X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=8c8bd2db17eb8562e3f25e371f6932419538095d;hb=0e0403151bbff57175d2b974ee2d14b8195f9234;hp=840465ab67855a5ff1ae52178168b9aee96770ef;hpb=38e48f549e7510ba0b5114ab79f91f528757a36d;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 840465ab..8c8bd2db 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -1,10 +1,10 @@ /*========================================================================= - + Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2004/12/09 10:11:38 $ - Version: $Revision: 1.4 $ + Date: $Date: 2005/01/31 03:22:26 $ + Version: $Revision: 1.38 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,14 +16,10 @@ =========================================================================*/ -////////////////// TEMPORARY NOTE -// look for "fixMem" and convert that to a member of this class -// Removing the prefix fixMem and dealing with allocations should do the trick -// -// grep PixelReadConvert everywhere and clean up ! - #include "gdcmDebug.h" -#include "gdcmHeader.h" +#include "gdcmFile.h" +#include "gdcmGlobal.h" +#include "gdcmTS.h" #include "gdcmPixelReadConvert.h" #include "gdcmDocEntry.h" #include "gdcmRLEFramesInfo.h" @@ -36,20 +32,6 @@ namespace gdcm { #define str2num(str, typeNum) *((typeNum *)(str)) -// For JPEG 2000, body in file gdcmJpeg2000.cxx -bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer); - -// For JPEG 8 Bits, body in file gdcmJpeg8.cxx -bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer); - -// For JPEG 12 Bits, body in file gdcmJpeg12.cxx -bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer); - -// For JPEG 16 Bits, body in file gdcmJpeg16.cxx -// Beware this is misleading there is no 16bits DCT algorithm, only -// jpeg lossless compression exist in 16bits. -bool gdcm_read_JPEG_file16 (std::ifstream* fp, void* image_buffer); - //----------------------------------------------------------------------------- // Constructor / Destructor @@ -57,8 +39,8 @@ PixelReadConvert::PixelReadConvert() { RGB = 0; RGBSize = 0; - Decompressed = 0; - DecompressedSize = 0; + Raw = 0; + RawSize = 0; LutRGBA = 0; LutRedData = 0; LutGreenData = 0; @@ -68,21 +50,15 @@ PixelReadConvert::PixelReadConvert() void PixelReadConvert::Squeeze() { if ( RGB ) - { delete [] RGB; - } RGB = 0; - if ( Decompressed ) - { - delete [] Decompressed; - } - Decompressed = 0; + if ( Raw ) + delete [] Raw; + Raw = 0; if ( LutRGBA ) - { delete [] LutRGBA; - } LutRGBA = 0; } @@ -93,29 +69,27 @@ PixelReadConvert::~PixelReadConvert() void PixelReadConvert::AllocateRGB() { - if ( RGB ) { + if ( RGB ) delete [] RGB; - } - RGB = new uint8_t[ RGBSize ]; + RGB = new uint8_t[RGBSize]; } -void PixelReadConvert::AllocateDecompressed() +void PixelReadConvert::AllocateRaw() { - if ( Decompressed ) { - delete [] Decompressed; - } - Decompressed = new uint8_t[ DecompressedSize ]; + if ( Raw ) + delete [] Raw; + Raw = new uint8_t[RawSize]; } /** * \brief Read from file a 12 bits per pixel image and decompress it * into a 16 bits per pixel image. */ -void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp ) +void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) throw ( FormatError ) { int nbPixels = XSize * YSize; - uint16_t* localDecompres = (uint16_t*)Decompressed; + uint16_t* localDecompres = (uint16_t*)Raw; for( int p = 0; p < nbPixels; p += 2 ) { @@ -157,39 +131,39 @@ void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp ) /** * \brief Try to deal with RLE 16 Bits. - * We assume the RLE has allready been parsed and loaded in - * Decompressed (through \ref ReadAndDecompressJPEGFile ). + * 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 decompressedSize = XSize * YSize * NumberOfFrames; + size_t pixelNumber = XSize * YSize; + size_t rawSize = XSize * YSize * NumberOfFrames; - // We assumed Decompressed contains the decoded RLE pixels but as + // 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 Decompressed and hence - // we copy it in a safe place, say copyDecompressed. + // per pixel we cannot work in place within Raw and hence + // we copy it in a safe place, say copyRaw. - uint8_t* copyDecompressed = new uint8_t[ decompressedSize * 2 ]; - memmove( copyDecompressed, Decompressed, decompressedSize * 2 ); + uint8_t* copyRaw = new uint8_t[rawSize * 2]; + memmove( copyRaw, Raw, rawSize * 2 ); - uint8_t* x = Decompressed; - uint8_t* a = copyDecompressed; - uint8_t* b = a + PixelNumber; + 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++ ) + for ( unsigned int j = 0; j < pixelNumber; j++ ) { *(x++) = *(b++); *(x++) = *(a++); } } - delete[] copyDecompressed; + delete[] copyRaw; /// \todo check that operator new []didn't fail, and sometimes return false return true; @@ -198,24 +172,24 @@ bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) /** * \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 subDecompressed Sub region of \ref Decompressed where the de - * decoded fragment should be placed. + * @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 decompressedSegmentSize The expected length of the fragment ONCE - * decompressed. + * @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* subDecompressed, +bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t *subRaw, long fragmentSize, - long decompressedSegmentSize, - std::ifstream* fp ) + long RawSegmentSize, + std::ifstream *fp ) { int8_t count; long numberOfOutputBytes = 0; long numberOfReadBytes = 0; - while( numberOfOutputBytes < decompressedSegmentSize ) + while( numberOfOutputBytes < RawSegmentSize ) { fp->read( (char*)&count, 1 ); numberOfReadBytes += 1; @@ -225,9 +199,9 @@ bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed, // signed integer of width N is 2^(N-1) - 1, which for int8_t // is 127]. { - fp->read( (char*)subDecompressed, count + 1); + fp->read( (char*)subRaw, count + 1); numberOfReadBytes += count + 1; - subDecompressed += count + 1; + subRaw += count + 1; numberOfOutputBytes += count + 1; } else @@ -239,9 +213,9 @@ bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed, numberOfReadBytes += 1; for( int i = 0; i < -count + 1; i++ ) { - subDecompressed[i] = newByte; + subRaw[i] = newByte; } - subDecompressed += -count + 1; + subRaw += -count + 1; numberOfOutputBytes += -count + 1; } } @@ -249,8 +223,7 @@ bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed, if ( numberOfReadBytes > fragmentSize ) { - dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we " - "read more bytes than the segment size."); + gdcmVerboseMacro( "Read more bytes than the segment size."); return false; } } @@ -264,27 +237,26 @@ bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed, * at which the pixel data should be copied * @return Boolean */ -bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp ) +bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream *fp ) { - uint8_t* subDecompressed = Decompressed; - long decompressedSegmentSize = XSize * YSize; + 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 ) + RLEFrame *frame = RLEInfo->GetFirstFrame(); + while( frame ) { // Loop on the fragments - for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ ) + for( unsigned int k = 1; k <= frame->GetNumberOfFragments(); k++ ) { - fp->seekg( (*it)->Offset[k] , std::ios::beg ); - (void)ReadAndDecompressRLEFragment( subDecompressed, - (*it)->Length[k], - decompressedSegmentSize, - fp ); - subDecompressed += decompressedSegmentSize; + fp->seekg(frame->GetOffset(k),std::ios::beg); + ReadAndDecompressRLEFragment(subRaw, + frame->GetLength(k), + RawSegmentSize, + fp); + subRaw += RawSegmentSize; } + frame = RLEInfo->GetNexttFrame(); } if ( BitsAllocated == 16 ) @@ -305,25 +277,21 @@ void PixelReadConvert::ConvertSwapZone() if( BitsAllocated == 16 ) { - uint16_t* im16 = (uint16_t*)Decompressed; + uint16_t *im16 = (uint16_t*)Raw; switch( SwapCode ) { - case 0: - case 12: case 1234: break; - case 21: case 3412: case 2143: case 4321: - for( i = 0; i < DecompressedSize / 2; i++ ) + for( i = 0; i < RawSize / 2; i++ ) { im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); } break; default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(16 bits) not allowed." ); + gdcmVerboseMacro("SwapCode value (16 bits) not allowed."); } } else if( BitsAllocated == 32 ) @@ -331,14 +299,13 @@ void PixelReadConvert::ConvertSwapZone() uint32_t s32; uint16_t high; uint16_t low; - uint32_t* im32 = (uint32_t*)Decompressed; + uint32_t* im32 = (uint32_t*)Raw; switch ( SwapCode ) { - case 0: case 1234: break; case 4321: - for( i = 0; i < DecompressedSize / 4; i++ ) + for( i = 0; i < RawSize / 4; i++ ) { low = im32[i] & 0x0000ffff; // 4321 high = im32[i] >> 16; @@ -349,7 +316,7 @@ void PixelReadConvert::ConvertSwapZone() } break; case 2143: - for( i = 0; i < DecompressedSize / 4; i++ ) + for( i = 0; i < RawSize / 4; i++ ) { low = im32[i] & 0x0000ffff; // 2143 high = im32[i] >> 16; @@ -360,7 +327,7 @@ void PixelReadConvert::ConvertSwapZone() } break; case 3412: - for( i = 0; i < DecompressedSize / 4; i++ ) + for( i = 0; i < RawSize / 4; i++ ) { low = im32[i] & 0x0000ffff; // 3412 high = im32[i] >> 16; @@ -369,14 +336,13 @@ void PixelReadConvert::ConvertSwapZone() } break; default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(32 bits) not allowed." ); + gdcmVerboseMacro("SwapCode value (32 bits) not allowed." ); } } } /** - * \brief Deal with endianity i.e. re-arange bytes inside the integer + * \brief Deal with endianness i.e. re-arange bytes inside the integer */ void PixelReadConvert::ConvertReorderEndianity() { @@ -386,12 +352,12 @@ void PixelReadConvert::ConvertReorderEndianity() } // Special kludge in order to deal with xmedcon broken images: - if ( ( BitsAllocated == 16 ) - && ( BitsStored < BitsAllocated ) - && ( ! PixelSign ) ) + if ( BitsAllocated == 16 + && BitsStored < BitsAllocated + && !PixelSign ) { - int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) ); - uint16_t *deb = (uint16_t *)Decompressed; + int l = (int)( RawSize / ( BitsAllocated / 8 ) ); + uint16_t *deb = (uint16_t *)Raw; for(int i = 0; iFragments.begin(); - it != JPEGInfo->Fragments.end(); - ++it ) + if ( IsJPEG2000 ) { - fp->seekg( (*it)->Offset, std::ios::beg); + 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 ( IsJPEG2000 ) - { - if ( ! gdcm_read_JPEG2000_file( fp,localDecompressed ) ) - { - return false; - } - } - else if ( BitsStored == 8) - { - // JPEG Lossy : call to IJG 6b - if ( ! gdcm_read_JPEG_file8( fp, localDecompressed ) ) - { - return false; - } - } - else if ( BitsStored <= 12) - { - // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file12 ( fp, localDecompressed ) ) - { - return false; - } - } - else if ( BitsStored <= 16) - { - // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file16 ( fp, localDecompressed ) ) - { - return false; - } - //assert( IsJPEGLossless ); - } - else - { - // other JPEG lossy not supported - dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown " - "jpeg lossy compression "); + 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; - } + } - // Advance to next free location in Decompressed - // for next fragment decompression (if any) - int length = XSize * YSize * SamplesPerPixel; - int numberBytes = BitsAllocated / 8; + // else ?? + // Precompute the offset localRaw will be shifted with + int length = XSize * YSize * SamplesPerPixel; + int numberBytes = BitsAllocated / 8; - localDecompressed += length * numberBytes; - } + JPEGInfo->DecompressJPEGFramesFromFile(fp, Raw, BitsStored, numberBytes, length ); return true; } @@ -478,12 +410,12 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) { if ( BitsStored != BitsAllocated ) { - int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) ); + int l = (int)( RawSize / ( BitsAllocated / 8 ) ); if ( BitsAllocated == 16 ) { uint16_t mask = 0xffff; mask = mask >> ( BitsAllocated - BitsStored ); - uint16_t* deb = (uint16_t*)Decompressed; + uint16_t* deb = (uint16_t*)Raw; for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; @@ -494,7 +426,7 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) { uint32_t mask = 0xffffffff; mask = mask >> ( BitsAllocated - BitsStored ); - uint32_t* deb = (uint32_t*)Decompressed; + uint32_t* deb = (uint32_t*)Raw; for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; @@ -503,23 +435,22 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) } else { - dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image"); - throw FormatError( "PixelReadConvert::ConvertReArrangeBits()", - "weird image !?" ); + gdcmVerboseMacro("Weird image"); + throw FormatError( "Weird image !?" ); } } return true; } /** - * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels + * \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* localDecompressed = Decompressed; - uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ]; - memmove( copyDecompressed, localDecompressed, DecompressedSize ); + 