X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=d3dfec5b671e7b81d405601c1fdff1fb8490829a;hb=f12e51a575034ba832a0ff3b9f9c5ba219fc8562;hp=3f99d2e897efba6c88363c61648794efdb4f0138;hpb=113b1e37913f5888168b7bbecf9aa4a6326a60c1;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 3f99d2e8..d3dfec5b 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -1,1367 +1,1007 @@ -/*========================================================================= - - Program: gdcm - Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ - Language: C++ - Date: $Date: 2004/12/13 06:22:43 $ - Version: $Revision: 1.7 $ - - Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de - l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. - - This software is distributed WITHOUT ANY WARRANTY; without even - the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR - PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ - -////////////////// 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 "gdcmPixelReadConvert.h" -#include "gdcmDocEntry.h" -#include "gdcmRLEFramesInfo.h" -#include "gdcmJPEGFragmentsInfo.h" - -#include -#include //for sscanf - -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() -{ - RGB = 0; - RGBSize = 0; - Raw = 0; - RawSize = 0; - LutRGBA = 0; - LutRedData = 0; - LutGreenData = 0; - LutBlueData =0; -} - -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 ) { - delete [] RGB; - } - RGB = new uint8_t[ RGBSize ]; -} - -void PixelReadConvert::AllocateRaw() -{ - 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 ) - throw ( FormatError ) -{ - int nbPixels = XSize * YSize; - uint16_t* localDecompres = (uint16_t*)Raw; - - for( int p = 0; p < nbPixels; p += 2 ) - { - uint8_t b0, b1, b2; - - fp->read( (char*)&b0, 1); - if ( fp->fail() || fp->eof() )//Fp->gcount() == 1 - { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound first block" ); - } - - fp->read( (char*)&b1, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound second block" ); - } - - fp->read( (char*)&b2, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound second block" ); - } - - // Two steps are necessary to please VC++ - // - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - // A B D - *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // F C E - *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - - /// \todo JPR Troubles expected on Big-Endian processors ? - } -} - -/** - * \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. - */ -void PixelReadConvert::ConvertSwapZone() -{ - unsigned int i; - - if( BitsAllocated == 16 ) - { - 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 < RawSize / 2; i++ ) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - break; - default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(16 bits) not allowed." ); - } - } - else if( BitsAllocated == 32 ) - { - uint32_t s32; - uint16_t high; - uint16_t low; - uint32_t* im32 = (uint32_t*)Raw; - switch ( SwapCode ) - { - case 0: - case 1234: - break; - case 4321: - for( i = 0; i < RawSize / 4; i++ ) - { - low = im32[i] & 0x0000ffff; // 4321 - high = im32[i] >> 16; - high = ( high >> 8 ) | ( high << 8 ); - low = ( low >> 8 ) | ( low << 8 ); - s32 = low; - im32[i] = ( s32 << 16 ) | high; - } - break; - case 2143: - for( i = 0; i < RawSize / 4; i++ ) - { - low = im32[i] & 0x0000ffff; // 2143 - high = im32[i] >> 16; - high = ( high >> 8 ) | ( high << 8 ); - low = ( low >> 8 ) | ( low << 8 ); - s32 = high; - im32[i] = ( s32 << 16 ) | low; - } - break; - case 3412: - for( i = 0; i < RawSize / 4; i++ ) - { - low = im32[i] & 0x0000ffff; // 3412 - high = im32[i] >> 16; - s32 = low; - im32[i] = ( s32 << 16 ) | high; - } - break; - default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(32 bits) not allowed." ); - } - } -} - -/** - * \brief Deal with endianity i.e. re-arange bytes inside the integer - */ -void PixelReadConvert::ConvertReorderEndianity() -{ - if ( BitsAllocated != 8 ) - { - ConvertSwapZone(); - } - - // Special kludge in order to deal with xmedcon broken images: - if ( ( BitsAllocated == 16 ) - && ( BitsStored < BitsAllocated ) - && ( ! PixelSign ) ) - { - int l = (int)( RawSize / ( BitsAllocated / 8 ) ); - uint16_t *deb = (uint16_t *)Raw; - for(int i = 0; iFragments.