1 /*=========================================================================
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4 Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
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6 Date: $Date: 2004/12/12 17:21:07 $
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7 Version: $Revision: 1.6 $
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9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
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10 l'Image). All rights reserved. See Doc/License.txt or
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11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
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13 This software is distributed WITHOUT ANY WARRANTY; without even
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14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 PURPOSE. See the above copyright notices for more information.
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17 =========================================================================*/
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19 ////////////////// TEMPORARY NOTE
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20 // look for "fixMem" and convert that to a member of this class
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21 // Removing the prefix fixMem and dealing with allocations should do the trick
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23 // grep PixelReadConvert everywhere and clean up !
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25 #include "gdcmDebug.h"
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26 #include "gdcmHeader.h"
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27 #include "gdcmPixelReadConvert.h"
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28 #include "gdcmDocEntry.h"
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29 #include "gdcmRLEFramesInfo.h"
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30 #include "gdcmJPEGFragmentsInfo.h"
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33 #include <stdio.h> //for sscanf
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37 #define str2num(str, typeNum) *((typeNum *)(str))
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39 // For JPEG 2000, body in file gdcmJpeg2000.cxx
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40 bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer);
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42 #define JOCTET uint8_t
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43 // For JPEG 8 Bits, body in file gdcmJpeg8.cxx
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44 bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer);
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45 bool gdcm_read_JPEG_memory8 (const JOCTET* buffer, const size_t buflen,
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47 size_t *howManyRead, size_t *howManyWritten);
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49 // For JPEG 12 Bits, body in file gdcmJpeg12.cxx
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50 bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer);
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51 bool gdcm_read_JPEG_memory12 (const JOCTET *buffer, const size_t buflen,
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53 size_t *howManyRead, size_t *howManyWritten);
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55 // For JPEG 16 Bits, body in file gdcmJpeg16.cxx
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56 // Beware this is misleading there is no 16bits DCT algorithm, only
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57 // jpeg lossless compression exist in 16bits.
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58 bool gdcm_read_JPEG_file16 (std::ifstream* fp, void* image_buffer);
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59 bool gdcm_read_JPEG_memory16 (const JOCTET *buffer, const size_t buflen,
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61 size_t *howManyRead, size_t *howManyWritten);
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64 //-----------------------------------------------------------------------------
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65 // Constructor / Destructor
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66 PixelReadConvert::PixelReadConvert()
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78 void PixelReadConvert::Squeeze()
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99 PixelReadConvert::~PixelReadConvert()
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104 void PixelReadConvert::AllocateRGB()
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109 RGB = new uint8_t[ RGBSize ];
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112 void PixelReadConvert::AllocateRaw()
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117 Raw = new uint8_t[ RawSize ];
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121 * \brief Read from file a 12 bits per pixel image and decompress it
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122 * into a 16 bits per pixel image.
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124 void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp )
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125 throw ( FormatError )
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127 int nbPixels = XSize * YSize;
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128 uint16_t* localDecompres = (uint16_t*)Raw;
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130 for( int p = 0; p < nbPixels; p += 2 )
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132 uint8_t b0, b1, b2;
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134 fp->read( (char*)&b0, 1);
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135 if ( fp->fail() || fp->eof() )//Fp->gcount() == 1
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137 throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
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138 "Unfound first block" );
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141 fp->read( (char*)&b1, 1 );
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142 if ( fp->fail() || fp->eof())//Fp->gcount() == 1
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144 throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
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145 "Unfound second block" );
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148 fp->read( (char*)&b2, 1 );
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149 if ( fp->fail() || fp->eof())//Fp->gcount() == 1
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151 throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
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152 "Unfound second block" );
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155 // Two steps are necessary to please VC++
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157 // 2 pixels 12bit = [0xABCDEF]
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158 // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
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160 *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
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162 *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
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164 /// \todo JPR Troubles expected on Big-Endian processors ?
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169 * \brief Try to deal with RLE 16 Bits.
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170 * We assume the RLE has allready been parsed and loaded in
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171 * Raw (through \ref ReadAndDecompressJPEGFile ).
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172 * We here need to make 16 Bits Pixels from Low Byte and
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173 * High Byte 'Planes'...(for what it may mean)
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176 bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )
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178 size_t PixelNumber = XSize * YSize;
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179 size_t RawSize = XSize * YSize * NumberOfFrames;
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181 // We assumed Raw contains the decoded RLE pixels but as
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182 // 8 bits per pixel. In order to convert those pixels to 16 bits
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183 // per pixel we cannot work in place within Raw and hence
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184 // we copy it in a safe place, say copyRaw.
