X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=6b9138b2ad26ea1e6d59b624994fc358ef04e202;hb=8ac4df8c7543a827c7b89fc9bbcf86625f3c1afe;hp=62051158b1acc18cb5bebfd277f9a013b749acb1;hpb=689f929ff0f35aabd30d81ffa75eb66fdf1a3c16;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 62051158..6b9138b2 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/09/29 17:33:17 $ - Version: $Revision: 1.132 $ + Date: $Date: 2004/10/01 12:40:57 $ + Version: $Revision: 1.134 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -519,66 +519,17 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) bool signedPixel = Header->IsSignedPixelData(); -// SPLIT ME -//////////////////////////////////////////////////////// -// ENDIANITY SECTION: re-arange bytes inside the integer - if ( numberBitsAllocated != 8 ) - { - SwapZone( destination, Header->GetSwapCode(), ImageDataSize, - numberBitsAllocated ); - } - - // to avoid pb with some xmedcon breakers images - if ( ( numberBitsAllocated == 16 ) - && ( numberBitsStored < numberBitsAllocated ) - && ( ! signedPixel ) ) - { - int l = (int)(ImageDataSize / (numberBitsAllocated/8)); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> ( numberBitsAllocated - numberBitsStored ); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; - deb++; - } - } - else if ( numberBitsAllocated == 32 ) - { - uint32_t mask = 0xffffffff; - mask = mask >> ( numberBitsAllocated - numberBitsStored ); - uint32_t *deb = (uint32_t *)destination; - for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; - deb++; - } - } - else - { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); - return 0; - } - } + ConvertReArrangeBits( (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + highBitPosition ); #ifdef GDCM_DEBUG FILE* DebugFile; @@ -608,98 +559,36 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( - int planConf = Header->GetPlanarConfiguration(); // 0028,0006 + int planConf = Header->GetPlanarConfiguration(); - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if ( Header->IsPaletteColor() ) + // Planar configuration = 2 ==> 1 gray Plane + 3 LUT + // ...and... + // whatever the Planar Configuration might be, "PALETTE COLOR " + // implies that we deal with the palette. + if ( ( planConf == 2 ) || Header->IsPaletteColor() ) { - planConf = 2; + return ImageDataSize; } - switch ( planConf ) - { - case 0: - // Pixels are already RGB - break; - case 1: - if ( Header->IsYBRFull() ) - { - // Warning : YBR_FULL_422 acts as RGB - // : we need to make RGB Pixels from Planes Y,cB,cR - - // 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 = Header->GetXSize() * Header->GetYSize(); - int nbFrames = Header->GetZSize(); - - uint8_t* newDest = new uint8_t[ImageDataSize]; - uint8_t* x = newDest; - uint8_t* a = (uint8_t*)destination; - uint8_t* b = a + l; - uint8_t* c = b + l; - double R,G,B; - - /// \todo : Replace by the 'well known' integer computation - /// counterpart - /// see 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; - - *(x++) = (uint8_t)R; - *(x++) = (uint8_t)G; - *(x++) = (uint8_t)B; - a++; b++; c++; - } - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - else - { - // need to make RGB Pixels from R,G,B Planes - // (all the Frames at a time) + // When planConf is 0, pixels are allready in RGB - int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); - - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *x = newDest; - uint8_t *a = (uint8_t *)destination; - uint8_t *b = a + l; - uint8_t *c = b + l; - - for (int j = 0; j < l; j++) - { - *(x++) = *(a++); - *(x++) = *(b++); - *(x++) = *(c++); - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - break; - case 2: - // Palettes were found - // Let the user deal with them ! - return ImageDataSize; + if ( planConf == 1 ) + { + uint8_t* newDest = new uint8_t[ImageDataSize]; + // Warning : YBR_FULL_422 acts as RGB + if ( Header->IsYBRFull() ) + { + ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest); + } + else + { + ConvertRGBPlanesToRGBPixels((uint8_t*)destination, newDest); + } + memmove(destination, newDest, ImageDataSize); + delete[] newDest; } + +/////////////////////////////////////////////////// // now, it's an RGB image // Lets's write it in the Header @@ -722,6 +611,154 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) return ImageDataSize; } +/** + * \brief Re-arrange the bits within the bytes. + */ +void gdcmFile::ConvertReArrangeBits( uint8_t* pixelZone, + size_t imageDataSize, + int numberBitsStored, + int numberBitsAllocated, + int highBitPosition) + throw ( gdcmFormatError ) +{ + if ( numberBitsStored != numberBitsAllocated ) + { + int l = (int)(imageDataSize / (numberBitsAllocated/8)); + if ( numberBitsAllocated == 16 ) + { + uint16_t mask = 0xffff; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint16_t* deb = (uint16_t*)pixelZone; + for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; + deb++; + } + } + else if ( numberBitsAllocated == 32 ) + { + uint32_t mask = 0xffffffff; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint32_t* deb = (uint32_t*)pixelZone; + for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; + deb++; + } + } + else + { + dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image"); + throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()", + "weird image !?" ); + } + } +} + +/** + * \brief Deal with endianity i.e. re-arange bytes inside the integer + */ +void gdcmFile::ConvertReorderEndianity( uint8_t* pixelZone, + size_t imageDataSize, + int numberBitsStored, + int numberBitsAllocated, + bool signedPixel) +{ + if ( numberBitsAllocated != 8 ) + { + SwapZone( pixelZone, Header->GetSwapCode(), ImageDataSize, + numberBitsAllocated ); + } + + // Special kludge in order to deal with xmedcon broken images: + if ( ( numberBitsAllocated == 16 ) + && ( numberBitsStored < numberBitsAllocated ) + && ( ! signedPixel ) ) + { + int l = (int)(ImageDataSize / (numberBitsAllocated/8)); + uint16_t *deb = (uint16_t *)pixelZone; + for(int i = 0; iGetXSize() * Header->GetYSize(); + int nbFrames = Header->GetZSize(); + + uint8_t* a = source; + uint8_t* b = source + l; + uint8_t* c = source + 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; + + *(destination++) = (uint8_t)R; + *(destination++) = (uint8_t)G; + *(destination++) = (uint8_t)B; + a++; + b++; + c++; + } + } +} + +/** + * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels + * \warning Works on all the frames at a time + */ +void gdcmFile::ConvertRGBPlanesToRGBPixels(uint8_t* source, + uint8_t* destination) +{ + int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); + + uint8_t* a = source; + uint8_t* b = source + l; + uint8_t* c = source + l + l; + + for (int j = 0; j < l; j++) + { + *(destination++) = *(a++); + *(destination++) = *(b++); + *(destination++) = *(c++); + } +} + /** * \brief Points the internal Pixel_Data pointer to the callers inData * image representation, BUT WITHOUT COPYING THE DATA. @@ -1014,32 +1051,12 @@ bool gdcmFile::ReadPixelData(void* destination) return false; } - // ---------------------- Compacted File (12 Bits Per Pixel) - // unpack 12 Bits pixels into 16 Bits pixels - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - if ( Header->GetBitsAllocated() == 12 ) { - int nbPixels = Header->GetXSize() * Header->GetYSize(); - uint8_t b0, b1, b2; - - uint16_t* pdestination = (uint16_t*)destination; - for(int p = 0; p < nbPixels; p += 2 ) - { - fread(&b0,1,1,fp); - fread(&b1,1,1,fp); - fread(&b2,1,1,fp); - - //Two steps is necessary to please VC++ - *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // A B D - *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - // F C E - - // Troubles expected on Big-Endian processors ? - } - + ConvertDecompress12BitsTo16Bits( (uint8_t*)destination, + Header->GetXSize(), + Header->GetYSize(), + fp); Header->CloseFile(); return true; } @@ -1072,22 +1089,13 @@ bool gdcmFile::ReadPixelData(void* destination) } // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) - { - nb = 16; - } - else + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) { - nb = atoi( str_nb.c_str() ); - if ( nb == 12 ) - { - nb = 16; // ?? 12 should be ACR-NEMA only - } + numberBitsAllocated = 16; } - int nBytes= nb/8; + int nBytes= numberBitsAllocated/8; int taille = Header->GetXSize() * Header->GetYSize() * Header->GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek @@ -1200,4 +1208,57 @@ bool gdcmFile::ReadPixelData(void* destination) Header->CloseFile(); return res; } + +/** + * \brief Read from file a 12 bits per pixel image and uncompress it + * into a 16 bits per pixel image. + */ +void gdcmFile::ConvertDecompress12BitsTo16Bits( + uint8_t* pixelZone, + int sizeX, + int sizeY, + FILE* filePtr) + throw ( gdcmFormatError ) +{ + int nbPixels = sizeX * sizeY; + uint16_t* destination = (uint16_t*)pixelZone; + + for( int p = 0; p < nbPixels; p += 2 ) + { + uint8_t b0, b1, b2; + size_t ItemRead; + + ItemRead = fread( &b0, 1, 1, filePtr); + if ( ItemRead != 1 ) + { + throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", + "Unfound first block" ); + } + + ItemRead = fread( &b1, 1, 1, filePtr); + if ( ItemRead != 1 ) + { + throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", + "Unfound second block" ); + } + + ItemRead = fread( &b2, 1, 1, filePtr); + if ( ItemRead != 1 ) + { + throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", + "Unfound second block" ); + } + + // Two steps are necessary to please VC++ + // + // 2 pixels 12bit = [0xABCDEF] + // 2 pixels 16bit = [0x0ABD] + [0x0FCE] + // A B D + *destination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); + // F C E + *destination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); + + /// \todo JPR Troubles expected on Big-Endian processors ? + } +} //-----------------------------------------------------------------------------