/*========================================================================= Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ Date: $Date: 2005/01/28 15:42:22 $ Version: $Revision: 1.37 $ 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. =========================================================================*/ #include "gdcmDebug.h" #include "gdcmFile.h" #include "gdcmGlobal.h" #include "gdcmTS.h" #include "gdcmPixelReadConvert.h" #include "gdcmDocEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" #include #include //for sscanf namespace gdcm { #define str2num(str, typeNum) *((typeNum *)(str)) //----------------------------------------------------------------------------- // Constructor / Destructor PixelReadConvert::PixelReadConvert() { RGB = 0; RGBSize = 0; Raw = 0; RawSize = 0; LutRGBA = 0; LutRedData = 0; LutGreenData = 0; LutBlueData =0; } void PixelReadConvert::Squeeze() { if ( RGB ) delete [] RGB; RGB = 0; if ( Raw ) delete [] Raw; Raw = 0; if ( LutRGBA ) delete [] LutRGBA; LutRGBA = 0; } PixelReadConvert::~PixelReadConvert() { Squeeze(); } void PixelReadConvert::AllocateRGB() { if ( RGB ) delete [] RGB; RGB = new uint8_t[RGBSize]; } void PixelReadConvert::AllocateRaw() { if ( Raw ) delete [] Raw; Raw = new uint8_t[RawSize]; } /** * \brief Read from file a 12 bits per pixel image and decompress it * into a 16 bits per pixel image. */ void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) throw ( FormatError ) { int nbPixels = XSize * YSize; uint16_t* localDecompres = (uint16_t*)Raw; 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( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound first block" ); } fp->read( (char*)&b1, 1 ); if ( fp->fail() || fp->eof())//Fp->gcount() == 1 { throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound second block" ); } fp->read( (char*)&b2, 1 ); if ( fp->fail() || fp->eof())//Fp->gcount() == 1 { throw FormatError( "PixelReadConvert::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 already been parsed and loaded in * Raw (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 PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) { size_t pixelNumber = XSize * YSize; size_t rawSize = XSize * YSize * NumberOfFrames; // We assumed Raw 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 Raw and hence // we copy it in a safe place, say copyRaw. uint8_t* copyRaw = new uint8_t[rawSize * 2]; memmove( copyRaw, Raw, rawSize * 2 ); uint8_t* x = Raw; uint8_t* a = copyRaw; 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[] copyRaw; /// \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 subRaw Sub region of \ref Raw where the decoded fragment * should be placed. * @param fragmentSize The length of the binary fragment as found on the disk. * @param RawSegmentSize The expected length of the fragment ONCE * Raw. * @param fp File Pointer: on entry the position should be the one of * the fragment to be decoded. */ bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t *subRaw, long fragmentSize, long RawSegmentSize, std::ifstream *fp ) { int8_t count; long numberOfOutputBytes = 0; long numberOfReadBytes = 0; while( numberOfOutputBytes < RawSegmentSize ) { 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*)subRaw, count + 1); numberOfReadBytes += count + 1; subRaw += 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++ ) { subRaw[i] = newByte; } subRaw += -count + 1; numberOfOutputBytes += -count + 1; } } // if count = 128 output nothing if ( numberOfReadBytes > fragmentSize ) { gdcmVerboseMacro( "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 PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream *fp ) { uint8_t *subRaw = Raw; long RawSegmentSize = XSize * YSize; // Loop on the frame[s] RLEFrame *frame = RLEInfo->GetFirstFrame(); while( frame ) { // Loop on the fragments for( unsigned int k = 1; k <= frame->GetNumberOfFragments(); k++ ) { fp->seekg(frame->GetOffset(k),std::ios::beg); ReadAndDecompressRLEFragment(subRaw, frame->GetLength(k), RawSegmentSize, fp); subRaw += RawSegmentSize; } frame = RLEInfo->GetNexttFrame(); } if ( BitsAllocated == 16 ) { // Try to deal with RLE 16 Bits (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); } return true; } /** * \brief Swap the bytes, according to \ref SwapCode. */ void PixelReadConvert::ConvertSwapZone() { unsigned int i; if( BitsAllocated == 16 ) { uint16_t *im16 = (uint16_t*)Raw; switch( SwapCode ) { case 1234: break; case 3412: case 2143: case 4321: for( i = 0; i < RawSize / 2; i++ ) { im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); } break; default: gdcmVerboseMacro("SwapCode value (16 bits) not allowed."); } } else if( BitsAllocated == 32 ) { uint32_t s32; uint16_t high; uint16_t low; uint32_t* im32 = (uint32_t*)Raw; switch ( SwapCode ) { case 1234: break; case 4321: for( i = 0; i < RawSize / 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 < RawSize / 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 < RawSize / 4; i++ ) { low = im32[i] & 0x0000ffff; // 3412 high = im32[i] >> 16; s32 = low; im32[i] = ( s32 << 16 ) | high; } break; default: gdcmVerboseMacro("SwapCode value (32 bits) not allowed." ); } } } /** * \brief Deal with endianness i.e. re-arange bytes inside the integer */ void PixelReadConvert::ConvertReorderEndianity() { if ( BitsAllocated != 8 ) { ConvertSwapZone(); } // Special kludge in order to deal with xmedcon broken images: if ( BitsAllocated == 16 && BitsStored < BitsAllocated && !PixelSign ) { int l = (int)( RawSize / ( BitsAllocated / 8 ) ); uint16_t *deb = (uint16_t *)Raw; for(int i = 0; iFragments.begin(); // it != JPEGInfo->Fragments.end(); // ++it ) // { // (*it)->DecompressJPEGFramesFromFile(fp, localRaw, BitsStored ); // // // Advance to next free location in Raw // // for next fragment decompression (if any) // // localRaw += length * numberBytes; // } JPEGInfo->DecompressJPEGFramesFromFile(fp, Raw, BitsStored, numberBytes, length ); return true; } /** * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated * file and decompress it. This function assumes that the dicom * image is a single frame split into several JPEG fragments. * Those fragments will be glued together into a memory buffer * before being read. * @param fp File Pointer * @return Boolean */ bool PixelReadConvert:: ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream *fp ) { // Loop on the fragment[s] to get total length size_t totalLength = JPEGInfo->GetFragmentsLength(); // Concatenate the jpeg fragments into a local buffer JOCTET *buffer = new JOCTET [totalLength]; // Fill in the buffer: JPEGInfo->ReadAllFragments(fp, buffer); // kludge: // FIXME JPEGFragment *fragment = JPEGInfo->GetFirstFragment(); fragment->DecompressJPEGSingleFrameFragmentsFromFile(buffer, totalLength, Raw, BitsStored); // free local buffer delete [] buffer; return true; } /** * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated * file and decompress it. This function handles the generic * and complex case where the DICOM contains several frames, * and some of the frames are possibly split into several JPEG * fragments. * @param fp File Pointer * @return Boolean */ bool PixelReadConvert:: ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream *fp ) { // Loop on the fragment[s] to get total length size_t totalLength = JPEGInfo->GetFragmentsLength(); // Concatenate the jpeg fragments into a local buffer JOCTET *buffer = new JOCTET [totalLength]; // Fill in the buffer: JPEGInfo->ReadAllFragments(fp, buffer); size_t howManyRead = 0; size_t howManyWritten = 0; size_t fragmentLength = 0; JPEGFragment *fragment = JPEGInfo->GetFirstFragment(); while( fragment ) { fragmentLength += fragment->GetLength(); if (howManyRead > fragmentLength) continue; fragment->DecompressJPEGFragmentedFramesFromFile(buffer, Raw, BitsStored, howManyRead, howManyWritten, totalLength); if (howManyRead < fragmentLength) howManyRead = fragmentLength; fragment = JPEGInfo->GetNextFragment(); } // free local buffer delete [] buffer; return true; } /** * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated * file and decompress it. * @param fp File Pointer * @return Boolean */ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) { if ( IsJPEG2000 ) { gdcmVerboseMacro( "Sorry, JPEG2000 not yet taken into account" ); fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg); // if ( ! gdcm_read_JPEG2000_file( fp,Raw ) ) return false; } if ( IsJPEGLS ) { gdcmVerboseMacro( "Sorry, JPEG-LS not yet taken into account" ); fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg); // if ( ! gdcm_read_JPEGLS_file( fp,Raw ) ) return false; } if ( ( ZSize == 1 ) && ( JPEGInfo->GetFragmentCount() > 1 ) ) { // we have one frame split into several fragments // we will pack those fragments into a single buffer and // read from it return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp ); } else if (JPEGInfo->GetFragmentCount() == (size_t)ZSize) { } // if ( ( ZSize == 1 ) && ( JPEGInfo->Fragments.size() > 1 ) ) // { // // we have one frame split into several fragments // // we will pack those fragments into a single buffer and // // read from it // return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp ); // } // else if (JPEGInfo->Fragments.size() == (size_t)ZSize) // { // suppose each fragment is a frame return ReadAndDecompressJPEGFramesFromFile( fp ); // } // else // { // // The dicom image contains frames containing fragments of images // // a more complex algorithm :-) // return ReadAndDecompressJPEGFragmentedFramesFromFile( fp ); // } } /** * \brief Re-arrange the bits within the bytes. * @return Boolean */ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) { if ( BitsStored != BitsAllocated ) { int l = (int)( RawSize / ( BitsAllocated / 8 ) ); if ( BitsAllocated == 16 ) { uint16_t mask = 0xffff; mask = mask >> ( BitsAllocated - BitsStored ); uint16_t* deb = (uint16_t*)Raw; 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*)Raw; for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; deb++; } } else { gdcmVerboseMacro("Weird image"); throw FormatError( "Weird image !?" ); } } return true; } /** * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels * \warning Works on all the frames at a time */ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() { uint8_t *localRaw = Raw; uint8_t *copyRaw = new uint8_t[ RawSize ]; memmove( copyRaw, localRaw, RawSize ); // 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 = copyRaw; uint8_t *b = copyRaw + l; uint8_t *c = copyRaw + 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; *(localRaw++) = (uint8_t)R; *(localRaw++) = (uint8_t)G; *(localRaw++) = (uint8_t)B; a++; b++; c++; } } delete[] copyRaw; } /** * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels * \warning Works on all the frames at a time */ void PixelReadConvert::ConvertRGBPlanesToRGBPixels() { uint8_t *localRaw = Raw; uint8_t *copyRaw = new uint8_t[ RawSize ]; memmove( copyRaw, localRaw, RawSize ); int l = XSize * YSize * ZSize; uint8_t* a = copyRaw; uint8_t* b = copyRaw + l; uint8_t* c = copyRaw + l + l; for (int j = 0; j < l; j++) { *(localRaw++) = *(a++); *(localRaw++) = *(b++); *(localRaw++) = *(c++); } delete[] copyRaw; } bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) { // ComputeRawAndRGBSizes is already made by // ::GrabInformationsFromfile. So, the structure sizes are // correct Squeeze(); ////////////////////////////////////////////////// //// First stage: get our hands on the Pixel Data. if ( !fp ) { gdcmVerboseMacro( "Unavailable file pointer." ); return false; } fp->seekg( PixelOffset, std::ios::beg ); if( fp->fail() || fp->eof()) { gdcmVerboseMacro( "Unable to find PixelOffset in file." ); return false; } AllocateRaw(); ////////////////////////////////////////////////// //// Second stage: read from disk dans decompress. if ( BitsAllocated == 12 ) { ReadAndDecompress12BitsTo16Bits( fp); } else if ( IsRaw ) { // This problem can be found when some obvious informations are found // after the field containing the image data. In this case, these // bad data are added to the size of the image (in the PixelDataLength // variable). But RawSize is the right size of the image ! if( PixelDataLength != RawSize) { gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." ); } if( PixelDataLength > RawSize) { fp->read( (char*)Raw, RawSize); } else { fp->read( (char*)Raw, PixelDataLength); } if ( fp->fail() || fp->eof()) { gdcmVerboseMacro( "Reading of Raw pixel data failed." ); return false; } } else if ( IsRLELossless ) { if ( ! ReadAndDecompressRLEFile( fp ) ) { gdcmVerboseMacro( "RLE decompressor failed." ); return false; } } else { // Default case concerns JPEG family if ( ! ReadAndDecompressJPEGFile( fp ) ) { gdcmVerboseMacro( "JPEG decompressor failed." ); return false; } } //////////////////////////////////////////// //// Third stage: twigle the bytes and bits. ConvertReorderEndianity(); ConvertReArrangeBits(); ConvertHandleColor(); return true; } void PixelReadConvert::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 will 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 ( ! IsRawRGB() ) { // [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 Raw) is RGB. * \note See comments of \ref ConvertHandleColor */ bool PixelReadConvert::IsRawRGB() { if ( IsMonochrome || PlanarConfiguration == 2 || IsPaletteColor ) { return false; } return true; } void PixelReadConvert::ComputeRawAndRGBSizes() { 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; } RawSize = XSize * YSize * ZSize * ( bitsAllocated / 8 ) * SamplesPerPixel; if ( HasLUT ) { RGBSize = 3 * RawSize; } else { RGBSize = RawSize; } } void PixelReadConvert::GrabInformationsFromFile( File *file ) { // Number of Bits Allocated for storing a Pixel is defaulted to 16 // when absent from the file. BitsAllocated = file->GetBitsAllocated(); if ( BitsAllocated == 0 ) { BitsAllocated = 16; } // Number of "Bits Stored", defaulted to number of "Bits Allocated" // when absent from the file. BitsStored = file->GetBitsStored(); if ( BitsStored == 0 ) { BitsStored = BitsAllocated; } // High Bit Position, defaulted to "Bits Allocated" - 1 HighBitPosition = file->GetHighBitPosition(); if ( HighBitPosition == 0 ) { HighBitPosition = BitsAllocated - 1; } XSize = file->GetXSize(); YSize = file->GetYSize(); ZSize = file->GetZSize(); SamplesPerPixel = file->GetSamplesPerPixel(); PixelSize = file->GetPixelSize(); PixelSign = file->IsSignedPixelData(); SwapCode = file->GetSwapCode(); std::string ts = file->GetTransferSyntax(); IsRaw = ( ! file->IsDicomV3() ) || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndianDLXGE || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian; IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts); IsJPEGLS = Global::GetTS()->IsJPEGLS(ts); IsJPEGLossy = Global::GetTS()->IsJPEGLossy(ts); IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts); IsRLELossless = Global::GetTS()->IsRLELossless(ts); PixelOffset = file->GetPixelOffset(); PixelDataLength = file->GetPixelAreaLength(); RLEInfo = file->GetRLEInfo(); JPEGInfo = file->GetJPEGInfo(); PlanarConfiguration = file->GetPlanarConfiguration(); IsMonochrome = file->IsMonochrome(); IsPaletteColor = file->IsPaletteColor(); IsYBRFull = file->IsYBRFull(); ///////////////////////////////////////////////////////////////// // LUT section: HasLUT = file->HasLUT(); if ( HasLUT ) { // Just in case some access to a File element requires disk access. LutRedDescriptor = file->GetEntryValue( 0x0028, 0x1101 ); LutGreenDescriptor = file->GetEntryValue( 0x0028, 0x1102 ); LutBlueDescriptor = file->GetEntryValue( 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 file // and when this fails we read the LUTs data directly 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 file->LoadEntryBinArea(0x0028, 0x1201); LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 ); if ( ! LutRedData ) { gdcmVerboseMacro( "Unable to read Red LUT data" ); } ////// Green round: file->LoadEntryBinArea(0x0028, 0x1202); LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 ); if ( ! LutGreenData) { gdcmVerboseMacro( "Unable to read Green LUT data" ); } ////// Blue round: file->LoadEntryBinArea(0x0028, 0x1203); LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 ); if ( ! LutBlueData ) { gdcmVerboseMacro( "Unable to read Blue LUT data" ); } } ComputeRawAndRGBSizes(); } /** * \brief Build Red/Green/Blue/Alpha LUT from File * 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 PixelReadConvert::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 ) { gdcmVerboseMacro( "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 ) { gdcmVerboseMacro( "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 ) { gdcmVerboseMacro( "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 Raw imagage and the LUTs. */ bool PixelReadConvert::BuildRGBImage() { if ( RGB ) { // The job is already done. return true; } if ( ! Raw ) { // 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 < RawSize; ++i ) { int j = Raw[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 PixelReadConvert::Print( std::ostream &os, std::string const & indent ) { 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( os, indent ); } else { gdcmVerboseMacro("Set as RLE file but NO RLEinfo present."); } } if ( IsJPEG2000 || IsJPEGLossless || IsJPEGLossy || IsJPEGLS ) { if ( JPEGInfo ) { JPEGInfo->Print( os, indent ); } else { gdcmVerboseMacro("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