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. - * @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; - for( JPEGFragmentsInfo::JPEGFragmentsList::iterator - 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; - - 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); - size_t len = (*it)->Length; - fp->read((char *)p,len); - p+=len; - } - - size_t howManyRead = 0; - size_t howManyWritten = 0; - size_t fragmentLength = 0; - - if ( BitsStored == 8) - { - if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw, - &howManyRead, &howManyWritten ) ) - { - dbg.Error( - "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 " - ); - delete [] buffer; - 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; - for( JPEGFragmentsInfo::JPEGFragmentsList::iterator - 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; - - 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); - 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( JPEGFragmentsInfo::JPEGFragmentsList::iterator - 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 ) ) - { - 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; - - 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() == 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 - */ -bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) -{ - if ( BitsStored != BitsAllocated ) - { - int l = (int)( RawSize / ( BitsAllocated / 8 ) ); - if ( BitsAllocated == 16 ) - { - uint16_t mask = 0xffff; - mask = mask >> ( BitsAllocated - BitsStored ); - uint16_t* deb = (uint16_t*)Raw; - for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; - deb++; - } - } - else if ( BitsAllocated == 32 ) - { - uint32_t mask = 0xffffffff; - mask = mask >> ( BitsAllocated - BitsStored ); - uint32_t* deb = (uint32_t*)Raw; - for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; - deb++; - } - } - else - { - dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image"); - throw FormatError( "PixelReadConvert::ConvertReArrangeBits()", - "weird image !?" ); - } - } - return true; -} - -/** - * \brief Convert (Y 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 ]; - 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 : - // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf - // and be *very* affraid - // - int l = XSize * YSize; - int nbFrames = ZSize; - - 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 - /// counterpart. Refer to - /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - /// for code optimisation. - - for ( int i = 0; i < nbFrames; i++ ) - { - for ( int j = 0; j < l; j++ ) - { - R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; - G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; - B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; - - if (R < 0.0) R = 0.0; - if (G < 0.0) G = 0.0; - if (B < 0.0) B = 0.0; - if (R > 255.0) R = 255.0; - if (G > 255.0) G = 255.0; - if (B > 255.0) B = 255.0; - - *(localRaw++) = (uint8_t)R; - *(localRaw++) = (uint8_t)G; - *(localRaw++) = (uint8_t)B; - a++; - b++; - c++; - } - } - delete[] copyRaw; -} - -/** - * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels - * \warning Works on all the frames at a time - */ -void PixelReadConvert::ConvertRGBPlanesToRGBPixels() -{ - uint8_t* localRaw = Raw; - uint8_t* copyRaw = new uint8_t[ RawSize ]; - memmove( copyRaw, localRaw, RawSize ); - - int l = XSize * YSize * ZSize; - - uint8_t* a = copyRaw; - uint8_t* b = copyRaw + l; - uint8_t* c = copyRaw + l + l; - - for (int j = 0; j < l; j++) - { - *(localRaw++) = *(a++); - *(localRaw++) = *(b++); - *(localRaw++) = *(c++); - } - delete[] copyRaw; -} - -bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) -{ - // ComputeRawAndRGBSizes is already made by - // ::GrabInformationsFromHeader. So, the structure sizes are - // correct - Squeeze(); - - ////////////////////////////////////////////////// - //// First stage: get our hands on the Pixel Data. - if ( !fp ) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "unavailable file pointer." ); - return false; - } - - fp->seekg( PixelOffset, std::ios::beg ); - if( fp->fail() || fp->eof()) //Fp->gcount() == 1 - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "unable to find PixelOffset in file." ); - return false; - } - - AllocateRaw(); - - ////////////////////////////////////////////////// - //// Second stage: read from disk dans decompress. - if ( BitsAllocated == 12 ) - { - ReadAndDecompress12BitsTo16Bits( 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 - // variable). But RawSize is the right size of the image ! - if( PixelDataLength != RawSize) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "Mismatch between PixelReadConvert and RawSize." ); - } - if( PixelDataLength > RawSize) - { - fp->read( (char*)Raw, RawSize); - } - else - { - fp->read( (char*)Raw, PixelDataLength); - } - - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "reading of Raw pixel data failed." ); - return false; - } - } - else if ( IsRLELossless ) - { - if ( ! ReadAndDecompressRLEFile( fp ) ) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "RLE decompressor failed." ); - return false; - } - } - else - { - // Default case concerns JPEG family - if ( ! ReadAndDecompressJPEGFile( fp ) ) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "JPEG