X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=35d29222c50ae044182c4c986f82939e233d3959;hb=27607c280b744ce7de6a1698935181e66aa2f3e6;hp=d3db30129b790697f13f0cf0b4ddbd0b19a9ce9d;hpb=145420342c6af4fc7a257c809a105ecd3d8d85cc;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index d3db3012..35d29222 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/01/28 15:42:22 $ - Version: $Revision: 1.37 $ + Date: $Date: 2005/02/02 16:34:55 $ + Version: $Revision: 1.45 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -30,36 +30,21 @@ namespace gdcm { +//----------------------------------------------------------------------------- #define str2num(str, typeNum) *((typeNum *)(str)) - //----------------------------------------------------------------------------- // Constructor / Destructor PixelReadConvert::PixelReadConvert() { - RGB = 0; - RGBSize = 0; - Raw = 0; - RawSize = 0; - LutRGBA = 0; - LutRedData = 0; + 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; + LutBlueData = 0; } PixelReadConvert::~PixelReadConvert() @@ -67,417 +52,317 @@ PixelReadConvert::~PixelReadConvert() Squeeze(); } -void PixelReadConvert::AllocateRGB() +//----------------------------------------------------------------------------- +// Public +/** + * \brief Predicate to know wether the image[s] (once Raw) is RGB. + * \note See comments of \ref ConvertHandleColor + */ +bool PixelReadConvert::IsRawRGB() { - if ( RGB ) - delete [] RGB; - RGB = new uint8_t[RGBSize]; + if ( IsMonochrome + || PlanarConfiguration == 2 + || IsPaletteColor ) + { + return false; + } + return true; } -void PixelReadConvert::AllocateRaw() +void PixelReadConvert::GrabInformationsFromFile( File *file ) { - if ( Raw ) - delete [] Raw; - Raw = new uint8_t[RawSize]; -} + // 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; + } -/** - * \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; + // Number of "Bits Stored", defaulted to number of "Bits Allocated" + // when absent from the file. + BitsStored = file->GetBitsStored(); + if ( BitsStored == 0 ) + { + BitsStored = BitsAllocated; + } - for( int p = 0; p < nbPixels; p += 2 ) + // High Bit Position, defaulted to "Bits Allocated" - 1 + HighBitPosition = file->GetHighBitPosition(); + if ( HighBitPosition == 0 ) { - uint8_t b0, b1, b2; + HighBitPosition = BitsAllocated - 1; + } - fp->read( (char*)&b0, 1); - if ( fp->fail() || fp->eof() )//Fp->gcount() == 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 ) { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound first block" ); + gdcmVerboseMacro( "Unable to read Red LUT data" ); } - fp->read( (char*)&b1, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + ////// Green round: + file->LoadEntryBinArea(0x0028, 0x1202); + LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 ); + if ( ! LutGreenData) { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound second block" ); + gdcmVerboseMacro( "Unable to read Green LUT data" ); } - fp->read( (char*)&b2, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + ////// Blue round: + file->LoadEntryBinArea(0x0028, 0x1203); + LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 ); + if ( ! LutBlueData ) { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound second block" ); + gdcmVerboseMacro( "Unable to read Blue LUT data" ); } - - // 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 ? } + + ComputeRawAndRGBSizes(); } -/** - * \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 ) +bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) { - 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; + // ComputeRawAndRGBSizes is already made by + // ::GrabInformationsFromfile. So, the structure sizes are + // correct + Squeeze(); - for ( int i = 0; i < NumberOfFrames; i++ ) + ////////////////////////////////////////////////// + //// First stage: get our hands on the Pixel Data. + if ( !fp ) { - for ( unsigned int j = 0; j < pixelNumber; j++ ) - { - *(x++) = *(b++); - *(x++) = *(a++); - } + gdcmVerboseMacro( "Unavailable file pointer." ); + return false; } - delete[] copyRaw; - - /// \todo check that operator new []didn't fail, and sometimes return false - return true; -} + fp->seekg( PixelOffset, std::ios::beg ); + if( fp->fail() || fp->eof()) + { + gdcmVerboseMacro( "Unable to find PixelOffset in file." ); + return false; + } -/** - * \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; + AllocateRaw(); - while( numberOfOutputBytes < RawSegmentSize ) + ////////////////////////////////////////////////// + //// Second stage: read from