X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=27ff8e2b83384398ebb43b587b4f63467d724c31;hb=0408b1aa8aaf0d1e17391984490ad2bbe89a922b;hp=2d6e0545343db63c889fafd913593a574c68624c;hpb=ee91cee9d641284ed6a410f2af286bb681829055;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 2d6e0545..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: 2004/12/16 11:37:03 $ - Version: $Revision: 1.12 $ + 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 @@ -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" @@ -34,33 +30,9 @@ 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); - -#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_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_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_memory16 (const JOCTET *buffer, const size_t buflen, - void* image_buffer, - size_t *howManyRead, size_t *howManyWritten); - - //----------------------------------------------------------------------------- // Constructor / Destructor PixelReadConvert::PixelReadConvert() @@ -75,53 +47,47 @@ 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]; } /** * \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; @@ -132,21 +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" ); @@ -165,146 +131,6 @@ 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 - * 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 de - * 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 ) - { - dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we " - "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)->NumberFragments; k++ ) - { - fp->seekg( (*it)->Offset[k] , std::ios::beg ); - (void)ReadAndDecompressRLEFragment( subRaw, - (*it)->Length[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. @@ -315,14 +141,11 @@ void PixelReadConvert::ConvertSwapZone() if( BitsAllocated == 16 ) { - uint16_t* im16 = (uint16_t*)Raw; + uint16_t *im16 = (uint16_t*)Raw; switch( SwapCode ) { - case 0: - case 12: case 1234: break; - case 21: case 3412: case 2143: case 4321: @@ -332,8 +155,7 @@ void PixelReadConvert::ConvertSwapZone() } break; default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(16 bits) not allowed." ); + gdcmVerboseMacro("SwapCode value (16 bits) not allowed."); } } else if( BitsAllocated == 32 ) @@ -344,7 +166,6 @@ void PixelReadConvert::ConvertSwapZone() uint32_t* im32 = (uint32_t*)Raw; switch ( SwapCode ) { - case 0: case 1234: break; case 4321: @@ -379,14 +200,13 @@ 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() { @@ -396,9 +216,9 @@ 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)( RawSize / ( BitsAllocated / 8 ) ); uint16_t *deb = (uint16_t *)Raw; @@ -413,298 +233,39 @@ void PixelReadConvert::ConvertReorderEndianity() } } - /** * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated - * file and decompress it. This funciton assumes that each - * jpeg fragment contains a whole frame (jpeg file). - * @param fp File Pointer - * @return Boolean - */ -bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream* fp ) -{ - uint8_t* localRaw = Raw; - // Loop on the fragment[s] - for( JPEGFragmentsInfo::JPEGFragmentsList::iterator - it = JPEGInfo->Fragments.begin(); - it != JPEGInfo->Fragments.end(); - ++it ) - { - fp->seekg( (*it)->Offset, std::ios::beg); - - if ( BitsStored == 8) - { - // JPEG Lossy : call to IJG 6b - if ( ! gdcm_read_JPEG_file8( fp, localRaw ) ) - { - return false; - } - } - else if ( BitsStored <= 12) - { - // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) ) - { - return false; - } - } - else if ( BitsStored <= 16) - { - // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) ) - { - return false; - } - //assert( IsJPEGLossless ); - } - else - { - // other JPEG lossy not supported - dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown " - "jpeg lossy compression "); - return false; - } - - // Advance to next free location in Raw - // for next fragment decompression (if any) - int length = XSize * YSize * SamplesPerPixel; - int numberBytes = BitsAllocated / 8; - - 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. + * file and decompress it. * @param fp File Pointer * @return Boolean */ -bool PixelReadConvert:: -ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream* fp ) +bool PixelReadConvert::ReadAndDecompressJPEGFile( 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 ) + if ( IsJPEG2000 ) { - fp->seekg( (*it)->Offset, std::ios::beg); - size_t len = (*it)->Length; - fp->read((char *)p,len); - p += len; + 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; } - size_t howManyRead = 0; - size_t howManyWritten = 0; - - if ( BitsStored == 8) + if ( IsJPEGLS ) { - if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw, - &howManyRead, &howManyWritten ) ) - { - dbg.Error( - "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 " - ); - delete [] buffer; + gdcmVerboseMacro( "Sorry, JPEG-LS not yet taken into account" ); + fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg); +// if ( ! gdcm_read_JPEGLS_file( fp,Raw ) ) return false; - } - } - else if ( BitsStored <= 12) - { - if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw, - &howManyRead, &howManyWritten ) ) - { - dbg.Error( - "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 " - ); - delete [] buffer; - return false; - } - } - else if ( BitsStored <= 