decompressor failed." ); - return false; - } - } - - //////////////////////////////////////////// - //// Third stage: twigle the bytes and bits. - ConvertReorderEndianity(); - ConvertReArrangeBits(); - ConvertHandleColor(); - - return true; -} - -void PixelReadConvert::ConvertHandleColor() -{ - ////////////////////////////////// - // Deal with the color decoding i.e. handle: - // - R, G, B planes (as opposed to RGB pixels) - // - YBR (various) encodings. - // - LUT[s] (or "PALETTE COLOR"). - // - // The classification in the color decoding schema is based on the blending - // of two Dicom tags values: - // * "Photometric Interpretation" for which we have the cases: - // - [Photo A] MONOCHROME[1|2] pictures, - // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB), - // - [Photo C] YBR_* (with the above exception of YBR_FULL_422) - // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s]. - // * "Planar Configuration" for which we have the cases: - // - [Planar 0] 0 then Pixels are already RGB - // - [Planar 1] 1 then we have 3 planes : R, G, B, - // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs - // - // Now in theory, one could expect some coherence when blending the above - // cases. For example we should not encounter files belonging at the - // time to case [Planar 0] and case [Photo D]. - // Alas, this was only theory ! Because in practice some odd (read ill - // 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 - // towards Dicom-non-conformance files: - // << whatever the "Planar Configuration" value might be, a - // "Photometric Interpretation" set to "PALETTE COLOR" forces - // a LUT intervention >> - // - // Now we are left with the following handling of the cases: - // - [Planar 0] OR [Photo A] no color decoding (since respectively - // Pixels are already RGB and monochrome pictures have no color :), - // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels() - // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels() - // - [Planar 2] OR [Photo D] requires LUT intervention. - - if ( ! IsRawRGB() ) - { - // [Planar 2] OR [Photo D]: LUT intervention done outside - return; - } - - if ( PlanarConfiguration == 1 ) - { - if ( IsYBRFull ) - { - // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB) - ConvertYcBcRPlanesToRGBPixels(); - } - else - { - // [Planar 1] AND [Photo C] - ConvertRGBPlanesToRGBPixels(); - } - return; - } - - // When planarConf is 0, and RLELossless (forbidden by Dicom norm) - // pixels need to be RGB-fied anyway - if (IsRLELossless) - { - ConvertRGBPlanesToRGBPixels(); - } - // In *normal *case, when planarConf is 0, pixels are already in RGB -} - -/** - * \brief Predicate to know wether the image[s] (once Raw) is RGB. - * \note See comments of \ref ConvertHandleColor - */ -bool PixelReadConvert::IsRawRGB() -{ - if ( IsMonochrome - || PlanarConfiguration == 2 - || IsPaletteColor ) - { - return false; - } - return true; -} - -void PixelReadConvert::ComputeRawAndRGBSizes() -{ - int bitsAllocated = BitsAllocated; - // Number of "Bits Allocated" is fixed to 16 when it's 12, since - // in this case we will expand the image to 16 bits (see - // \ref ReadAndDecompress12BitsTo16Bits() ) - if ( BitsAllocated == 12 ) - { - bitsAllocated = 16; - } - - RawSize = XSize * YSize * ZSize - * ( bitsAllocated / 8 ) - * SamplesPerPixel; - if ( HasLUT ) - { - RGBSize = 3 * RawSize; - } - else - { - RGBSize = RawSize; - } -} - -void PixelReadConvert::GrabInformationsFromHeader( Header* header ) -{ - // Number of Bits Allocated for storing a Pixel is defaulted to 16 - // when absent from the header. - BitsAllocated = header->GetBitsAllocated(); - if ( BitsAllocated == 0 ) - { - BitsAllocated = 16; - } - - // Number of "Bits Stored" defaulted to number of "Bits Allocated" - // when absent from the header. - BitsStored = header->GetBitsStored(); - if ( BitsStored == 0 ) - { - BitsStored = BitsAllocated; - } - - // High Bit Position - HighBitPosition = header->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(); - 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(); - - ///////////////////////////////////////////////////////////////// - // LUT section: - HasLUT = header->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 ); - - // 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. - /// 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 - /// within the [Bin|Val]Entry class itself. The only problem - /// is that the [Bin|Val]Entry is unaware of the FILE* is was - /// parsed from. Fix that. FIXME. - - ////// Red round - header->LoadEntryBinArea(0x0028, 0x1201); - LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 ); - if ( ! LutRedData ) - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read