disk dans decompress. + if ( BitsAllocated == 12 ) + { + ReadAndDecompress12BitsTo16Bits( fp); + } + else if ( IsRaw ) { - 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]. + // 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) { - fp->read( (char*)subRaw, count + 1); - numberOfReadBytes += count + 1; - subRaw += count + 1; - numberOfOutputBytes += count + 1; + gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." ); + } + if( PixelDataLength > RawSize) + { + fp->read( (char*)Raw, RawSize); } 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; - } + fp->read( (char*)Raw, PixelDataLength); } - // if count = 128 output nothing - - if ( numberOfReadBytes > fragmentSize ) + + if ( fp->fail() || fp->eof()) { - gdcmVerboseMacro( "Read more bytes than the segment size."); + gdcmVerboseMacro( "Reading of Raw pixel data failed." ); 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 ) + } + else if ( IsRLELossless ) { - // Loop on the fragments - for( unsigned int k = 1; k <= frame->GetNumberOfFragments(); k++ ) + if ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) { - fp->seekg(frame->GetOffset(k),std::ios::beg); - ReadAndDecompressRLEFragment(subRaw, - frame->GetLength(k), - RawSegmentSize, - fp); - subRaw += RawSegmentSize; + gdcmVerboseMacro( "RLE decompressor failed." ); + return false; } - frame = RLEInfo->GetNexttFrame(); } - - if ( BitsAllocated == 16 ) + else { - // Try to deal with RLE 16 Bits - (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); + // 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; } -/** - * \brief Swap the bytes, according to \ref SwapCode. - */ -void PixelReadConvert::ConvertSwapZone() +void PixelReadConvert::Squeeze() { - 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." ); - } - } + if ( RGB ) + delete [] RGB; + RGB = 0; + + if ( Raw ) + delete [] Raw; + Raw = 0; + + if ( LutRGBA ) + delete [] LutRGBA; + LutRGBA = 0; } /** - * \brief Deal with endianness i.e. re-arange bytes inside the integer + * \brief Build the RGB image from the Raw imagage and the LUTs. */ -void PixelReadConvert::ConvertReorderEndianity() +bool PixelReadConvert::BuildRGBImage() { - if ( BitsAllocated != 8 ) + if ( RGB ) { - ConvertSwapZone(); + // The job is already done. + return true; } - // Special kludge in order to deal with xmedcon broken images: - if ( BitsAllocated == 16 - && BitsStored < BitsAllocated - && !PixelSign ) + if ( ! Raw ) { - 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 ); + 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; } +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private /** - * \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 + * \brief Read from file a 12 bits per pixel image and decompress it + * into a 16 bits per pixel image. */ -bool PixelReadConvert:: -ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream *fp ) +void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) + throw ( FormatError ) { - // Loop on the fragment[s] to get total length - size_t totalLength = JPEGInfo->GetFragmentsLength(); + int nbPixels = XSize * YSize; + uint16_t *localDecompres = (uint16_t*)Raw; - // Concatenate the jpeg fragments into a local buffer - JOCTET *buffer = new JOCTET [totalLength]; - // Fill in the buffer: - JPEGInfo->ReadAllFragments(fp, buffer); + for( int p = 0; p < nbPixels; p += 2 ) + { + uint8_t b0, b1, b2; - // kludge: // FIXME - JPEGFragment *fragment = JPEGInfo->GetFirstFragment(); - fragment->DecompressJPEGSingleFrameFragmentsFromFile(buffer, totalLength, Raw, BitsStored); + fp->read( (char*)&b0, 1); + if ( fp->fail() || fp->eof() ) + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound first block" ); + } - // free local buffer - delete [] buffer; - - return true; -} + fp->read( (char*)&b1, 1 ); + if ( fp->fail() || fp->eof()) + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); + } -/** - * \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(); + fp->read( (char*)&b2, 1 ); + if ( fp->fail() || fp->eof()) + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); + } - // Concatenate the jpeg fragments into a local buffer - JOCTET *buffer = new JOCTET [totalLength]; - // Fill in the buffer: - JPEGInfo->ReadAllFragments(fp, buffer); + // 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); - 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(); + /// \todo JPR Troubles expected on Big-Endian processors ? } - - // free local buffer - delete [] buffer; - - return true; } /** @@ -504,632 +389,485 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) 