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186 uint8_t* copyRaw = new uint8_t[ RawSize * 2 ];
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187 memmove( copyRaw, Raw, RawSize * 2 );
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190 uint8_t* a = copyRaw;
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191 uint8_t* b = a + PixelNumber;
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193 for ( int i = 0; i < NumberOfFrames; i++ )
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195 for ( unsigned int j = 0; j < PixelNumber; j++ )
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204 /// \todo check that operator new []didn't fail, and sometimes return false
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209 * \brief Implementation of the RLE decoding algorithm for decompressing
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210 * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86]
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211 * @param subRaw Sub region of \ref Raw where the de
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212 * decoded fragment should be placed.
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213 * @param fragmentSize The length of the binary fragment as found on the disk.
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214 * @param RawSegmentSize The expected length of the fragment ONCE
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216 * @param fp File Pointer: on entry the position should be the one of
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217 * the fragment to be decoded.
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219 bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subRaw,
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221 long RawSegmentSize,
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222 std::ifstream* fp )
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225 long numberOfOutputBytes = 0;
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226 long numberOfReadBytes = 0;
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228 while( numberOfOutputBytes < RawSegmentSize )
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230 fp->read( (char*)&count, 1 );
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231 numberOfReadBytes += 1;
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233 // Note: count <= 127 comparison is always true due to limited range
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234 // of data type int8_t [since the maximum of an exact width
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235 // signed integer of width N is 2^(N-1) - 1, which for int8_t
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238 fp->read( (char*)subRaw, count + 1);
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239 numberOfReadBytes += count + 1;
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240 subRaw += count + 1;
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241 numberOfOutputBytes += count + 1;
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245 if ( ( count <= -1 ) && ( count >= -127 ) )
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248 fp->read( (char*)&newByte, 1);
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249 numberOfReadBytes += 1;
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250 for( int i = 0; i < -count + 1; i++ )
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252 subRaw[i] = newByte;
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254 subRaw += -count + 1;
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255 numberOfOutputBytes += -count + 1;
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258 // if count = 128 output nothing
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260 if ( numberOfReadBytes > fragmentSize )
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262 dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we "
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263 "read more bytes than the segment size.");
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271 * \brief Reads from disk the Pixel Data of 'Run Length Encoded'
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272 * Dicom encapsulated file and decompress it.
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273 * @param fp already open File Pointer
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274 * at which the pixel data should be copied
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277 bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp )
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279 uint8_t* subRaw = Raw;
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280 long RawSegmentSize = XSize * YSize;
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282 // Loop on the frame[s]
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283 for( RLEFramesInfo::RLEFrameList::iterator
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284 it = RLEInfo->Frames.begin();
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285 it != RLEInfo->Frames.end();
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288 // Loop on the fragments
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289 for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ )
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291 fp->seekg( (*it)->Offset[k] , std::ios::beg );
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292 (void)ReadAndDecompressRLEFragment( subRaw,
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296 subRaw += RawSegmentSize;
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300 if ( BitsAllocated == 16 )
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302 // Try to deal with RLE 16 Bits
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303 (void)DecompressRLE16BitsFromRLE8Bits( ZSize );
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310 * \brief Swap the bytes, according to \ref SwapCode.