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 : @@ -529,9 +460,9 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() int l = XSize * YSize; int nbFrames = ZSize; - uint8_t* a = copyDecompressed; - uint8_t* b = copyDecompressed + l; - uint8_t* c = copyDecompressed + l + l; + 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 @@ -554,15 +485,15 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() if (G > 255.0) G = 255.0; if (B > 255.0) B = 255.0; - *(localDecompressed++) = (uint8_t)R; - *(localDecompressed++) = (uint8_t)G; - *(localDecompressed++) = (uint8_t)B; + *(localRaw++) = (uint8_t)R; + *(localRaw++) = (uint8_t)G; + *(localRaw++) = (uint8_t)B; a++; b++; c++; } } - delete[] copyDecompressed; + delete[] copyRaw; } /** @@ -571,29 +502,29 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() */ void PixelReadConvert::ConvertRGBPlanesToRGBPixels() { - uint8_t* localDecompressed = Decompressed; - uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ]; - memmove( copyDecompressed, localDecompressed, DecompressedSize ); + uint8_t *localRaw = Raw; + uint8_t *copyRaw = new uint8_t[ RawSize ]; + memmove( copyRaw, localRaw, RawSize ); int l = XSize * YSize * ZSize; - uint8_t* a = copyDecompressed; - uint8_t* b = copyDecompressed + l; - uint8_t* c = copyDecompressed + l + l; + uint8_t* a = copyRaw; + uint8_t* b = copyRaw + l; + uint8_t* c = copyRaw + l + l; for (int j = 0; j < l; j++) { - *(localDecompressed++) = *(a++); - *(localDecompressed++) = *(b++); - *(localDecompressed++) = *(c++); + *(localRaw++) = *(a++); + *(localRaw++) = *(b++); + *(localRaw++) = *(c++); } - delete[] copyDecompressed; + delete[] copyRaw; } -bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) +bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) { - // ComputeDecompressedAndRGBSizes is already made by - // ::GrabInformationsFromHeader. So, the structure sizes are + // ComputeRawAndRGBSizes is already made by + // ::GrabInformationsFromfile. So, the structure sizes are // correct Squeeze(); @@ -601,20 +532,18 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) //// First stage: get our hands on the Pixel Data. if ( !fp ) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "unavailable file pointer." ); + gdcmVerboseMacro( "Unavailable file pointer." ); return false; } fp->seekg( PixelOffset, std::ios::beg ); - if( fp->fail() || fp->eof()) //Fp->gcount() == 1 + if( fp->fail() || fp->eof()) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "unable to find PixelOffset in file." ); + gdcmVerboseMacro( "Unable to find PixelOffset in file." ); return false; } - AllocateDecompressed(); + AllocateRaw(); ////////////////////////////////////////////////// //// Second stage: read from disk dans decompress. @@ -622,30 +551,28 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) { ReadAndDecompress12BitsTo16Bits( fp); } - else if ( IsDecompressed ) + else if ( IsRaw ) { // This problem can be found when some obvious informations are found - // after the field containing the image datas. In this case, these - // bad datas are added to the size of the image (in the PixelDataLength - // variable). But DecompressedSize is the right size of the image ! - if( PixelDataLength != DecompressedSize) + // 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) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "Mismatch between PixelReadConvert and DecompressedSize." ); + gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." ); } - if( PixelDataLength > DecompressedSize) + if( PixelDataLength > RawSize) { - fp->read( (char*)Decompressed, DecompressedSize); + fp->read( (char*)Raw, RawSize); } else { - fp->read( (char*)Decompressed, PixelDataLength); + fp->read( (char*)Raw, PixelDataLength); } - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + if ( fp->fail() || fp->eof()) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "reading of decompressed pixel data failed." ); + gdcmVerboseMacro( "Reading of Raw pixel data failed." ); return false; } } @@ -653,8 +580,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) { if ( ! ReadAndDecompressRLEFile( fp ) ) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "RLE decompressor failed." ); + gdcmVerboseMacro( "RLE decompressor failed." ); return false; } } @@ -663,8 +589,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) // Default case concerns JPEG family if ( ! ReadAndDecompressJPEGFile( fp ) ) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "JPEG decompressor failed." ); + gdcmVerboseMacro( "JPEG decompressor failed." ); return false; } } @@ -705,7 +630,7 @@ void PixelReadConvert::ConvertHandleColor() // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter: // - "Planar Configuration" = 0, // - "Photometric Interpretation" = "PALETTE COLOR". - // Hence gdcm shall use the folowing "heuristic" in order to be tolerant + // 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 @@ -718,7 +643,7 @@ void PixelReadConvert::ConvertHandleColor() // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels() // - [Planar 2] OR [Photo D] requires LUT intervention. - if ( ! IsDecompressedRGB() ) + if ( ! IsRawRGB() ) { // [Planar 2] OR [Photo D]: LUT intervention done outside return; @@ -749,10 +674,10 @@ void PixelReadConvert::ConvertHandleColor() } /** - * \brief Predicate to know wether the image[s] (once decompressed) is RGB. + * \brief Predicate to know wether the image[s] (once Raw) is RGB. * \note See comments of \ref ConvertHandleColor */ -bool PixelReadConvert::IsDecompressedRGB() +bool PixelReadConvert::IsRawRGB() { if ( IsMonochrome || PlanarConfiguration == 2 @@ -763,7 +688,7 @@ bool PixelReadConvert::IsDecompressedRGB() return true; } -void PixelReadConvert::ComputeDecompressedAndRGBSizes() +void PixelReadConvert::ComputeRawAndRGBSizes() { int bitsAllocated = BitsAllocated; // Number of "Bits Allocated" is fixed to 16 when it's 12, since @@ -774,90 +699,93 @@ void PixelReadConvert::ComputeDecompressedAndRGBSizes() bitsAllocated = 16; } - DecompressedSize = XSize * YSize * ZSize + RawSize = XSize * YSize * ZSize * ( bitsAllocated / 8 ) * SamplesPerPixel; if ( HasLUT ) { - RGBSize = 3 * DecompressedSize; + RGBSize = 3 * RawSize; } else { - RGBSize = DecompressedSize; + RGBSize = RawSize; } } -void PixelReadConvert::GrabInformationsFromHeader( Header* 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(); + // 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 - HighBitPosition = header->GetHighBitPosition(); + // High Bit Position, defaulted to "Bits Allocated" - 1 + 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(); - TransferSyntaxType ts = header->GetTransferSyntax(); - IsDecompressed = - ( ! header->IsDicomV3() ) - || ts == ImplicitVRLittleEndian - || ts == ImplicitVRLittleEndianDLXGE - || ts == ExplicitVRLittleEndian - || ts == ExplicitVRBigEndian - || ts == DeflatedExplicitVRLittleEndian; - IsJPEG2000 = header->IsJPEG2000(); - IsJPEGLossless = header->IsJPEGLossless(); - IsRLELossless = ( ts == RLELossless ); - PixelOffset = header->GetPixelOffset(); - PixelDataLength = header->GetPixelAreaLength(); - RLEInfo = header->GetRLEInfo(); - JPEGInfo = header->GetJPEGInfo(); - - PlanarConfiguration = header->GetPlanarConfiguration(); - IsMonochrome = header->IsMonochrome(); - IsPaletteColor = header->IsPaletteColor(); - IsYBRFull = header->IsYBRFull(); + 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 = header->HasLUT(); + HasLUT = file->HasLUT(); if ( HasLUT ) { - // Just in case some access to a Header element requires disk access. - // Note: gdcmDocument::Fp is leaved open after OpenFile. - LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 ); - LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 ); - LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 ); + // 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 header - // and when this fails we read the LUTs data directely from disk. - /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge. + // 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 @@ -866,38 +794,35 @@ void PixelReadConvert::GrabInformationsFromHeader( Header* header ) /// parsed from. Fix that. FIXME. ////// Red round - header->LoadEntryBinArea(0x0028, 0x1201); - LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 ); + file->LoadEntryBinArea(0x0028, 0x1201); + LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 ); if ( ! LutRedData ) { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read red LUT data" ); + gdcmVerboseMacro( "Unable to read Red LUT data" ); } ////// Green round: - header->LoadEntryBinArea(0x0028, 