16) - { - - if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw, - &howManyRead, &howManyWritten ) ) - { - dbg.Error( - "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 " - ); - delete [] buffer; - return false; - } - } - else - { - // other JPEG lossy not supported - dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: 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; + // else ?? + // Precompute the offset localRaw will be shifted with + int length = XSize * YSize * SamplesPerPixel; + int numberBytes = BitsAllocated / 8; - if ( BitsStored == 8) - { - if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead, - Raw+howManyWritten, - &howManyRead, &howManyWritten ) ) - { - dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: 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 ) ) - { - dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: 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 ) ) - { - dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 "); - delete [] buffer; - return false; - } - } - else - { - // other JPEG lossy not supported - dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown " - "jpeg lossy compression "); - delete [] buffer; - return false; - } - - if (howManyRead < fragmentLength) - howManyRead = fragmentLength; - } - - // free local buffer - delete [] buffer; - + JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length ); 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 @@ -738,22 +299,21 @@ 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* localRaw = Raw; - uint8_t* copyRaw = new uint8_t[ RawSize ]; + 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, @@ -764,9 +324,9 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() int l = XSize * YSize; int nbFrames = ZSize; - uint8_t* a = copyRaw; - uint8_t* b = copyRaw + l; - uint8_t* c = copyRaw + 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 @@ -806,8 +366,8 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() */ void PixelReadConvert::ConvertRGBPlanesToRGBPixels() { - uint8_t* localRaw = Raw; - uint8_t* copyRaw = new uint8_t[ RawSize ]; + uint8_t *localRaw = Raw; + uint8_t *copyRaw = new uint8_t[ RawSize ]; memmove( copyRaw, localRaw, RawSize ); int l = XSize * YSize * ZSize; @@ -825,10 +385,10 @@ void PixelReadConvert::ConvertRGBPlanesToRGBPixels() delete[] copyRaw; } -bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) +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(); @@ -836,16 +396,14 @@ 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; } @@ -860,13 +418,12 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) 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 + // 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 RawSize." ); + gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." ); } if( PixelDataLength > RawSize) { @@ -877,19 +434,17 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) 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 Raw pixel data failed." ); + gdcmVerboseMacro( "Reading of Raw pixel data failed." ); return false; } } else if ( IsRLELossless ) { - if ( ! ReadAndDecompressRLEFile( fp ) ) + if ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "RLE decompressor failed." ); + gdcmVerboseMacro( "RLE decompressor failed." ); return false; } } @@ -898,8 +453,7 @@ 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; } } @@ -940,7 +494,7 @@ 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 @@ -1022,77 +576,80 @@ void PixelReadConvert::ComputeRawAndRGBSizes() } } -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(); + 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() ) - || 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(); + ( ! 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 @@ -1101,30 +658,27 @@ 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" ); } } @@ -1132,7 +686,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header* header ) } /** - * \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 @@ -1177,7 +731,7 @@ 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 @@ -1188,7 +742,7 @@ 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 @@ -1199,7 +753,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthB, &debB, &nbitsB ); if( nbRead != 3 ) { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor"); + gdcmVerboseMacro( "Wrong Blue LUT descriptor" ); } //////////////////////////////////////////////////////// @@ -1212,9 +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; @@ -1234,7 +787,7 @@ 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; @@ -1303,21 +856,20 @@ bool PixelReadConvert::BuildRGBImage() return true; } -/** - * \brief Print self. - * @param os Stream to print to. - */ -void PixelReadConvert::Print( std::ostream &os ) -{ - Print("",os); -} +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private +//----------------------------------------------------------------------------- +// Print /** * \brief Print self. * @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 -------------------------" @@ -1333,29 +885,28 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) { 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."); } } } +//----------------------------------------------------------------------------- } // end namespace gdcm // NOTES on File internal calls