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312 void PixelReadConvert::ConvertSwapZone()
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316 if( BitsAllocated == 16 )
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318 uint16_t* im16 = (uint16_t*)Raw;
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329 for( i = 0; i < RawSize / 2; i++ )
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331 im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
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335 dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "
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336 "(16 bits) not allowed." );
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339 else if( BitsAllocated == 32 )
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344 uint32_t* im32 = (uint32_t*)Raw;
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345 switch ( SwapCode )
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351 for( i = 0; i < RawSize / 4; i++ )
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353 low = im32[i] & 0x0000ffff; // 4321
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354 high = im32[i] >> 16;
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355 high = ( high >> 8 ) | ( high << 8 );
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356 low = ( low >> 8 ) | ( low << 8 );
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358 im32[i] = ( s32 << 16 ) | high;
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362 for( i = 0; i < RawSize / 4; i++ )
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364 low = im32[i] & 0x0000ffff; // 2143
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365 high = im32[i] >> 16;
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366 high = ( high >> 8 ) | ( high << 8 );
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367 low = ( low >> 8 ) | ( low << 8 );
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369 im32[i] = ( s32 << 16 ) | low;
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373 for( i = 0; i < RawSize / 4; i++ )
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375 low = im32[i] & 0x0000ffff; // 3412
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376 high = im32[i] >> 16;
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378 im32[i] = ( s32 << 16 ) | high;
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382 dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "
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383 "(32 bits) not allowed." );
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389 * \brief Deal with endianity i.e. re-arange bytes inside the integer
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391 void PixelReadConvert::ConvertReorderEndianity()
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393 if ( BitsAllocated != 8 )
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398 // Special kludge in order to deal with xmedcon broken images:
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399 if ( ( BitsAllocated == 16 )
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400 && ( BitsStored < BitsAllocated )
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401 && ( ! PixelSign ) )
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403 int l = (int)( RawSize / ( BitsAllocated / 8 ) );
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404 uint16_t *deb = (uint16_t *)Raw;
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405 for(int i = 0; i<l; i++)
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407 if( *deb == 0xffff )
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418 * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
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419 * file and decompress it. This funciton assumes that each
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420 * jpeg fragment contains a whole frame (jpeg file).
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421 * @param fp File Pointer
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424 bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream* fp )
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426 uint8_t* localRaw = Raw;
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427 // Loop on the fragment[s]
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428 for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
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429 it = JPEGInfo->Fragments.begin();
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430 it != JPEGInfo->Fragments.end();
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433 fp->seekg( (*it)->Offset, std::ios::beg);
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435 if ( BitsStored == 8)
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437 // JPEG Lossy : call to IJG 6b
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438 if ( ! gdcm_read_JPEG_file8( fp, localRaw ) )
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443 else if ( BitsStored <= 12)
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445 // Reading Fragment pixels
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446 if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) )
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451 else if ( BitsStored <= 16)
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453 // Reading Fragment pixels
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454 if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) )
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458 //assert( IsJPEGLossless );
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462 // other JPEG lossy not supported
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463 dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown "
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464 "jpeg lossy compression ");
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468 // Advance to next free location in Raw
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469 // for next fragment decompression (if any)
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470 int length = XSize * YSize * SamplesPerPixel;
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471 int numberBytes = BitsAllocated / 8;
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473 localRaw += length * numberBytes;
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479 * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
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480 * file and decompress it. This function assumes that the dicom
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481 * image is a single frame split into several JPEG fragments.
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482 * Those fragments will be glued together into a memory buffer
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483 * before being read.
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484 * @param fp File Pointer
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487 bool PixelReadConvert::
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488 ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream* fp )
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490 // Loop on the fragment[s] to get total length
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491 size_t totalLength = 0;
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492 for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
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493 it = JPEGInfo->Fragments.begin();
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494 it != JPEGInfo->Fragments.end();
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497 totalLength += (*it)->Length;
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500 // Concatenate the jpeg fragments into a local buffer
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501 JOCTET *buffer = new JOCTET [totalLength];
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502 JOCTET *p = buffer;
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504 uint8_t* localRaw = Raw;
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505 // Loop on the fragment[s]
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506 for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
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507 it = JPEGInfo->Fragments.begin();
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508 it != JPEGInfo->Fragments.end();
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511 fp->seekg( (*it)->Offset, std::ios_base::beg);
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512 size_t len = (*it)->Length;
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513 fp->read((char *)p,len);
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517 size_t howManyRead = 0;
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518 size_t howManyWritten = 0;
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519 size_t fragmentLength = 0;
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521 if ( BitsStored == 8)
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523 if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw,
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524 &howManyRead, &howManyWritten ) )
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527 "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 "
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533 else if ( BitsStored <= 12)
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535 if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw,
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536 &howManyRead, &howManyWritten ) )
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539 "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 "
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545 else if ( BitsStored <= 16)
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548 if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw,
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549 &howManyRead, &howManyWritten ) )
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552 "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 "
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560 // other JPEG lossy not supported
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561 dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "
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562 "jpeg lossy compression ");