0x1202); - LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 ); + file->LoadEntryBinArea(0x0028, 0x1202); + LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 ); if ( ! LutGreenData) { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read green LUT data" ); + gdcmVerboseMacro( "Unable to read Green LUT data" ); } ////// Blue round: - header->LoadEntryBinArea(0x0028, 0x1203); - LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 ); + file->LoadEntryBinArea(0x0028, 0x1203); + LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 ); if ( ! LutBlueData ) { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read blue LUT data" ); + gdcmVerboseMacro( "Unable to read Blue LUT data" ); } } - ComputeDecompressedAndRGBSizes(); + ComputeRawAndRGBSizes(); } /** - * \brief Build Red/Green/Blue/Alpha LUT from Header + * \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 @@ -942,7 +867,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthR, &debR, &nbitsR ); if( nbRead != 3 ) { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor"); + gdcmVerboseMacro( "Wrong Red LUT descriptor" ); } int lengthG; // Green LUT length in Bytes @@ -953,7 +878,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthG, &debG, &nbitsG ); if( nbRead != 3 ) { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor"); + gdcmVerboseMacro( "Wrong Green LUT descriptor" ); } int lengthB; // Blue LUT length in Bytes @@ -964,7 +889,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthB, &debB, &nbitsB ); if( nbRead != 3 ) { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor"); + gdcmVerboseMacro( "Wrong Blue LUT descriptor" ); } //////////////////////////////////////////////////////// @@ -977,9 +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; @@ -999,7 +923,7 @@ void PixelReadConvert::BuildLUTRGBA() // 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 + // We give up the checking to avoid some (useless ?) overhead // (optimistic asumption) int i; uint8_t* a = LutRGBA + 0; @@ -1032,7 +956,7 @@ void PixelReadConvert::BuildLUTRGBA() } /** - * \brief Build the RGB image from the Decompressed imagage and the LUTs. + * \brief Build the RGB image from the Raw imagage and the LUTs. */ bool PixelReadConvert::BuildRGBImage() { @@ -1042,7 +966,7 @@ bool PixelReadConvert::BuildRGBImage() return true; } - if ( ! Decompressed ) + if ( ! Raw ) { // The job can't be done return false; @@ -1058,9 +982,9 @@ bool PixelReadConvert::BuildRGBImage() // Build RGB Pixels AllocateRGB(); uint8_t* localRGB = RGB; - for (size_t i = 0; i < DecompressedSize; ++i ) + for (size_t i = 0; i < RawSize; ++i ) { - int j = Decompressed[i] * 4; + int j = Raw[i] * 4; *localRGB++ = LutRGBA[j]; *localRGB++ = LutRGBA[j+1]; *localRGB++ = LutRGBA[j+2]; @@ -1073,41 +997,39 @@ bool PixelReadConvert::BuildRGBImage() * @param indent Indentation string to be prepended during printing. * @param os Stream to print to. */ -void PixelReadConvert::Print( std::string indent, std::ostream &os ) +void PixelReadConvert::Print( std::ostream &os, std::string const & indent ) { os << indent << "--- Pixel information -------------------------" << std::endl; os << indent << "Pixel Data: offset " << PixelOffset - << " x" << std::hex << PixelOffset << std::dec - << " length " << PixelDataLength - << " x" << std::hex << PixelDataLength << std::dec - << std::endl; + << " x(" << std::hex << PixelOffset << std::dec + << ") length " << PixelDataLength + << " x(" << std::hex << PixelDataLength << std::dec + << ")" << std::endl; if ( IsRLELossless ) { if ( RLEInfo ) { - RLEInfo->Print( indent, os ); + RLEInfo->Print( os, indent ); } else { - dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file " - "but NO RLEinfo present."); + gdcmVerboseMacro("Set as RLE file but NO RLEinfo present."); } } - if ( IsJPEG2000 || IsJPEGLossless ) + if ( IsJPEG2000 || IsJPEGLossless || IsJPEGLossy || IsJPEGLS ) { if ( JPEGInfo ) { - JPEGInfo->Print( indent, os ); + JPEGInfo->Print( os, indent ); } else { - dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file " - "but NO JPEGinfo present."); + gdcmVerboseMacro("Set as JPEG file but NO JPEGinfo present."); } } } @@ -1123,3 +1045,4 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) // User // ---> GetImageDataRaw // ---> GetImageDataIntoVectorRaw +