/*========================================================================= Program: gdcm Module: $RCSfile: gdcmPixelConvert.cxx,v $ Language: C++ Date: $Date: 2004/11/16 11:19:51 $ Version: $Revision: 1.30 $ 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" #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 PixelConvert::PixelConvert() { RGB = 0; RGBSize = 0; Decompressed = 0; DecompressedSize = 0; LutRGBA = 0; LutRedData = 0; LutGreenData = 0; LutBlueData =0; } void PixelConvert::Squeeze() { if ( RGB ) { delete [] RGB; } RGB = 0; if ( Decompressed ) { delete [] Decompressed; } Decompressed = 0; if ( LutRGBA ) { delete [] LutRGBA; } LutRGBA = 0; } 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 decompress it * into a 16 bits per pixel image. */ void PixelConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp ) throw ( FormatError ) { int nbPixels = XSize * YSize; uint16_t* localDecompres = (uint16_t*)Decompressed; for( int p = 0; p < nbPixels; p += 2 ) { uint8_t b0, b1, b2; fp->read( (char*)&b0, 1); if ( fp->fail() || fp->eof() )//Fp->gcount() == 1 { throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound first block" ); } fp->read( (char*)&b1, 1 ); if ( fp->fail() || fp->eof())//Fp->gcount() == 1 { throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound second block" ); } fp->read( (char*)&b2, 1 ); if ( fp->fail() || fp->eof())//Fp->gcount() == 1 { throw FormatError( "PixelConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound second block" ); } // 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); /// \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 * 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 PixelConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) { size_t PixelNumber = XSize * YSize; size_t decompressedSize = XSize * YSize * NumberOfFrames; // 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 Decompressed and hence // we copy it in a safe place, say copyDecompressed. uint8_t* copyDecompressed = new uint8_t[ decompressedSize * 2 ]; memmove( copyDecompressed, Decompressed, decompressedSize * 2 ); uint8_t* x = Decompressed; uint8_t* a = copyDecompressed; uint8_t* b = a + PixelNumber; for ( int i = 0; i < NumberOfFrames; i++ ) { for ( unsigned int j = 0; j < PixelNumber; j++ ) { *(x++) = *(b++); *(x++) = *(a++); } } delete[] copyDecompressed; /// \todo check that operator new []didn't fail, and sometimes return false return true; } /** * \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 PixelConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed, long fragmentSize, long decompressedSegmentSize, std::ifstream* fp ) { int8_t count; long numberOfOutputBytes = 0; long numberOfReadBytes = 0; while( numberOfOutputBytes < decompressedSegmentSize ) { fp->read( (char*)&count, 1 ); 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]. { fp->read( (char*)subDecompressed, count + 1); numberOfReadBytes += count + 1; subDecompressed += count + 1; numberOfOutputBytes += count + 1; } else { if ( ( count <= -1 ) && ( count >= -127 ) ) { int8_t newByte; fp->read( (char*)&newByte, 1); numberOfReadBytes += 1; for( int i = 0; i < -count + 1; i++ ) { subDecompressed[i] = newByte; } subDecompressed += -count + 1; numberOfOutputBytes += -count + 1; } } // if count = 128 output nothing if ( numberOfReadBytes > fragmentSize ) { dbg.Verbose(0, "PixelConvert::ReadAndDecompressRLEFragment: 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 decompress it. * @param fp already open File Pointer * at which the pixel data should be copied * @return Boolean */ bool PixelConvert::ReadAndDecompressRLEFile( std::ifstream* fp ) { uint8_t* subDecompressed = Decompressed; long decompressedSegmentSize = 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( unsigned int k = 1; k <= (*it)->NumberFragments; k++ ) { 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)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(); AllocateDecompressed(); ////////////////////////////////////////////////// //// 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; } ////////////////////////////////////////////////// //// 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; } } 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 == 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" ); return; } } ////// 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" ); return; } } ////// 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" ); return; } } } 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