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567 // free local buffer
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574 * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
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575 * file and decompress it. This function handles the generic
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576 * and complex case where the DICOM contains several frames,
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577 * and some of the frames are possibly split into several JPEG
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579 * @param fp File Pointer
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582 bool PixelReadConvert::
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583 ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream* fp )
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585 // Loop on the fragment[s] to get total length
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586 size_t totalLength = 0;
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587 for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
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588 it = JPEGInfo->Fragments.begin();
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589 it != JPEGInfo->Fragments.end();
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592 totalLength += (*it)->Length;
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595 // Concatenate the jpeg fragments into a local buffer
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596 JOCTET *buffer = new JOCTET [totalLength];
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597 JOCTET *p = buffer;
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599 uint8_t* localRaw = Raw;
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600 // Loop on the fragment[s]
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601 for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
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602 it = JPEGInfo->Fragments.begin();
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603 it != JPEGInfo->Fragments.end();
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606 fp->seekg( (*it)->Offset, std::ios_base::beg);
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607 size_t len = (*it)->Length;
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608 fp->read((char *)p,len);
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612 size_t howManyRead = 0;
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613 size_t howManyWritten = 0;
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614 size_t fragmentLength = 0;
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616 for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
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617 it = JPEGInfo->Fragments.begin() ;
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618 (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength);
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621 fragmentLength += (*it)->Length;
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623 if (howManyRead > fragmentLength) continue;
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625 if ( BitsStored == 8)
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627 if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead,
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628 Raw+howManyWritten,
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629 &howManyRead, &howManyWritten ) )
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631 dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 ");
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636 else if ( BitsStored <= 12)
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639 if ( ! gdcm_read_JPEG_memory12( buffer+howManyRead, totalLength-howManyRead,
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640 Raw+howManyWritten,
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641 &howManyRead, &howManyWritten ) )
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643 dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 ");
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648 else if ( BitsStored <= 16)
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651 if ( ! gdcm_read_JPEG_memory16( buffer+howManyRead, totalLength-howManyRead,
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652 Raw+howManyWritten,
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653 &howManyRead, &howManyWritten ) )
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655 dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 ");
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662 // other JPEG lossy not supported
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663 dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "
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664 "jpeg lossy compression ");
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669 if (howManyRead < fragmentLength)
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670 howManyRead = fragmentLength;
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673 // free local buffer
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680 * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
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681 * file and decompress it.
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682 * @param fp File Pointer
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685 bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp )
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689 fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios_base::beg);
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690 if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
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694 if ( ( ZSize == 1 ) && ( JPEGInfo->Fragments.size() > 1 ) )
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696 // we have one frame split into several fragments
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697 // we will pack those fragments into a single buffer and
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699 return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp );
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701 else if (JPEGInfo->Fragments.size() == ZSize)
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703 // suppose each fragment is a frame
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704 return ReadAndDecompressJPEGFramesFromFile( fp );
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708 // The dicom image contains frames containing fragments of images
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709 // a more complex algorithm :-)
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710 return ReadAndDecompressJPEGFragmentedFramesFromFile( fp );
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715 * \brief Re-arrange the bits within the bytes.
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718 bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
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720 if ( BitsStored != BitsAllocated )
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722 int l = (int)( RawSize / ( BitsAllocated / 8 ) );
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723 if ( BitsAllocated == 16 )
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725 uint16_t mask = 0xffff;
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726 mask = mask >> ( BitsAllocated - BitsStored );
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727 uint16_t* deb = (uint16_t*)Raw;
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728 for(int i = 0; i<l; i++)
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730 *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
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734 else if ( BitsAllocated == 32 )
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736 uint32_t mask = 0xffffffff;
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737 mask = mask >> ( BitsAllocated - BitsStored );
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738 uint32_t* deb = (uint32_t*)Raw;
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739 for(int i = 0; i<l; i++)
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741 *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
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747 dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image");
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748 throw FormatError( "PixelReadConvert::ConvertReArrangeBits()",
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749 "weird image !?" );
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756 * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
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757 * \warning Works on all the frames at a time
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759 void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
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761 uint8_t* localRaw = Raw;
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762 uint8_t* copyRaw = new uint8_t[ RawSize ];
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763 memmove( copyRaw, localRaw, RawSize );
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765 // to see the tricks about YBR_FULL, YBR_FULL_422,
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766 // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
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767 // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
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768 // and be *very* affraid
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770 int l = XSize * YSize;
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771 int nbFrames = ZSize;
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773 uint8_t* a = copyRaw;
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774 uint8_t* b = copyRaw + l;
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775 uint8_t* c = copyRaw + l + l;
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778 /// \todo : Replace by the 'well known' integer computation
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779 /// counterpart. Refer to
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780 /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
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781 /// for code optimisation.
