X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=424514ed153305253a807297cde5445f564ae18b;hb=8e10ae94ea66aca5adf40e66521fba9c736628c4;hp=9338248a130141a5161773f0c6c32536862062c6;hpb=1dd2c40c0da9098b444ad53b0e3c23da808997fa;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 9338248a..424514ed 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/01/31 04:00:05 $ - Version: $Revision: 1.39 $ + Date: $Date: 2005/02/03 17:12:46 $ + Version: $Revision: 1.47 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -30,21 +30,238 @@ 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; + LutBlueData = 0; +} + +PixelReadConvert::~PixelReadConvert() +{ + Squeeze(); +} + +//----------------------------------------------------------------------------- +// Public +/** + * \brief Predicate to know whether 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; +} +/** + * \brief Gets various usefull informations from the file header + * @param file gdcm::File pointer + */ +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(); +} + +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 : " + << PixelDataLength << " and RawSize : " << 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 ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) + { + 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::Squeeze() @@ -62,25 +279,48 @@ void PixelReadConvert::Squeeze() LutRGBA = 0; } -PixelReadConvert::~PixelReadConvert() +/** + * \brief Build the RGB image from the Raw imagage and the LUTs. + */ +bool PixelReadConvert::BuildRGBImage() { - Squeeze(); -} + if ( RGB ) + { + // The job is already done. + return true; + } -void PixelReadConvert::AllocateRGB() -{ - if ( RGB ) - delete [] RGB; - RGB = new uint8_t[RGBSize]; -} + if ( ! Raw ) + { + // The job can't be done + return false; + } -void PixelReadConvert::AllocateRaw() -{ - if ( Raw ) - delete [] Raw; - Raw = new uint8_t[RawSize]; + 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 Read from file a 12 bits per pixel image and decompress it * into a 16 bits per pixel image. @@ -89,7 +329,7 @@ void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) throw ( FormatError ) { int nbPixels = XSize * YSize; - uint16_t* localDecompres = (uint16_t*)Raw; + uint16_t *localDecompres = (uint16_t*)Raw; for( int p = 0; p < nbPixels; p += 2 ) { @@ -130,142 +370,170 @@ void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) } /** - * \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) + * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated + * file and decompress it. + * @param fp File Pointer * @return Boolean */ -bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) +bool PixelReadConvert::ReadAndDecompressJPEGFile( 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; - - for ( int i = 0; i < NumberOfFrames; i++ ) + if ( IsJPEG2000 ) { - for ( unsigned int j = 0; j < pixelNumber; j++ ) - { - *(x++) = *(b++); - *(x++) = *(a++); - } + 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; } - delete[] copyRaw; - - /// \todo check that operator new []didn't fail, and sometimes 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; + } + + // 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 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. + * \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::ReadAndDecompressRLEFragment( uint8_t *subRaw, - long fragmentSize, - long RawSegmentSize, - std::ifstream *fp ) +void PixelReadConvert::BuildLUTRGBA() { - int8_t count; - long numberOfOutputBytes = 0; - long numberOfReadBytes = 0; + 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; + } - while( numberOfOutputBytes < RawSegmentSize ) + //////////////////////////////////////////// + // 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 ) { - 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 + gdcmVerboseMacro( "Wrong Red LUT descriptor" ); + } - if ( numberOfReadBytes > fragmentSize ) - { - gdcmVerboseMacro( "Read more bytes than the segment size."); - return false; - } + 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; } - 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; + //////////////////////////////////////////////// + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha) + if ( !LutRGBA ) + return; - // Loop on the frame[s] - RLEFrame *frame = RLEInfo->GetFirstFrame(); - while( frame ) + memset( LutRGBA, 0, 1024 ); + + int mult; + if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) ) { - // 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(); + // when LUT item size is different than pixel size + mult = 2; // high byte must be = low byte } - - if ( BitsAllocated == 16 ) + else { - // Try to deal with RLE 16 Bits - (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); + // 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; } - - return true; } /** @@ -299,7 +567,7 @@ void PixelReadConvert::ConvertSwapZone() uint32_t s32; uint16_t high; uint16_t low; - uint32_t* im32 = (uint32_t*)Raw; + uint32_t *im32 = (uint32_t*)Raw; switch ( SwapCode ) { case 1234: @@ -369,39 +637,6 @@ void PixelReadConvert::ConvertReorderEndianity() } } -/** - * \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; - } - - // else ?? - // Precompute the offset localRaw will be shifted with - int length = XSize * YSize * SamplesPerPixel; - int numberBytes = BitsAllocated / 8; - - JPEGInfo->DecompressJPEGFramesFromFile(fp, Raw, BitsStored, numberBytes, length ); - return true; -} - /** * \brief Re-arrange the bits within the bytes. * @return Boolean @@ -415,7 +650,7 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) { uint16_t mask = 0xffff; mask = mask >> ( BitsAllocated - BitsStored ); - uint16_t* deb = (uint16_t*)Raw; + uint16_t *deb = (uint16_t*)Raw; for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; @@ -426,7 +661,7 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) { uint32_t mask = 0xffffffff; mask = mask >> ( BitsAllocated - BitsStored ); - uint32_t* deb = (uint32_t*)Raw; + uint32_t *deb = (uint32_t*)Raw; for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; @@ -442,6 +677,31 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) return true; } +/** + * \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; +} + /** * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels * \warning Works on all the frames at a time @@ -496,114 +756,7 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() 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() +void PixelReadConvert::ConvertHandleColor() { ////////////////////////////////// // Deal with the color decoding i.e. handle: @@ -673,21 +826,6 @@ void PixelReadConvert::ConvertHandleColor() // 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; @@ -712,292 +850,28 @@ void PixelReadConvert::ComputeRawAndRGBSizes() } } -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() +void PixelReadConvert::AllocateRGB() { - 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; - } + if ( RGB ) + delete [] RGB; + RGB = new uint8_t[RGBSize]; } -/** - * \brief Build the RGB image from the Raw imagage and the LUTs. - */ -bool PixelReadConvert::BuildRGBImage() +void PixelReadConvert::AllocateRaw() { - 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; + 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 -------------------------" @@ -1034,6 +908,7 @@ void PixelReadConvert::Print( std::ostream &os, std::string const & indent ) } } +//----------------------------------------------------------------------------- } // end namespace gdcm // NOTES on File internal calls