X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=27ff8e2b83384398ebb43b587b4f63467d724c31;hb=7350639601914cd8ab02bfb0d6668c5bf56ce2f4;hp=b94a76a82cb57149e26450a1673bafd2d0dd37bb;hpb=a4cff04fcd2023f798a9f1ef6bc9307269abd185;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index b94a76a8..27ff8e2b 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/01/26 11:42:02 $ - Version: $Revision: 1.35 $ + Date: $Date: 2005/02/01 10:29:55 $ + Version: $Revision: 1.43 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -30,9 +30,9 @@ namespace gdcm { +//----------------------------------------------------------------------------- #define str2num(str, typeNum) *((typeNum *)(str)) - //----------------------------------------------------------------------------- // Constructor / Destructor PixelReadConvert::PixelReadConvert() @@ -47,46 +47,40 @@ PixelReadConvert::PixelReadConvert() LutBlueData =0; } +PixelReadConvert::~PixelReadConvert() +{ + Squeeze(); +} + +//----------------------------------------------------------------------------- +// Public 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 ) { + if ( RGB ) delete [] RGB; - } - RGB = new uint8_t[ RGBSize ]; + RGB = new uint8_t[RGBSize]; } void PixelReadConvert::AllocateRaw() { - if ( Raw ) { + if ( Raw ) delete [] Raw; - } - Raw = new uint8_t[ RawSize ]; + Raw = new uint8_t[RawSize]; } /** @@ -104,21 +98,21 @@ void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) uint8_t b0, b1, b2; fp->read( (char*)&b0, 1); - if ( fp->fail() || fp->eof() )//Fp->gcount() == 1 + if ( fp->fail() || fp->eof() ) { throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound first block" ); } fp->read( (char*)&b1, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + if ( fp->fail() || fp->eof()) { throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound second block" ); } fp->read( (char*)&b2, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + if ( fp->fail() || fp->eof()) { throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", "Unfound second block" ); @@ -137,145 +131,6 @@ 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) - * @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] - for( RLEFramesInfo::RLEFrameList::iterator - it = RLEInfo->Frames.begin(); - it != RLEInfo->Frames.end(); - ++it ) - { - // Loop on the fragments - for( unsigned int k = 1; k <= (*it)->GetNumberOfFragments(); k++ ) - { - fp->seekg( (*it)->GetOffset(k) , std::ios::beg ); - (void)ReadAndDecompressRLEFragment( subRaw, - (*it)->GetLength(k), - RawSegmentSize, - fp ); - subRaw += RawSegmentSize; - } - } - - if ( BitsAllocated == 16 ) - { - // Try to deal with RLE 16 Bits - (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); - } - - return true; -} /** * \brief Swap the bytes, according to \ref SwapCode. @@ -378,115 +233,6 @@ void PixelReadConvert::ConvertReorderEndianity() } } - -/** - * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated - * file and decompress it. This function assumes that each - * jpeg fragment contains a whole frame (jpeg file). - * @param fp File Pointer - * @return Boolean - */ -bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream *fp ) -{ - // Pointer to the Raw image - //uint8_t *localRaw = Raw; - - // Precompute the offset localRaw will be shifted with - int length = XSize * YSize * SamplesPerPixel; - int numberBytes = BitsAllocated / 8; - -// // Loop on the fragment[s] -// for( JPEGFragmentsInfo::JPEGFragmentsList::iterator -// it = JPEGInfo->Fragments.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 - JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it = JPEGInfo->Fragments.begin(); - (*it)->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; - - JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it; - for( it = JPEGInfo->Fragments.begin() ; - (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength); - ++it ) - { - fragmentLength += (*it)->GetLength(); - - if (howManyRead > fragmentLength) continue; - - (*it)->DecompressJPEGFragmentedFramesFromFile(buffer, Raw, BitsStored, howManyRead, howManyWritten, totalLength); - - if (howManyRead < fragmentLength) - howManyRead = fragmentLength; - } - - // free local buffer - delete [] buffer; - - return true; -} - /** * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated * file and decompress it. @@ -498,48 +244,26 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) if ( IsJPEG2000 ) { gdcmVerboseMacro( "Sorry, JPEG2000 not yet taken into account" ); - fp->seekg( (*JPEGInfo->Fragments.begin())->GetOffset(), std::ios::beg); + fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg); // if ( ! gdcm_read_JPEG2000_file( fp,Raw ) ) - gdcmVerboseMacro( "Wrong Blue LUT descriptor" ); return false; } if ( IsJPEGLS ) { gdcmVerboseMacro( "Sorry, JPEG-LS not yet taken into account" ); - fp->seekg( (*JPEGInfo->Fragments.begin())->GetOffset(), std::ios::beg); + fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg); // if ( ! gdcm_read_JPEGLS_file( fp,Raw ) ) return false; } - 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) - { - } -// 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; } /** @@ -664,7 +388,7 @@ void PixelReadConvert::ConvertRGBPlanesToRGBPixels() bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) { // ComputeRawAndRGBSizes is already made by - // ::GrabInformationsFromHeader. So, the structure sizes are + // ::GrabInformationsFromfile. So, the structure sizes are // correct Squeeze(); @@ -718,7 +442,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) } else if ( IsRLELossless ) { - if ( ! ReadAndDecompressRLEFile( fp ) ) + if ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) { gdcmVerboseMacro( "RLE decompressor failed." ); return false; @@ -852,41 +576,41 @@ void PixelReadConvert::ComputeRawAndRGBSizes() } } -void PixelReadConvert::GrabInformationsFromHeader( File *header ) +void PixelReadConvert::GrabInformationsFromFile( File *file ) { // Number of Bits Allocated for storing a Pixel is defaulted to 16 - // when absent from the header. - BitsAllocated = header->GetBitsAllocated(); + // 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 header. - BitsStored = header->GetBitsStored(); + // when absent from the file. + BitsStored = file->GetBitsStored(); if ( BitsStored == 0 ) { BitsStored = BitsAllocated; } // High Bit Position, defaulted to "Bits Allocated" - 1 - HighBitPosition = header->GetHighBitPosition(); + HighBitPosition = file->GetHighBitPosition(); if ( HighBitPosition == 0 ) { HighBitPosition = BitsAllocated - 1; } - XSize = header->GetXSize(); - YSize = header->GetYSize(); - ZSize = header->GetZSize(); - SamplesPerPixel = header->GetSamplesPerPixel(); - PixelSize = header->GetPixelSize(); - PixelSign = header->IsSignedPixelData(); - SwapCode = header->GetSwapCode(); - std::string ts = header->GetTransferSyntax(); + 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 = - ( ! header->IsDicomV3() ) + ( ! file->IsDicomV3() ) || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndianDLXGE || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian @@ -899,25 +623,25 @@ void PixelReadConvert::GrabInformationsFromHeader( File *header ) IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts); IsRLELossless = Global::GetTS()->IsRLELossless(ts); - PixelOffset = header->GetPixelOffset(); - PixelDataLength = header->GetPixelAreaLength(); - RLEInfo = header->GetRLEInfo(); - JPEGInfo = header->GetJPEGInfo(); - - PlanarConfiguration = header->GetPlanarConfiguration(); - IsMonochrome = header->IsMonochrome(); - IsPaletteColor = header->IsPaletteColor(); - IsYBRFull = header->IsYBRFull(); + 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 = header->HasLUT(); + HasLUT = file->HasLUT(); if ( HasLUT ) { // Just in case some access to a File element requires disk access. - LutRedDescriptor = header->GetEntryValue( 0x0028, 0x1101 ); - LutGreenDescriptor = header->GetEntryValue( 0x0028, 0x1102 ); - LutBlueDescriptor = header->GetEntryValue( 0x0028, 0x1103 ); + 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 @@ -934,24 +658,24 @@ void PixelReadConvert::GrabInformationsFromHeader( File *header ) /// parsed from. Fix that. FIXME. ////// Red round - header->LoadEntryBinArea(0x0028, 0x1201); - LutRedData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1201 ); + file->LoadEntryBinArea(0x0028, 0x1201); + LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 ); if ( ! LutRedData ) { gdcmVerboseMacro( "Unable to read Red LUT data" ); } ////// Green round: - header->LoadEntryBinArea(0x0028, 0x1202); - LutGreenData = (uint8_t*)header->GetEntryBinArea(0x0028, 0x1202 ); + file->LoadEntryBinArea(0x0028, 0x1202); + LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 ); if ( ! LutGreenData) { gdcmVerboseMacro( "Unable to read Green LUT data" ); } ////// Blue round: - header->LoadEntryBinArea(0x0028, 0x1203); - LutBlueData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1203 ); + file->LoadEntryBinArea(0x0028, 0x1203); + LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 ); if ( ! LutBlueData ) { gdcmVerboseMacro( "Unable to read Blue LUT data" ); @@ -1042,9 +766,8 @@ void PixelReadConvert::BuildLUTRGBA() // 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; @@ -1133,6 +856,14 @@ bool PixelReadConvert::BuildRGBImage() return true; } +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private + +//----------------------------------------------------------------------------- +// Print /** * \brief Print self. * @param indent Indentation string to be prepended during printing. @@ -1175,6 +906,7 @@ void PixelReadConvert::Print( std::ostream &os, std::string const & indent ) } } +//----------------------------------------------------------------------------- } // end namespace gdcm // NOTES on File internal calls