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 ); -// } + // else ?? + // Precompute the offset localRaw will be shifted with + int length = XSize * YSize * SamplesPerPixel; + int numberBytes = BitsAllocated / 8; + + JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length ); + return true; } /** - * \brief Re-arrange the bits within the bytes. - * @return Boolean + * \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 */ -bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) +void PixelReadConvert::BuildLUTRGBA() { - if ( BitsStored != BitsAllocated ) + if ( LutRGBA ) { - 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; + } + // 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; } - 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++ ) + //////////////////////////////////////////// + // 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 ) { - 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++; - } + gdcmVerboseMacro( "Wrong Red LUT descriptor" ); } - 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++) + + 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 ) { - *(localRaw++) = *(a++); - *(localRaw++) = *(b++); - *(localRaw++) = *(c++); + gdcmVerboseMacro( "Wrong Green LUT descriptor" ); } - 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 ) + + 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( "Unavailable file pointer." ); - return false; + gdcmVerboseMacro( "Wrong Blue LUT descriptor" ); } - - fp->seekg( PixelOffset, std::ios::beg ); - if( fp->fail() || fp->eof()) + + //////////////////////////////////////////////////////// + if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) ) { - gdcmVerboseMacro( "Unable to find PixelOffset in file." ); - return false; + return; } - AllocateRaw(); + //////////////////////////////////////////////// + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha) + if ( !LutRGBA ) + return; - ////////////////////////////////////////////////// - //// Second stage: read from disk dans decompress. - if ( BitsAllocated == 12 ) + memset( LutRGBA, 0, 1024 ); + + int mult; + if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) ) { - ReadAndDecompress12BitsTo16Bits( fp); + // when LUT item size is different than pixel size + mult = 2; // high byte must be = low byte } - else if ( IsRaw ) + else { - // 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 ) + // 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 ) { - if ( ! ReadAndDecompressRLEFile( fp ) ) - { - gdcmVerboseMacro( "RLE decompressor failed." ); - return false; - } + *a = LutRedData[i*mult+1]; + a += 4; } - else + + a = LutRGBA + 1; + for( i=0; i < lengthG; ++i) { - // Default case concerns JPEG family - if ( ! ReadAndDecompressJPEGFile( fp ) ) - { - gdcmVerboseMacro( "JPEG decompressor failed." ); - return false; - } + *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; } - - //////////////////////////////////////////// - //// Third stage: twigle the bytes and bits. - ConvertReorderEndianity(); - ConvertReArrangeBits(); - ConvertHandleColor(); - - return true; } -void PixelReadConvert::ConvertHandleColor() +/** + * \brief Swap the bytes, according to \ref SwapCode. + */ +void PixelReadConvert::ConvertSwapZone() { - ////////////////////////////////// - // 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. + 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." ); + } + } +} - if ( ! IsRawRGB() ) +/** + * \brief Deal with endianness i.e. re-arange bytes inside the integer + */ +void PixelReadConvert::ConvertReorderEndianity() +{ + if ( BitsAllocated != 8 ) { - // [Planar 2] OR [Photo D]: LUT intervention done outside - return; + ConvertSwapZone(); } - - if ( PlanarConfiguration == 1 ) + + // Special kludge in order to deal with xmedcon broken images: + if ( BitsAllocated == 16 + && BitsStored < BitsAllocated + && !PixelSign ) { - if ( IsYBRFull ) - { - // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB) - ConvertYcBcRPlanesToRGBPixels(); - } - else + int l = (int)( RawSize / ( BitsAllocated / 8 ) ); + uint16_t *deb = (uint16_t *)Raw; + for(int i = 0; i> ( 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; } -void PixelReadConvert::ComputeRawAndRGBSizes() +/** + * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels + * \warning Works on all the frames at a time + */ +void PixelReadConvert::ConvertRGBPlanesToRGBPixels() { - 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; - } -} + uint8_t *localRaw = Raw; + uint8_t *copyRaw = new uint8_t[ RawSize ]; + memmove( copyRaw, localRaw, 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; - } + int l = XSize * YSize * ZSize; - // Number of "Bits Stored", defaulted to number of "Bits Allocated" - // when absent from the file. - BitsStored = file->GetBitsStored(); - if ( BitsStored == 0 ) - { - BitsStored = BitsAllocated; - } + uint8_t *a = copyRaw; + uint8_t *b = copyRaw + l; + uint8_t *c = copyRaw + l + l; - // High Bit Position, defaulted to "Bits Allocated" - 1 - HighBitPosition = file->GetHighBitPosition(); - if ( HighBitPosition == 0 ) + for (int j = 0; j < l; j++) { - HighBitPosition = BitsAllocated - 1; + *(localRaw++) = *(a++); + *(localRaw++) = *(b++); + *(localRaw++) = *(c++); } + delete[] copyRaw; +} - 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(); +/** + * \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 ); - PlanarConfiguration = file->GetPlanarConfiguration(); - IsMonochrome = file->IsMonochrome(); - IsPaletteColor = file->IsPaletteColor(); - IsYBRFull = file->IsYBRFull(); + // 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; - ///////////////////////////////////////////////////////////////// - // 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" ); - } + uint8_t *a = copyRaw; + uint8_t *b = copyRaw + l; + uint8_t *c = copyRaw + l + l; + double R, G, B; - ////// Green round: - file->LoadEntryBinArea(0x0028, 0x1202); - LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 ); - if ( ! LutGreenData) - { - gdcmVerboseMacro( "Unable to read Green LUT data" ); - } + /// \todo : Replace by the 'well known' integer computation + /// counterpart. Refer to + /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf + /// for code optimisation. - ////// Blue round: - file->LoadEntryBinArea(0x0028, 0x1203); - LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 ); - if ( ! LutBlueData ) + for ( int i = 0; i < nbFrames; i++ ) + { + for ( int j = 0; j < l; j++ ) { - gdcmVerboseMacro( "Unable to read Blue LUT data" ); + 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++; } } - - ComputeRawAndRGBSizes(); + delete[] copyRaw; } -/** - * \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() +void PixelReadConvert::ConvertHandleColor() { - if ( LutRGBA ) + ////////////////////////////////// + // 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; } - // Not so easy : see - // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables - if ( ! IsPaletteColor ) + 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; } - if ( LutRedDescriptor == GDCM_UNFOUND - || LutGreenDescriptor == GDCM_UNFOUND - || LutBlueDescriptor == GDCM_UNFOUND ) + // When planarConf is 0, and RLELossless (forbidden by Dicom norm) + // pixels need to be RGB-fied anyway + if (IsRLELossless) { - return; + ConvertRGBPlanesToRGBPixels(); } + // In *normal *case, when planarConf is 0, pixels are already in RGB +} - //////////////////////////////////////////// - // 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 ) ) +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 ) { - return; + bitsAllocated = 16; } - - //////////////////////////////////////////////// - // 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 ) ) + RawSize = XSize * YSize * ZSize + * ( bitsAllocated / 8 ) + * SamplesPerPixel; + if ( HasLUT ) { - // when LUT item size is different than pixel size - mult = 2; // high byte must be = low byte + RGBSize = 3 * RawSize; } 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; + RGBSize = RawSize; } } -/** - * \brief Build the RGB image from the Raw imagage and the LUTs. - */ -bool PixelReadConvert::BuildRGBImage() +void PixelReadConvert::AllocateRGB() { - if ( RGB ) - { - // The job is already done. - return true; - } - - if ( ! Raw ) - { - // The job can't be done - return false; - } + if ( RGB ) + delete [] RGB; + RGB = new uint8_t[RGBSize]; +} - 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; +void PixelReadConvert::AllocateRaw() +{ + if ( Raw ) + delete [] Raw; + Raw = new uint8_t[RawSize]; } +//----------------------------------------------------------------------------- +// Print /** * \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 ) +void PixelReadConvert::Print( std::ostream &os, std::string const &indent ) { os << indent << "--- Pixel information -------------------------" @@ -1166,6 +904,7 @@ void PixelReadConvert::Print( std::ostream &os, std::string const & indent ) } } +//----------------------------------------------------------------------------- } // end namespace gdcm // NOTES on File internal calls