red LUT data" ); - } - - ////// Green round: - header->LoadEntryBinArea(0x0028, 0x1202); - LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 ); - if ( ! LutGreenData) - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read green LUT data" ); - } - - ////// Blue round: - header->LoadEntryBinArea(0x0028, 0x1203); - LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 ); - if ( ! LutBlueData ) - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read blue LUT data" ); - } - } - - ComputeRawAndRGBSizes(); -} - -/** - * \brief Build Red/Green/Blue/Alpha LUT from Header - * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] - * and (0028,1101),(0028,1102),(0028,1102) - * - xxx Palette Color Lookup Table Descriptor - are found - * and (0028,1201),(0028,1202),(0028,1202) - * - xxx Palette Color Lookup Table Data - are found - * \warning does NOT deal with : - * 0028 1100 Gray Lookup Table Descriptor (Retired) - * 0028 1221 Segmented Red Palette Color Lookup Table Data - * 0028 1222 Segmented Green Palette Color Lookup Table Data - * 0028 1223 Segmented Blue Palette Color Lookup Table Data - * no known Dicom reader deals with them :-( - * @return a RGBA Lookup Table - */ -void PixelReadConvert::BuildLUTRGBA() -{ - if ( LutRGBA ) - { - return; - } - // Not so easy : see - // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables - - if ( ! IsPaletteColor ) - { - return; - } - - if ( LutRedDescriptor == GDCM_UNFOUND - || LutGreenDescriptor == GDCM_UNFOUND - || LutBlueDescriptor == GDCM_UNFOUND ) - { - return; - } - - //////////////////////////////////////////// - // Extract the info from the LUT descriptors - int lengthR; // Red LUT length in Bytes - int debR; // Subscript of the first Lut Value - int nbitsR; // Lut item size (in Bits) - int nbRead = sscanf( LutRedDescriptor.c_str(), - "%d\\%d\\%d", - &lengthR, &debR, &nbitsR ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor"); - } - - int lengthG; // Green LUT length in Bytes - int debG; // Subscript of the first Lut Value - int nbitsG; // Lut item size (in Bits) - nbRead = sscanf( LutGreenDescriptor.c_str(), - "%d\\%d\\%d", - &lengthG, &debG, &nbitsG ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor"); - } - - int lengthB; // Blue LUT length in Bytes - int debB; // Subscript of the first Lut Value - int nbitsB; // Lut item size (in Bits) - nbRead = sscanf( LutRedDescriptor.c_str(), - "%d\\%d\\%d", - &lengthB, &debB, &nbitsB ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor"); - } - - //////////////////////////////////////////////////////// - if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) ) - { - return; - } - - //////////////////////////////////////////////// - // 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; - if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) ) - { - // when LUT item size is different than pixel size - mult = 2; // high byte must be = low byte - } - else - { - // See PS 3.3-2003 C.11.1.1.2 p 619 - mult = 1; - } - - // if we get a black image, let's just remove the '+1' - // from 'i*mult+1' and check again - // 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 - // (optimistic asumption) - int i; - uint8_t* a = LutRGBA + 0; - for( i=0; i < lengthR; ++i ) - { - *a = LutRedData[i*mult+1]; - a += 4; - } - - a = LutRGBA + 1; - for( i=0; i < lengthG; ++i) - { - *a = LutGreenData[i*mult+1]; - a += 4; - } - - a = LutRGBA + 2; - for(i=0; i < lengthB; ++i) - { - *a = LutBlueData[i*mult+1]; - a += 4; - } - - a = LutRGBA + 3; - for(i=0; i < 256; ++i) - { - *a = 1; // Alpha component - a += 4; - } -} - -/** - * \brief Build the RGB image from the Raw imagage and the LUTs. - */ -bool PixelReadConvert::BuildRGBImage() -{ - if ( RGB ) - { - // The job is already done. - return true; - } - - if ( ! Raw ) - { - // The job can't be done - return false; - } - - BuildLUTRGBA(); - if ( ! LutRGBA ) - { - // The job can't be done - return false; - } - - // Build RGB Pixels - AllocateRGB(); - uint8_t* localRGB = RGB; - for (size_t i = 0; i < RawSize; ++i ) - { - int j = Raw[i] * 4; - *localRGB++ = LutRGBA[j]; - *localRGB++ = LutRGBA[j+1]; - *localRGB++ = LutRGBA[j+2]; - } - return true; -} - -/** - * \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 ) -{ - 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; - - if ( IsRLELossless ) - { - if ( RLEInfo ) - { - RLEInfo->Print( indent, os ); - } - else - { - dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file " - "but NO RLEinfo present."); - } - } - - if ( IsJPEG2000 || IsJPEGLossless ) - { - if ( JPEGInfo ) - { - JPEGInfo->Print( indent, os ); - } - else - { - dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file " - "but NO JPEGinfo present."); - } - } -} - -} // end namespace gdcm - -// NOTES on File internal calls -// User -// ---> GetImageData -// ---> GetImageDataIntoVector -// |---> GetImageDataIntoVectorRaw -// | lut intervention -// User -// ---> GetImageDataRaw -// ---> GetImageDataIntoVectorRaw - +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ + Language: C++ + Date: $Date: 2005/02/23 09:54:59 $ + Version: $Revision: 1.53 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#include "gdcmDebug.h" +#include "gdcmFile.h" +#include "gdcmGlobal.h" +#include "gdcmTS.h" +#include "gdcmPixelReadConvert.h" +#include "gdcmDocEntry.