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783 for ( int i = 0; i < nbFrames; i++ )
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785 for ( int j = 0; j < l; j++ )
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787 R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
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788 G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
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789 B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
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791 if (R < 0.0) R = 0.0;
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792 if (G < 0.0) G = 0.0;
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793 if (B < 0.0) B = 0.0;
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794 if (R > 255.0) R = 255.0;
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795 if (G > 255.0) G = 255.0;
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796 if (B > 255.0) B = 255.0;
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798 *(localRaw++) = (uint8_t)R;
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799 *(localRaw++) = (uint8_t)G;
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800 *(localRaw++) = (uint8_t)B;
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810 * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
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811 * \warning Works on all the frames at a time
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813 void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
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815 uint8_t* localRaw = Raw;
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816 uint8_t* copyRaw = new uint8_t[ RawSize ];
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817 memmove( copyRaw, localRaw, RawSize );
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819 int l = XSize * YSize * ZSize;
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821 uint8_t* a = copyRaw;
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822 uint8_t* b = copyRaw + l;
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823 uint8_t* c = copyRaw + l + l;
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825 for (int j = 0; j < l; j++)
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827 *(localRaw++) = *(a++);
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828 *(localRaw++) = *(b++);
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829 *(localRaw++) = *(c++);
\r
834 bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp )
\r
836 // ComputeRawAndRGBSizes is already made by
\r
837 // ::GrabInformationsFromHeader. So, the structure sizes are
\r
841 //////////////////////////////////////////////////
\r
842 //// First stage: get our hands on the Pixel Data.
\r
845 dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
\r
846 "unavailable file pointer." );
\r
850 fp->seekg( PixelOffset, std::ios::beg );
\r
851 if( fp->fail() || fp->eof()) //Fp->gcount() == 1
\r
853 dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
\r
854 "unable to find PixelOffset in file." );
\r
860 //////////////////////////////////////////////////
\r
861 //// Second stage: read from disk dans decompress.
\r
862 if ( BitsAllocated == 12 )
\r
864 ReadAndDecompress12BitsTo16Bits( fp);
\r
868 // This problem can be found when some obvious informations are found
\r
869 // after the field containing the image datas. In this case, these
\r
870 // bad datas are added to the size of the image (in the PixelDataLength
\r
871 // variable). But RawSize is the right size of the image !
\r
872 if( PixelDataLength != RawSize)
\r
874 dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
\r
875 "Mismatch between PixelReadConvert and RawSize." );
\r
877 if( PixelDataLength > RawSize)
\r
879 fp->read( (char*)Raw, RawSize);
\r
883 fp->read( (char*)Raw, PixelDataLength);
\r
886 if ( fp->fail() || fp->eof())//Fp->gcount() == 1
\r
888 dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
\r
889 "reading of Raw pixel data failed." );
\r
893 else if ( IsRLELossless )
\r
895 if ( ! ReadAndDecompressRLEFile( fp ) )
\r
897 dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
\r
898 "RLE decompressor failed." );
\r
904 // Default case concerns JPEG family
\r
905 if ( ! ReadAndDecompressJPEGFile( fp ) )
\r
907 dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
\r
908 "JPEG decompressor failed." );
\r
913 ////////////////////////////////////////////
\r
914 //// Third stage: twigle the bytes and bits.
\r
915 ConvertReorderEndianity();
\r
916 ConvertReArrangeBits();
\r
917 ConvertHandleColor();
\r
922 void PixelReadConvert::ConvertHandleColor()
\r
924 //////////////////////////////////
\r
925 // Deal with the color decoding i.e. handle:
\r
926 // - R, G, B planes (as opposed to RGB pixels)
\r
927 // - YBR (various) encodings.
\r
928 // - LUT[s] (or "PALETTE COLOR").
\r
930 // The classification in the color decoding schema is based on the blending
\r
931 // of two Dicom tags values:
\r
932 // * "Photometric Interpretation" for which we have the cases:
\r
933 // - [Photo A] MONOCHROME[1|2] pictures,
\r
934 // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB),
\r
935 // - [Photo C] YBR_* (with the above exception of YBR_FULL_422)
\r
936 // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s].
