColor() +{ + ////////////////////////////////// + // 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 ( ! IsDecompressedRGB() ) + { + // [Planar 2] OR [Photo D]: LUT intervention done outside + return; + } + + if ( PlanarConfiguration == 1 ) + { + if ( IsYBRFull ) + { + // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB) + ConvertYcBcRPlanesToRGBPixels(); + } + else + { + // [Planar 1] AND [Photo C] + ConvertRGBPlanesToRGBPixels(); + } + return; } + // When planarConf is 0, and RLELossless (forbidden by Dicom norm) + // pixels need to be RGB-fied anyway + if (IsRLELossless) + { + ConvertRGBPlanesToRGBPixels(); + } + // In *normal *case, when planarConf is 0, pixels are already in RGB +} + +/** + * \brief Predicate to know wether the image[s] (once decompressed) is RGB. + * \note See comments of \ref ConvertHandleColor + */ +bool PixelConvert::IsDecompressedRGB() +{ + if ( IsMonochrome + || PlanarConfiguration == 2 + || IsPaletteColor ) + { + return false; + } return true; } +void PixelConvert::ComputeDecompressedAndRGBSizes() +{ + int bitsAllocated = 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; + if ( HasLUT ) + { + RGBSize = 3 * DecompressedSize; + } + else + { + RGBSize = DecompressedSize; + } +} + +void PixelConvert::GrabInformationsFromHeader( Header* header ) +{ + // Just in case some access to a Header element requires disk access. + // Note: gdcmDocument::Fp is leaved open after OpenFile. + std::ifstream* fp = header->OpenFile(); + // Number of Bits Allocated for storing a Pixel is defaulted to 16 + // when absent from the header. + BitsAllocated = header->GetBitsAllocated(); + if ( BitsAllocated == 0 ) + { + BitsAllocated = 16; + } + + // Number of "Bits Stored" defaulted to number of "Bits Allocated" + // when absent from the header. + BitsStored = header->GetBitsStored(); + if ( BitsStored == 0 ) + { + BitsStored = BitsAllocated; + } + + // High Bit Position + HighBitPosition = header->GetHighBitPosition(); + if ( HighBitPosition == 0 ) + { + HighBitPosition = BitsAllocated - 1; + } + + XSize = header->GetXSize(); + YSize = header->GetYSize(); + ZSize = header->GetZSize(); + SamplesPerPixel = header->GetSamplesPerPixel(); + PixelSize = header->GetPixelSize(); + PixelSign = header->IsSignedPixelData(); + SwapCode = header->GetSwapCode(); + TransferSyntaxType ts = header->GetTransferSyntax(); + IsDecompressed = + ( ! header->IsDicomV3() ) + || ts == ImplicitVRLittleEndian + || ts == ImplicitVRLittleEndianDLXGE + || ts == ExplicitVRLittleEndian + || ts == ExplicitVRBigEndian + || ts == DeflatedExplicitVRLittleEndian; + IsJPEG2000 = header->IsJPEG2000(); + IsJPEGLossless = header->IsJPEGLossless(); + IsRLELossless = ( ts == RLELossless ); + PixelOffset = header->GetPixelOffset(); + PixelDataLength = header->GetPixelAreaLength(); + RLEInfo = header->GetRLEInfo(); + JPEGInfo = header->GetJPEGInfo(); + + PlanarConfiguration = header->GetPlanarConfiguration(); + IsMonochrome = header->IsMonochrome(); + IsPaletteColor = header->IsPaletteColor(); + IsYBRFull = header->IsYBRFull(); + + ///////////////////////////////////////////////////////////////// + // LUT section: + HasLUT = header->HasLUT(); + if ( HasLUT ) + { + LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 ); + LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 ); + LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 ); + + // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE + // [ refer to invocation of Document::SetMaxSizeLoadEntry() in + // Document::Document() ], the loading of the value (content) of a + // [Bin|Val]Entry occurence migth have been hindered (read simply NOT + // loaded). Hence, we first try to obtain the LUTs data from the header + // and when this fails we read the LUTs data