X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=9ef62cd05b34fabe0e113d1bc2cfb20b400757ad;hb=35d345304e70ddd87907ab52018ca992eb360e87;hp=d4c57abfb1f7cd21b0f55cd2eec75b323946a238;hpb=2bb60efea83f2bfa1823f27b2a5536a0e6cfd8c0;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index d4c57abf..9ef62cd0 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -1,10 +1,10 @@ /*========================================================================= - + Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2004/12/03 10:21:55 $ - Version: $Revision: 1.1 $ + Date: $Date: 2005/01/12 15:22:23 $ + Version: $Revision: 1.25 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,9 +23,16 @@ // grep PixelReadConvert everywhere and clean up ! #include "gdcmDebug.h" +#include "gdcmHeader.h" +#include "gdcmGlobal.h" +#include "gdcmTS.h" #include "gdcmPixelReadConvert.h" +#include "gdcmDocEntry.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" + #include -#include +#include //for sscanf namespace gdcm { @@ -34,16 +41,26 @@ namespace gdcm // For JPEG 2000, body in file gdcmJpeg2000.cxx bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer); +#define JOCTET uint8_t // For JPEG 8 Bits, body in file gdcmJpeg8.cxx -bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer); - +bool gdcm_read_JPEG_file8 (std::ifstream *fp, void *image_buffer); +bool gdcm_read_JPEG_memory8 (const JOCTET *buffer, const size_t buflen, + void *image_buffer, + size_t *howManyRead, size_t *howManyWritten); +// // For JPEG 12 Bits, body in file gdcmJpeg12.cxx -bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer); +bool gdcm_read_JPEG_file12 (std::ifstream *fp, void *image_buffer); +bool gdcm_read_JPEG_memory12 (const JOCTET *buffer, const size_t buflen, + void *image_buffer, + size_t *howManyRead, size_t *howManyWritten); // 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); +bool gdcm_read_JPEG_file16 (std::ifstream *fp, void *image_buffer); +bool gdcm_read_JPEG_memory16 (const JOCTET *buffer, const size_t buflen, + void* image_buffer, + size_t *howManyRead, size_t *howManyWritten); //----------------------------------------------------------------------------- @@ -52,8 +69,8 @@ PixelReadConvert::PixelReadConvert() { RGB = 0; RGBSize = 0; - Decompressed = 0; - DecompressedSize = 0; + Raw = 0; + RawSize = 0; LutRGBA = 0; LutRedData = 0; LutGreenData = 0; @@ -68,11 +85,11 @@ void PixelReadConvert::Squeeze() } RGB = 0; - if ( Decompressed ) + if ( Raw ) { - delete [] Decompressed; + delete [] Raw; } - Decompressed = 0; + Raw = 0; if ( LutRGBA ) { @@ -94,23 +111,23 @@ void PixelReadConvert::AllocateRGB() RGB = new uint8_t[ RGBSize ]; } -void PixelReadConvert::AllocateDecompressed() +void PixelReadConvert::AllocateRaw() { - if ( Decompressed ) { - delete [] Decompressed; + if ( Raw ) { + delete [] Raw; } - Decompressed = new uint8_t[ DecompressedSize ]; + 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 ) { @@ -152,39 +169,39 @@ 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; @@ -193,24 +210,24 @@ 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 + * @param subRaw Sub region of \ref Raw where the de * 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; @@ -220,9 +237,9 @@ 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 @@ -234,9 +251,9 @@ 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; } } @@ -244,8 +261,7 @@ 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; } } @@ -259,10 +275,10 @@ 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 @@ -274,11 +290,11 @@ bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp ) for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ ) { fp->seekg( (*it)->Offset[k] , std::ios::beg ); - (void)ReadAndDecompressRLEFragment( subDecompressed, + (void)ReadAndDecompressRLEFragment( subRaw, (*it)->Length[k], - decompressedSegmentSize, + RawSegmentSize, fp ); - subDecompressed += decompressedSegmentSize; + subRaw += RawSegmentSize; } } @@ -300,25 +316,21 @@ 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 ) @@ -326,14 +338,13 @@ 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; @@ -344,7 +355,7 @@ 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; @@ -355,7 +366,7 @@ 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; @@ -364,8 +375,7 @@ void PixelReadConvert::ConvertSwapZone() } break; default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(32 bits) not