\r
937 // * "Planar Configuration" for which we have the cases:
\r
938 // - [Planar 0] 0 then Pixels are already RGB
\r
939 // - [Planar 1] 1 then we have 3 planes : R, G, B,
\r
940 // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs
\r
942 // Now in theory, one could expect some coherence when blending the above
\r
943 // cases. For example we should not encounter files belonging at the
\r
944 // time to case [Planar 0] and case [Photo D].
\r
945 // Alas, this was only theory ! Because in practice some odd (read ill
\r
946 // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:
\r
947 // - "Planar Configuration" = 0,
\r
948 // - "Photometric Interpretation" = "PALETTE COLOR".
\r
949 // Hence gdcm shall use the folowing "heuristic" in order to be tolerant
\r
950 // towards Dicom-non-conformance files:
\r
951 // << whatever the "Planar Configuration" value might be, a
\r
952 // "Photometric Interpretation" set to "PALETTE COLOR" forces
\r
953 // a LUT intervention >>
\r
955 // Now we are left with the following handling of the cases:
\r
956 // - [Planar 0] OR [Photo A] no color decoding (since respectively
\r
957 // Pixels are already RGB and monochrome pictures have no color :),
\r
958 // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels()
\r
959 // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
\r
960 // - [Planar 2] OR [Photo D] requires LUT intervention.
\r
962 if ( ! IsRawRGB() )
\r
964 // [Planar 2] OR [Photo D]: LUT intervention done outside
\r
968 if ( PlanarConfiguration == 1 )
\r
972 // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
\r
973 ConvertYcBcRPlanesToRGBPixels();
\r
977 // [Planar 1] AND [Photo C]
\r
978 ConvertRGBPlanesToRGBPixels();
\r
983 // When planarConf is 0, and RLELossless (forbidden by Dicom norm)
\r
984 // pixels need to be RGB-fied anyway
\r
987 ConvertRGBPlanesToRGBPixels();
\r
989 // In *normal *case, when planarConf is 0, pixels are already in RGB
\r
993 * \brief Predicate to know wether the image[s] (once Raw) is RGB.
\r
994 * \note See comments of \ref ConvertHandleColor
\r
996 bool PixelReadConvert::IsRawRGB()
\r
999 || PlanarConfiguration == 2
\r
1000 || IsPaletteColor )
\r
1007 void PixelReadConvert::ComputeRawAndRGBSizes()
\r
1009 int bitsAllocated = BitsAllocated;
\r
1010 // Number of "Bits Allocated" is fixed to 16 when it's 12, since
\r
1011 // in this case we will expand the image to 16 bits (see
\r
1012 // \ref ReadAndDecompress12BitsTo16Bits() )
\r
1013 if ( BitsAllocated == 12 )
\r
1015 bitsAllocated = 16;
\r
1018 RawSize = XSize * YSize * ZSize
\r
1019 * ( bitsAllocated / 8 )
\r
1020 * SamplesPerPixel;
\r
1023 RGBSize = 3 * RawSize;
\r
1027 RGBSize = RawSize;
\r
1031 void PixelReadConvert::GrabInformationsFromHeader( Header* header )
\r
1033 // Number of Bits Allocated for storing a Pixel is defaulted to 16
\r
1034 // when absent from the header.
\r
1035 BitsAllocated = header->GetBitsAllocated();
\r
1036 if ( BitsAllocated == 0 )
\r
1038 BitsAllocated = 16;
\r
1041 // Number of "Bits Stored" defaulted to number of "Bits Allocated"
\r
1042 // when absent from the header.