directely from disk. + /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge. + /// We should NOT bypass the [Bin|Val]Entry class. Instead + /// an access to an UNLOADED content of a [Bin|Val]Entry occurence + /// (e.g. BinEntry::GetBinArea()) should force disk access from + /// within the [Bin|Val]Entry class itself. The only problem + /// is that the [Bin|Val]Entry is unaware of the FILE* is was + /// parsed from. Fix that. FIXME. + + ////// Red round: + LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 ); + if ( ! LutRedData ) + { + // Read the Lut Data from disk + DocEntry* lutRedDataEntry = header->GetDocEntryByNumber( 0x0028, + 0x1201 ); + LutRedData = new uint8_t[ lutRedDataEntry->GetLength() ]; + fp->seekg( lutRedDataEntry->GetOffset() ,std::ios_base::beg ); + fp->read( (char*)LutRedData, (size_t)lutRedDataEntry->GetLength()); + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + { + dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: " + "unable to read red LUT data" ); + } + } + + ////// Green round: + LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 ); + if ( ! LutGreenData) + { + // Read the Lut Data from disk + DocEntry* lutGreenDataEntry = header->GetDocEntryByNumber( 0x0028, + 0x1202 ); + LutGreenData = new uint8_t[ lutGreenDataEntry->GetLength() ]; + fp->seekg( lutGreenDataEntry->GetOffset() , std::ios_base::beg ); + fp->read( (char*)LutGreenData, (size_t)lutGreenDataEntry->GetLength() ); + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + { + dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: " + "unable to read green LUT data" ); + } + } + + ////// Blue round: + LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 ); + if ( ! LutBlueData ) + { + // Read the Lut Data from disk + DocEntry* lutBlueDataEntry = header->GetDocEntryByNumber( 0x0028, + 0x1203 ); + LutBlueData = new uint8_t[ lutBlueDataEntry->GetLength() ]; + fp->seekg( lutBlueDataEntry->GetOffset() , std::ios_base::beg ); + fp->read( (char*)LutBlueData, (size_t)lutBlueDataEntry->GetLength() ); + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + { + dbg.Verbose(0, "PixelConvert::GrabInformationsFromHeader: " + "unable to read blue LUT data" ); + } + } + } + + ComputeDecompressedAndRGBSizes(); + + if(fp) + { + header->CloseFile(); + } +} + +/** + * \brief Build Red/Green/Blue/Alpha LUT from Header + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * and (0028,1101),(0028,1102),(0028,1102) + * - xxx Palette Color Lookup Table Descriptor - are found + * and (0028,1201),(0028,1202),(0028,1202) + * - xxx Palette Color Lookup Table Data - are found + * \warning does NOT deal with : + * 0028 1100 Gray Lookup Table Descriptor (Retired) + * 0028 1221 Segmented Red Palette Color Lookup Table Data + * 0028 1222 Segmented Green Palette Color Lookup Table Data + * 0028 1223 Segmented Blue Palette Color Lookup Table Data + * no known Dicom reader deals with them :-( + * @return a RGBA Lookup Table + */ +void PixelConvert::BuildLUTRGBA() +{ + if ( LutRGBA ) + { + return; + } + // Not so easy : see + // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables + + if ( ! IsPaletteColor ) + { + return; + } + + if ( LutRedDescriptor == GDCM_UNFOUND + || LutGreenDescriptor == GDCM_UNFOUND + || LutBlueDescriptor == GDCM_UNFOUND ) + { + return; + } + + //////////////////////////////////////////// + // Extract the info from the LUT descriptors + int lengthR; // Red LUT length in Bytes + int debR; // Subscript of the first Lut Value + int nbitsR; // Lut item size (in Bits) + int nbRead = sscanf( LutRedDescriptor.c_str(), + "%d\\%d\\%d", + &lengthR, &debR, &nbitsR ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "PixelConvert::BuildLUTRGBA: wrong red LUT descriptor"); + } + + int lengthG; // Green