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" + +#include +#include //for sscanf + +namespace gdcm +{ +//----------------------------------------------------------------------------- +#define str2num(str, typeNum) *((typeNum *)(str)) + +//----------------------------------------------------------------------------- +// Constructor / Destructor +/// Constructor +PixelReadConvert::PixelReadConvert() +{ + RGB = 0; + RGBSize = 0; + Raw = 0; + RawSize = 0; + LutRGBA = 0; + LutRedData = 0; + LutGreenData = 0; + LutBlueData = 0; +} + +/// Canonical Destructor +PixelReadConvert::~PixelReadConvert() +{ + Squeeze(); +} + +//----------------------------------------------------------------------------- +// Public +/** + * \brief Predicate to know whether the image[s] (once Raw) is RGB. + * \note See comments of \ref ConvertHandleColor + */ +bool PixelReadConvert::IsRawRGB() +{ + if ( IsMonochrome + || PlanarConfiguration == 2 + || IsPaletteColor ) + { + return false; + } + return true; +} +/** + * \brief Gets various usefull informations from the file header + * @param file gdcm::File pointer + */ +void PixelReadConvert::GrabInformationsFromFile( File *file ) +{ + // Number of Bits Allocated for storing a Pixel is defaulted to 16 + // 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 file. + BitsStored = file->GetBitsStored(); + if ( BitsStored == 0 ) + { + BitsStored = BitsAllocated; + } + + // High Bit Position, defaulted to "Bits Allocated" - 1 + HighBitPosition = file->GetHighBitPosition(); + if ( HighBitPosition == 0 ) + { + HighBitPosition = BitsAllocated - 1; + } + + 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(); + + IsMonochrome = file->IsMonochrome(); + IsMonochrome1 = file->IsMonochrome1(); + IsPaletteColor = file->IsPaletteColor(); + IsYBRFull = file->IsYBRFull(); + + PlanarConfiguration = file->GetPlanarConfiguration(); + + ///////////////////////////////////////////////////////////////// + // LUT section: + HasLUT = file->HasLUT(); + if ( HasLUT ) + { + // 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 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 + // within the [Bin|Val]Entry class itself. The only problem + // is that the [Bin|Val]Entry is unaware of the FILE* is was + // parsed from. Fix that. FIXME. + + // //// Red round + file->LoadEntryBinArea(0x0028, 0x1201); + LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 ); + if ( ! LutRedData ) + { + gdcmWarningMacro( "Unable to read Red LUT data" ); + } + + // //// Green round: + file->LoadEntryBinArea(0x0028, 0x1202); + LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 ); + if ( ! LutGreenData) + { + gdcmWarningMacro( "Unable to read Green LUT data" ); + } + + // //// Blue round: + file->LoadEntryBinArea(0x0028, 0x1203); + LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 ); + if ( ! LutBlueData ) + { + gdcmWarningMacro( "Unable to read Blue LUT data" ); + } + } + + ComputeRawAndRGBSizes(); +} + +/// \brief Reads from disk and decompresses Pixels +bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) +{ + // ComputeRawAndRGBSizes is already made by + // ::GrabInformationsFromfile. So, the structure sizes are + // correct + Squeeze(); + + ////////////////////////////////////////////////// + //// First stage: get our hands on the Pixel Data. + if ( !fp ) + { + gdcmWarningMacro( "Unavailable file pointer." ); + return false; + } + + fp->seekg( PixelOffset, std::ios::beg ); + if( fp->fail() || fp->eof()) + { + gdcmWarningMacro( "Unable to find PixelOffset in file." ); + return false; + } + + AllocateRaw(); + + ////////////////////////////////////////////////// + //// Second stage: read from disk dans decompress. + if ( BitsAllocated == 12 ) + { + ReadAndDecompress12BitsTo16Bits( fp); + } + else if ( IsRaw ) + { + // This problem can be found when some obvious informations are found + // 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) + { + gdcmWarningMacro( "Mismatch between PixelReadConvert : " + << PixelDataLength << " and RawSize : " << RawSize ); + } + if( PixelDataLength > RawSize) + { + fp->read( (char*)Raw, RawSize); + } + else + { + fp->read( (char*)Raw, PixelDataLength); + } + + if ( fp->fail() || fp->eof()) + { + gdcmWarningMacro( "Reading of Raw pixel data failed." ); + return false; + } + } + else if ( IsRLELossless ) + { + if ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) + { + gdcmWarningMacro( "RLE decompressor failed." ); + return false; + } + } + else + { + // Default case concerns JPEG family + if ( ! ReadAndDecompressJPEGFile( fp ) ) + { + gdcmWarningMacro( "JPEG decompressor failed." ); + return false; + } + } + + //////////////////////////////////////////// + //// Third stage: twigle the bytes and bits. + ConvertReorderEndianity(); + ConvertReArrangeBits(); + ConvertFixGreyLevels(); + ConvertHandleColor(); + + return true; +} + +/// Deletes Pixels Area +void PixelReadConvert::Squeeze() +{ + if ( RGB ) + delete [] RGB; + RGB = 0; + + if ( Raw ) + delete [] Raw; + Raw = 0; + + if ( LutRGBA ) + delete [] LutRGBA; + LutRGBA = 0; +} + +/** + * \brief Build the RGB image from the Raw imagage and the LUTs. + */ +bool PixelReadConvert::BuildRGBImage() +{ + if ( RGB ) + { + // The job is already done. + return true; + } + + if ( ! Raw ) + { + // The job can't be done + return false; + } + + BuildLUTRGBA(); + if ( ! LutRGBA ) + { + // The job can't be done + return false; + } + + // Build RGB Pixels + AllocateRGB(); + uint8_t *localRGB = RGB; + for (size_t i = 0; i < RawSize; ++i ) + { + int j = Raw[i] * 4; + *localRGB++ = LutRGBA[j]; + *localRGB++ = LutRGBA[j+1]; + *localRGB++ = LutRGBA[j+2]; + } + return true; +} + +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private +/** + * \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 ) + throw ( FormatError ) +{ + int nbPixels = XSize * YSize; + uint16_t *localDecompres = (uint16_t*)Raw; + + for( int p = 0; p < nbPixels; p += 2 ) + { + uint8_t b0, b1, b2; + + fp->read( (char*)&b0, 1); + if ( fp->fail() || fp->eof() ) + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound first block" ); + } + + fp->read( (char*)&b1, 1 ); + if ( fp->fail() || fp->eof()) + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); + } + + fp->read( (char*)&b2, 1 ); + if ( fp->fail() || fp->eof()) + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); + } + + // Two steps are necessary to please VC++ + // + // 2 pixels 12bit = [0xABCDEF] + // 2 pixels 16bit = [0x0ABD] + [0x0FCE] + // A B D + *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); + // F C E + *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); + + /// \todo JPR Troubles expected on Big-Endian processors ? + } +} + +/** + * \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 ) + { + gdcmWarningMacro( "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 ( IsJPEGLS ) + { + gdcmWarningMacro( "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 ?? + // Precompute the offset localRaw will be shifted with + int length = XSize * YSize * SamplesPerPixel; + int numberBytes = BitsAllocated / 8; + + JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length ); + return true; +} + +/** + * \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 + * and (0028,1201),(0028,1202),(0028,1202) + * - xxx Palette Color Lookup Table Data - are found + * \warning does NOT deal with : + * 0028 1100 Gray Lookup Table Descriptor (Retired) + * 0028 1221 Segmented Red Palette Color Lookup Table Data + * 0028 1222 Segmented Green Palette Color Lookup Table Data + * 0028 1223 Segmented Blue Palette Color Lookup Table Data + * no known Dicom reader deals with them :-( + * @return a RGBA Lookup Table + */ +void PixelReadConvert::BuildLUTRGBA() +{ + if ( LutRGBA ) + { + return; + } + // Not so easy : see + // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables + + if ( ! IsPaletteColor ) + { + return; + } + + if ( LutRedDescriptor == GDCM_UNFOUND + || LutGreenDescriptor == GDCM_UNFOUND + || LutBlueDescriptor == GDCM_UNFOUND ) + { + return; + } + + //////////////////////////////////////////// + // Extract the info from the LUT descriptors + int lengthR; // Red LUT length in Bytes + int debR; // Subscript of the first Lut Value + int nbitsR; // Lut item size (in Bits) + int nbRead = sscanf( LutRedDescriptor.c_str(), + "%d\\%d\\%d", + &lengthR, &debR, &nbitsR ); + if( nbRead != 3 ) + { + gdcmWarningMacro( "Wrong Red LUT descriptor" ); + } + + int lengthG; // Green LUT length in Bytes + int debG; // Subscript of the first Lut Value + int nbitsG; // Lut item size (in Bits) + nbRead = sscanf( LutGreenDescriptor.c_str(), + "%d\\%d\\%d", + &lengthG, &debG, &nbitsG ); + if( nbRead != 3 ) + { + gdcmWarningMacro( "Wrong Green LUT descriptor" ); + } + + int lengthB; // Blue LUT length in Bytes + int debB; // Subscript of the first Lut Value + int nbitsB; // Lut item size (in Bits) + nbRead = sscanf( LutRedDescriptor.c_str(), + "%d\\%d\\%d", + &lengthB, &debB, &nbitsB ); + if( nbRead != 3 ) + { + gdcmWarningMacro( "Wrong Blue LUT descriptor" ); + } + + //////////////////////////////////////////////////////// + if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) ) + { + return; + } + + //////////////////////////////////////////////// + // 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; + if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) ) + { + // when LUT item size is different than pixel size + mult = 2; // high byte must be = low byte + } + else + { + // See PS 3.3-2003 C.11.1.1.2 p 619 + mult = 1; + } + + // if we get a black image, let's just remove the '+1' + // from 'i*mult+1' and check again + // 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 + // (optimistic asumption) + int i; + uint8_t *a = LutRGBA + 0; + for( i=0; i < lengthR; ++i ) + { + *a = LutRedData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 1; + for( i=0; i < lengthG; ++i) + { + *a = LutGreenData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 2; + for(i=0; i < lengthB; ++i) + { + *a = LutBlueData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 3; + for(i=0; i < 256; ++i) + { + *a = 1; // Alpha component + a += 4; + } +} + +/** + * \brief Swap the bytes, according to \ref SwapCode. + */ +void PixelReadConvert::ConvertSwapZone() +{ + unsigned int i; + + if( BitsAllocated == 16 ) + { + uint16_t *im16 = (uint16_t*)Raw; + switch( SwapCode ) + { + case 1234: + break; + case 3412: + case 2143: + case 4321: + for( i = 0; i < RawSize / 2; i++ ) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } + break; + default: + gdcmWarningMacro("SwapCode value (16 bits) not allowed."); + } + } + else if( BitsAllocated == 32 ) + { + uint32_t s32; + uint16_t high; + uint16_t low; + uint32_t *im32 = (uint32_t*)Raw; + switch ( SwapCode ) + { + case 1234: + break; + case 4321: + for( i = 0; i < RawSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 4321 + high = im32[i] >> 16; + high = ( high >> 8 ) | ( high << 8 ); + low = ( low >> 8 ) | ( low << 8 ); + s32 = low; + im32[i] = ( s32 << 16 ) | high; + } + break; + case 2143: + for( i = 0; i < RawSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 2143 + high = im32[i] >> 16; + high = ( high >> 8 ) | ( high << 8 ); + low = ( low >> 8 ) | ( low << 8 ); + s32 = high; + im32[i] = ( s32 << 16 ) | low; + } + break; + case 3412: + for( i = 0; i < RawSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 3412 + high = im32[i] >> 16; + s32 = low; + im32[i] = ( s32 << 16 ) | high; + } + break; + default: + gdcmWarningMacro("SwapCode value (32 bits) not allowed." ); + } + } +} + +/** + * \brief Deal with endianness i.e. re-arange bytes inside the integer + */ +void PixelReadConvert::ConvertReorderEndianity() +{ + if ( BitsAllocated != 8 ) + { + ConvertSwapZone(); + } + + // Special kludge in order to deal with xmedcon broken images: + if ( BitsAllocated == 16 + && BitsStored < BitsAllocated + && !PixelSign ) + { + int l = (int)( RawSize / ( BitsAllocated / 8 ) ); + uint16_t *deb = (uint16_t *)Raw; + for(int i = 0; i> ( BitsAllocated - BitsStored ); + uint16_t *deb = (uint16_t*)Raw; + for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; + deb++; + } + } + else if ( BitsAllocated == 32 ) + { + uint32_t mask = 0xffffffff; + mask = mask >> ( BitsAllocated - BitsStored ); + uint32_t *deb = (uint32_t*)Raw; + for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; + deb++; + } + } + else + { + gdcmWarningMacro("Weird image"); + throw FormatError( "Weird image !?" ); + } + } + return true; +} + +/** + * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels + * \warning Works on all the frames at a time + */ +void PixelReadConvert::ConvertRGBPlanesToRGBPixels() +{ + uint8_t *localRaw = Raw; + uint8_t *copyRaw = new uint8_t[ RawSize ]; + memmove( copyRaw, localRaw, RawSize ); + + int l = XSize * YSize * ZSize; + + uint8_t *a = copyRaw; + uint8_t *b = copyRaw + l; + uint8_t *c = copyRaw + l + l; + + for (int j = 0; j < l; j++) + { + *(localRaw++) = *(a++); + *(localRaw++) = *(b++); + *(localRaw++) = *(c++); + } + delete[] copyRaw; +} + +/** + * \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 ]; + 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 : + // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf + // and be *very* affraid + // + int l = XSize * YSize; + int nbFrames = ZSize; + + 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 + /// counterpart. Refer to + /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf + /// for code optimisation. + + for ( int i = 0; i < nbFrames; i++ ) + { + for ( int j = 0; j < l; j++ ) + { + R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; + G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; + B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; + + if (R < 0.0) R = 0.0; + if (G < 0.0) G = 0.0; + if (B < 0.0) B = 0.0; + if (R > 255.0) R = 255.0; + if (G > 255.0) G = 255.0; + if (B > 255.0) B = 255.0; + + *(localRaw++) = (uint8_t)R; + *(localRaw++) = (uint8_t)G; + *(localRaw++) = (uint8_t)B; + a++; + b++; + c++; + } + } + delete[] copyRaw; +} + +/// \brief Deals with the color decoding i.e. handle: +/// - R, G, B planes (as opposed to RGB pixels) +/// - YBR (various) encodings. +/// - LUT[s] (or "PALETTE COLOR"). + +void PixelReadConvert::ConvertHandleColor() +{ + ////////////////////////////////// + // Deal with the color decoding i.e. handle: + // - R, G, B planes (as opposed to RGB pixels) + // - YBR (various) encodings. + // - LUT[s] (or "PALETTE COLOR"). + // + // The classification in the color decoding schema is based on the blending + // of two Dicom tags values: + // * "Photometric Interpretation" for which we have the cases: + // - [Photo A] MONOCHROME[1|2] pictures, + // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB), + // - [Photo C] YBR_* (with the above exception of YBR_FULL_422) + // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s]. + // * "Planar Configuration" for which we have the cases: + // - [Planar 0] 0 then Pixels are already RGB + // - [Planar 1] 1 then we have 3 planes : R, G, B, + // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs + // + // Now in theory, one could expect some coherence when blending the above + // cases. For example we should not encounter files belonging at the + // time to case [Planar 0] and case [Photo D]. + // Alas, this was only theory ! Because in practice some odd (read ill + // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter: + // - "Planar Configuration" = 0, + // - "Photometric Interpretation" = "PALETTE COLOR". + // 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 + // a LUT intervention >> + // + // Now we are left with the following handling of the cases: + // - [Planar 0] OR [Photo A] no color decoding (since respectively + // Pixels are already RGB and monochrome pictures have no color :), + // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels() + // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels() + // - [Planar 2] OR [Photo D] requires LUT intervention. + + if ( ! IsRawRGB() ) + { + // [Planar 2] OR [Photo D]: LUT intervention done outside + return; + } + + if ( PlanarConfiguration == 1 ) + { + if ( IsYBRFull ) + { + // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB) + ConvertYcBcRPlanesToRGBPixels(); + } + else + { + // [Planar 1] AND [Photo C] + ConvertRGBPlanesToRGBPixels(); + } + return; + } + + // When planarConf is 0, and RLELossless (forbidden by Dicom norm) + // pixels need to be RGB-fied anyway + if (IsRLELossless) + { + ConvertRGBPlanesToRGBPixels(); + } + // In *normal *case, when planarConf is 0, pixels are already in RGB +} + +/// Computes the Pixels Size +void PixelReadConvert::ComputeRawAndRGBSizes() +{ + int bitsAllocated = BitsAllocated; + // Number of "Bits Allocated" is fixed to 16 when it's 12, since + // in this case we will expand the image to 16 bits (see + // \ref ReadAndDecompress12BitsTo16Bits() ) + if ( BitsAllocated == 12 ) + { + bitsAllocated = 16; + } + + RawSize = XSize * YSize * ZSize + * ( bitsAllocated / 8 ) + * SamplesPerPixel; + if ( HasLUT ) + { + RGBSize = 3 * RawSize; + } + else + { + RGBSize = RawSize; + } +} + +/// Allocates room for RGB Pixels +void PixelReadConvert::AllocateRGB() +{ + if ( RGB ) + delete [] RGB; + RGB = new uint8_t[RGBSize]; +} + +/// Allocates room for RAW Pixels +void PixelReadConvert::AllocateRaw() +{ + if ( Raw ) + delete [] Raw; + Raw = new uint8_t[RawSize]; +} + +//----------------------------------------------------------------------------- +// Print +/** + * \brief Print self. + * @param indent Indentation string to be prepended during printing. + * @param os Stream to print to. + */ +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; + + if ( IsRLELossless ) + { + if ( RLEInfo ) + { + RLEInfo->Print( os, indent ); + } + else + { + gdcmWarningMacro("Set as RLE file but NO RLEinfo present."); + } + } + + if ( IsJPEG2000 || IsJPEGLossless || IsJPEGLossy || IsJPEGLS ) + { + if ( JPEGInfo ) + { + JPEGInfo->Print( os, indent ); + } + else + { + gdcmWarningMacro("Set as JPEG file but NO JPEGinfo present."); + } + } +} + +//----------------------------------------------------------------------------- +} // end namespace gdcm + +// NOTES on File internal calls +// User +// ---> GetImageData +// ---> GetImageDataIntoVector +// |---> GetImageDataIntoVectorRaw +// | lut intervention +// User +// ---> GetImageDataRaw +// ---> GetImageDataIntoVectorRaw +