X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=9338248a130141a5161773f0c6c32536862062c6;hb=1dd2c40c0da9098b444ad53b0e3c23da808997fa;hp=b94a76a82cb57149e26450a1673bafd2d0dd37bb;hpb=a4cff04fcd2023f798a9f1ef6bc9307269abd185;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index b94a76a8..9338248a 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: 2005/01/31 04:00:05 $ + Version: $Revision: 1.39 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -50,21 +50,15 @@ PixelReadConvert::PixelReadConvert() void PixelReadConvert::Squeeze() { if ( RGB ) - { delete [] RGB; - } RGB = 0; if ( Raw ) - { delete [] Raw; - } Raw = 0; if ( LutRGBA ) - { delete [] LutRGBA; - } LutRGBA = 0; } @@ -75,18 +69,16 @@ PixelReadConvert::~PixelReadConvert() 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 +96,21 @@ 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" ); @@ -155,7 +147,7 @@ bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) // 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 ]; + uint8_t* copyRaw = new uint8_t[rawSize * 2]; memmove( copyRaw, Raw, rawSize * 2 ); uint8_t* x = Raw; @@ -251,21 +243,20 @@ bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream *fp ) long RawSegmentSize = XSize * YSize; // Loop on the frame[s] - for( RLEFramesInfo::RLEFrameList::iterator - it = RLEInfo->Frames.begin(); - it != RLEInfo->Frames.end(); - ++it ) + RLEFrame *frame = RLEInfo->GetFirstFrame(); + while( frame ) { // Loop on the fragments - for( unsigned int k = 1; k <= (*it)->GetNumberOfFragments(); k++ ) + for( unsigned int k = 1; k <= frame->GetNumberOfFragments(); k++ ) { - fp->seekg( (*it)->GetOffset(k) , std::ios::beg ); - (void)ReadAndDecompressRLEFragment( subRaw, - (*it)->GetLength(k), - RawSegmentSize, - fp ); + fp->seekg(frame->GetOffset(k),std::ios::beg); + ReadAndDecompressRLEFragment(subRaw, + frame->GetLength(k), + RawSegmentSize, + fp); subRaw += RawSegmentSize; } + frame = RLEInfo->GetNexttFrame(); } if ( BitsAllocated == 16 ) @@ -378,115 +369,6 @@ 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 +380,26 @@ 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->DecompressJPEGFramesFromFile(fp, Raw, BitsStored, numberBytes, length ); + return true; } /** @@ -664,7 +524,7 @@ 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(); @@ -852,41 +712,41 @@ 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 +759,25 @@ 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 +794,24 @@ 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 +902,8 @@ 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;