LUT length in Bytes + int debG; // Subscript of the first Lut Value + int nbitsG; // Lut item size (in Bits) + nbRead = sscanf( LutGreenDescriptor.c_str(), + "%d\\%d\\%d", + &lengthG, &debG, &nbitsG ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "PixelConvert::BuildLUTRGBA: wrong green LUT descriptor"); + } + + int lengthB; // Blue LUT length in Bytes + int debB; // Subscript of the first Lut Value + int nbitsB; // Lut item size (in Bits) + nbRead = sscanf( LutRedDescriptor.c_str(), + "%d\\%d\\%d", + &lengthB, &debB, &nbitsB ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "PixelConvert::BuildLUTRGBA: wrong blue LUT descriptor"); + } + + //////////////////////////////////////////////////////// + if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) ) + { + return; + } + + //////////////////////////////////////////////// + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha) + if ( !LutRGBA ) + { + return; + } + memset( LutRGBA, 0, 1024 ); + + int mult; + if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) ) + { + // when LUT item size is different than pixel size + mult = 2; // high byte must be = low byte + } + else + { + // See PS 3.3-2003 C.11.1.1.2 p 619 + mult = 1; + } + + // if we get a black image, let's just remove the '+1' + // from 'i*mult+1' and check again + // if it works, we shall have to check the 3 Palettes + // to see which byte is ==0 (first one, or second one) + // and fix the code + // We give up the checking to avoid some (useless ?)overhead + // (optimistic asumption) + int i; + uint8_t* a = LutRGBA + 0; + for( i=0; i < lengthR; ++i ) + { + *a = LutRedData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 1; + for( i=0; i < lengthG; ++i) + { + *a = LutGreenData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 2; + for(i=0; i < lengthB; ++i) + { + *a = LutBlueData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 3; + for(i=0; i < 256; ++i) + { + *a = 1; // Alpha component + a += 4; + } +} + +/** + * \brief Build the RGB image from the Decompressed imagage and the LUTs. + */ +bool PixelConvert::BuildRGBImage() +{ + if ( RGB ) + { + // The job is already done. + return true; + } + + if ( ! Decompressed ) + { + // The job can't be done + return false; + } + + BuildLUTRGBA(); + if ( ! LutRGBA ) + { + // The job can't be done + return false; + } + + // Build RGB Pixels + AllocateRGB(); + uint8_t* localRGB = RGB; + for (size_t i = 0; i < DecompressedSize; ++i ) + { + int j = Decompressed[i] * 4; + *localRGB++ = LutRGBA[j]; + *localRGB++ = LutRGBA[j+1]; + *localRGB++ = LutRGBA[j+2]; + } + return true; +} + +/** + * \brief Print self. + * @param indent Indentation string to be prepended during printing. + * @param os Stream to print to. + */ +void PixelConvert::Print( std::string indent, std::ostream &os ) +{ + os << indent + << "--- Pixel information -------------------------" + << std::endl; + os << indent + << "Pixel Data: offset " << PixelOffset + << " x" << std::hex << PixelOffset << std::dec + << " length " << PixelDataLength + << " x" << std::hex << PixelDataLength << std::dec + << std::endl; + + if ( IsRLELossless ) + { + if ( RLEInfo ) + { + RLEInfo->Print( indent, os ); + } + else + { + dbg.Verbose(0, "PixelConvert::Print: set as RLE file " + "but NO RLEinfo present."); + } + } + + if ( IsJPEG2000 || IsJPEGLossless ) + { + if ( JPEGInfo ) + { + JPEGInfo->Print( indent, os ); + } + else + { + dbg.Verbose(0, "PixelConvert::Print: set as JPEG file " + "but NO JPEGinfo present."); + } + } +} + +} // end namespace gdcm + +// NOTES on File internal calls +// User +// ---> GetImageData +// ---> GetImageDataIntoVector +// |---> GetImageDataIntoVectorRaw +// | lut intervention +// User +// ---> GetImageDataRaw +// ---> GetImageDataIntoVectorRaw