allowed." ); + gdcmVerboseMacro("SwapCode value (32 bits) not allowed." ); } } } @@ -385,8 +395,8 @@ void PixelReadConvert::ConvertReorderEndianity() && ( 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(); @@ -415,17 +427,10 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp ) { fp->seekg( (*it)->Offset, std::ios::beg); - if ( IsJPEG2000 ) - { - if ( ! gdcm_read_JPEG2000_file( fp,localDecompressed ) ) - { - return false; - } - } - else if ( BitsStored == 8) + if ( BitsStored == 8) { // JPEG Lossy : call to IJG 6b - if ( ! gdcm_read_JPEG_file8( fp, localDecompressed ) ) + if ( ! gdcm_read_JPEG_file8( fp, localRaw ) ) { return false; } @@ -433,7 +438,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp ) else if ( BitsStored <= 12) { // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file12 ( fp, localDecompressed ) ) + if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) ) { return false; } @@ -441,30 +446,251 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp ) else if ( BitsStored <= 16) { // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file16 ( fp, localDecompressed ) ) + if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) ) { return false; } - //assert( IsJPEGLossless ); + //gdcmAssertMacro( IsJPEGLossless ); } else { // other JPEG lossy not supported - dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown " - "jpeg lossy compression "); + gdcmErrorMacro( "Unknown jpeg lossy compression "); return false; } - // Advance to next free location in Decompressed + // Advance to next free location in Raw // for next fragment decompression (if any) int length = XSize * YSize * SamplesPerPixel; int numberBytes = BitsAllocated / 8; - localDecompressed += length * numberBytes; + localRaw += length * numberBytes; } 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 = 0; + JPEGFragmentsInfo::JPEGFragmentsList::iterator it; + for( it = JPEGInfo->Fragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + totalLength += (*it)->Length; + } + + // Concatenate the jpeg fragments into a local buffer + JOCTET *buffer = new JOCTET [totalLength]; + JOCTET *p = buffer; + + // Loop on the fragment[s] + for( it = JPEGInfo->Fragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + fp->seekg( (*it)->Offset, std::ios::beg); + size_t len = (*it)->Length; + fp->read((char *)p,len); + p += len; + } + + size_t howManyRead = 0; + size_t howManyWritten = 0; + + if ( BitsStored == 8) + { + if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw, + &howManyRead, &howManyWritten ) ) + { + gdcmErrorMacro( "Failed to read jpeg8 "); + delete [] buffer; + return false; + } + } + else if ( BitsStored <= 12) + { + if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw, + &howManyRead, &howManyWritten ) ) + { + gdcmErrorMacro( "Failed to read jpeg12 "); + delete [] buffer; + return false; + } + } + else if ( BitsStored <= 16) + { + + if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw, + &howManyRead, &howManyWritten ) ) + { + gdcmErrorMacro( "Failed to read jpeg16 "); + delete [] buffer; + return false; + } + } + else + { + // other JPEG lossy not supported + gdcmErrorMacro( "Unknown jpeg lossy compression "); + delete [] buffer; + return false; + } + + // 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 = 0; + JPEGFragmentsInfo::JPEGFragmentsList::iterator it; + for( it = JPEGInfo->Fragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + totalLength += (*it)->Length; + } + + // Concatenate the jpeg fragments into a local buffer + JOCTET *buffer = new JOCTET [totalLength]; + JOCTET *p = buffer; + + // Loop on the fragment[s] + for( it = JPEGInfo->Fragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + fp->seekg( (*it)->Offset, std::ios::beg); + size_t len = (*it)->Length; + fp->read((char *)p,len); + p+=len; + } + + size_t howManyRead = 0; + size_t howManyWritten = 0; + size_t fragmentLength = 0; + + for( it = JPEGInfo->Fragments.begin() ; + (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength); + ++it ) + { + fragmentLength += (*it)->Length; + + if (howManyRead > fragmentLength) continue; + + if ( BitsStored == 8) + { + if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead, + Raw+howManyWritten, + &howManyRead, &howManyWritten ) ) + { + gdcmErrorMacro( "Failed to read jpeg8"); + delete [] buffer; + return false; + } + } + else if ( BitsStored <= 12) + { + + if ( ! gdcm_read_JPEG_memory12( buffer+howManyRead, totalLength-howManyRead, + Raw+howManyWritten, + &howManyRead, &howManyWritten ) ) + { + gdcmErrorMacro( "Failed to read jpeg12"); + delete [] buffer; + return false; + } + } + else if ( BitsStored <= 16) + { + + if ( ! gdcm_read_JPEG_memory16( buffer+howManyRead, totalLength-howManyRead, + Raw+howManyWritten, + &howManyRead, &howManyWritten ) ) + { + gdcmErrorMacro( "Failed to read jpeg16 "); + delete [] buffer; + return false; + } + } + else + { + // other JPEG lossy not supported + gdcmErrorMacro( "Unknown jpeg lossy compression "); + delete [] buffer; + return false; + } + + 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. + * @param fp File Pointer + * @return Boolean + */ +bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) +{ + if ( IsJPEG2000 ) + { + fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg); + if ( ! gdcm_read_JPEG2000_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) + { + // 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 ); + } +} + /** * \brief Re-arrange the bits within the bytes. * @return Boolean @@ -473,12 +699,12 @@ 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; @@ -489,7 +715,7 @@ 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; @@ -498,9 +724,8 @@ 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; @@ -512,9 +737,9 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) */ 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 : @@ -524,9 +749,9 @@ 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 @@ -549,15 +774,15 @@ 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; } /** @@ -566,28 +791,28 @@ 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 + // ComputeRawAndRGBSizes is already made by // ::GrabInformationsFromHeader. So, the structure sizes are // correct Squeeze(); @@ -596,20 +821,18 @@ 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. @@ -617,30 +840,28 @@ 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) + // 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; } } @@ -648,8 +869,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) { if ( ! ReadAndDecompressRLEFile( fp ) ) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "RLE decompressor failed." ); + gdcmVerboseMacro( "RLE decompressor failed." ); return false; } } @@ -658,8 +878,7 @@ 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; } } @@ -713,7 +932,7 @@ 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; @@ -744,10 +963,10 @@ 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 @@ -758,7 +977,7 @@ 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 @@ -769,24 +988,21 @@ 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::GrabInformationsFromHeader( Header *header ) { - // Just in case some access to a Header element requires disk access. - // Note: gdcmDocument::Fp is leaved open after OpenFile. - std::ifstream* fp = header->OpenFile(); // Number of Bits Allocated for storing a Pixel is defaulted to 16 // when absent from the header. BitsAllocated = header->GetBitsAllocated(); @@ -817,17 +1033,17 @@ void PixelReadConvert::GrabInformationsFromHeader( Header* header ) PixelSize = header->GetPixelSize(); PixelSign = header->IsSignedPixelData(); SwapCode = header->GetSwapCode(); - TransferSyntaxType ts = header->GetTransferSyntax(); - IsDecompressed = + std::string ts = header->GetTransferSyntax(); + IsRaw = ( ! header->IsDicomV3() ) - || ts == ImplicitVRLittleEndian - || ts == ImplicitVRLittleEndianDLXGE - || ts == ExplicitVRLittleEndian - || ts == ExplicitVRBigEndian - || ts == DeflatedExplicitVRLittleEndian; - IsJPEG2000 = header->IsJPEG2000(); - IsJPEGLossless = header->IsJPEGLossless(); - IsRLELossless = ( ts == RLELossless ); + || 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); + IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts); + IsRLELossless = Global::GetTS()->IsRLELossless(ts); PixelOffset = header->GetPixelOffset(); PixelDataLength = header->GetPixelAreaLength(); RLEInfo = header->GetRLEInfo(); @@ -843,9 +1059,10 @@ void PixelReadConvert::GrabInformationsFromHeader( Header* header ) HasLUT = header->HasLUT(); if ( HasLUT ) { - LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 ); - LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 ); - LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 ); + // Just in case some access to a Header element requires disk access. + LutRedDescriptor = header->GetEntry( 0x0028, 0x1101 ); + LutGreenDescriptor = header->GetEntry( 0x0028, 0x1102 ); + LutBlueDescriptor = header->GetEntry( 0x0028, 0x1103 ); // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE // [ refer to invocation of Document::SetMaxSizeLoadEntry() in @@ -861,64 +1078,32 @@ void PixelReadConvert::GrabInformationsFromHeader( Header* header ) /// is that the [Bin|Val]Entry is unaware of the FILE* is was /// parsed from. Fix that. FIXME. - ////// Red round: - LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 ); + ////// Red round + header->LoadEntryBinArea(0x0028, 0x1201); + LutRedData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1201 ); if ( ! LutRedData ) { - // Read the Lut Data from disk - DocEntry* lutRedDataEntry = header->GetDocEntryByNumber( 0x0028, - 0x1201 ); - LutRedData = new uint8_t[ lutRedDataEntry->GetLength() ]; - fp->seekg( lutRedDataEntry->GetOffset() ,std::ios::beg ); - fp->read( (char*)LutRedData, (size_t)lutRedDataEntry->GetLength()); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read red LUT data" ); - } + gdcmVerboseMacro( "Unable to read red LUT data" ); } ////// Green round: - LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 ); + header->LoadEntryBinArea(0x0028, 0x1202); + LutGreenData = (uint8_t*)header->GetEntryBinArea(0x0028, 0x1202 ); if ( ! LutGreenData) { - // Read the Lut Data from disk - DocEntry* lutGreenDataEntry = header->GetDocEntryByNumber( 0x0028, - 0x1202 ); - LutGreenData = new uint8_t[ lutGreenDataEntry->GetLength() ]; - fp->seekg( lutGreenDataEntry->GetOffset() , std::ios::beg ); - fp->read( (char*)LutGreenData, (size_t)lutGreenDataEntry->GetLength() ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read green LUT data" ); - } + gdcmVerboseMacro( "Unable to read green LUT data" ); } ////// Blue round: - LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 ); + header->LoadEntryBinArea(0x0028, 0x1203); + LutBlueData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1203 ); if ( ! LutBlueData ) { - // Read the Lut Data from disk - DocEntry* lutBlueDataEntry = header->GetDocEntryByNumber( 0x0028, - 0x1203 ); - LutBlueData = new uint8_t[ lutBlueDataEntry->GetLength() ]; - fp->seekg( lutBlueDataEntry->GetOffset() , std::ios::beg ); - fp->read( (char*)LutBlueData, (size_t)lutBlueDataEntry->GetLength() ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read blue LUT data" ); - } + gdcmVerboseMacro( "Unable to read blue LUT data" ); } } - ComputeDecompressedAndRGBSizes(); - - if(fp) - { - header->CloseFile(); - } + ComputeRawAndRGBSizes(); } /** @@ -967,7 +1152,7 @@ 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 @@ -978,7 +1163,7 @@ 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 @@ -989,7 +1174,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthB, &debB, &nbitsB ); if( nbRead != 3 ) { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor"); + gdcmVerboseMacro( "Wrong blue LUT descriptor" ); } //////////////////////////////////////////////////////// @@ -1057,7 +1242,7 @@ 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() { @@ -1067,7 +1252,7 @@ bool PixelReadConvert::BuildRGBImage() return true; } - if ( ! Decompressed ) + if ( ! Raw ) { // The job can't be done return false; @@ -1083,9 +1268,9 @@ 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]; @@ -1093,6 +1278,15 @@ bool PixelReadConvert::BuildRGBImage() return true; } +/** + * \brief Print self. + * @param os Stream to print to. + */ +void PixelReadConvert::Print( std::ostream &os ) +{ + Print("",os); +} + /** * \brief Print self. * @param indent Indentation string to be prepended during printing. @@ -1105,10 +1299,10 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) << 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 ) { @@ -1118,8 +1312,7 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) } else { - dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file " - "but NO RLEinfo present."); + gdcmVerboseMacro("Set as RLE file but NO RLEinfo present."); } } @@ -1131,8 +1324,7 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) } else { - dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file " - "but NO JPEGinfo present."); + gdcmVerboseMacro("Set as JPEG file but NO JPEGinfo present."); } } } @@ -1148,3 +1340,4 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) // User // ---> GetImageDataRaw // ---> GetImageDataIntoVectorRaw +