\r
1043 BitsStored = header->GetBitsStored();
\r
1044 if ( BitsStored == 0 )
\r
1046 BitsStored = BitsAllocated;
\r
1049 // High Bit Position
\r
1050 HighBitPosition = header->GetHighBitPosition();
\r
1051 if ( HighBitPosition == 0 )
\r
1053 HighBitPosition = BitsAllocated - 1;
\r
1056 XSize = header->GetXSize();
\r
1057 YSize = header->GetYSize();
\r
1058 ZSize = header->GetZSize();
\r
1059 SamplesPerPixel = header->GetSamplesPerPixel();
\r
1060 PixelSize = header->GetPixelSize();
\r
1061 PixelSign = header->IsSignedPixelData();
\r
1062 SwapCode = header->GetSwapCode();
\r
1063 TransferSyntaxType ts = header->GetTransferSyntax();
\r
1065 ( ! header->IsDicomV3() )
\r
1066 || ts == ImplicitVRLittleEndian
\r
1067 || ts == ImplicitVRLittleEndianDLXGE
\r
1068 || ts == ExplicitVRLittleEndian
\r
1069 || ts == ExplicitVRBigEndian
\r
1070 || ts == DeflatedExplicitVRLittleEndian;
\r
1071 IsJPEG2000 = header->IsJPEG2000();
\r
1072 IsJPEGLossless = header->IsJPEGLossless();
\r
1073 IsRLELossless = ( ts == RLELossless );
\r
1074 PixelOffset = header->GetPixelOffset();
\r
1075 PixelDataLength = header->GetPixelAreaLength();
\r
1076 RLEInfo = header->GetRLEInfo();
\r
1077 JPEGInfo = header->GetJPEGInfo();
\r
1079 PlanarConfiguration = header->GetPlanarConfiguration();
\r
1080 IsMonochrome = header->IsMonochrome();
\r
1081 IsPaletteColor = header->IsPaletteColor();
\r
1082 IsYBRFull = header->IsYBRFull();
\r
1084 /////////////////////////////////////////////////////////////////
\r
1086 HasLUT = header->HasLUT();
\r
1089 // Just in case some access to a Header element requires disk access.
\r
1090 // Note: gdcmDocument::Fp is leaved open after OpenFile.
\r
1091 LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 );
\r
1092 LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 );
\r
1093 LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 );
\r
1095 // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE
\r
1096 // [ refer to invocation of Document::SetMaxSizeLoadEntry() in
\r
1097 // Document::Document() ], the loading of the value (content) of a
\r
1098 // [Bin|Val]Entry occurence migth have been hindered (read simply NOT
\r
1099 // loaded). Hence, we first try to obtain the LUTs data from the header
\r
1100 // and when this fails we read the LUTs data directely from disk.
\r
1101 /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge.
\r
1102 /// We should NOT bypass the [Bin|Val]Entry class. Instead
\r
1103 /// an access to an UNLOADED content of a [Bin|Val]Entry occurence
\r
1104 /// (e.g. BinEntry::GetBinArea()) should force disk access from
\r
1105 /// within the [Bin|Val]Entry class itself. The only problem
\r
1106 /// is that the [Bin|Val]Entry is unaware of the FILE* is was
\r
1107 /// parsed from. Fix that. FIXME.
\r
1110 header->LoadEntryBinArea(0x0028, 0x1201);
\r
1111 LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 );
\r
1112 if ( ! LutRedData )
\r
1114 dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
\r
1115 "unable to read red LUT data" );
\r
1118 ////// Green round:
\r
1119 header->LoadEntryBinArea(0x0028, 0x1202);
\r
1120 LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 );
\r
1121 if ( ! LutGreenData)
\r
1123 dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
\r
1124 "unable to read green LUT data" );
\r
1127 ////// Blue round:
\r
1128 header->LoadEntryBinArea(0x0028, 0x1203);
\r
1129 LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 );
\r
1130 if ( ! LutBlueData )
\r
1132 dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
\r
1133 "unable to read blue LUT data" );
\r
1137 ComputeRawAndRGBSizes();
\r
1141 * \brief Build Red/Green/Blue/Alpha LUT from Header
\r
1142 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
\r
1143 * and (0028,1101),(0028,1102),(0028,1102)
\r
1144 * - xxx Palette Color Lookup Table Descriptor - are found
\r
1145 * and (0028,1201),(0028,1202),(0028,1202)
\r
1146 * - xxx Palette Color Lookup Table Data - are found
\r
1147 * \warning does NOT deal with :
\r
1148 * 0028 1100 Gray Lookup Table Descriptor (Retired)
\r
1149 * 0028 1221 Segmented Red Palette Color Lookup Table Data
\r
1150 * 0028 1222 Segmented Green Palette Color Lookup Table Data
\r
1151 * 0028 1223 Segmented Blue Palette Color Lookup Table Data
\r
1152 * no known Dicom reader deals with them :-(
\r
1153 * @return a RGBA Lookup Table
\r
1155 void PixelReadConvert::BuildLUTRGBA()
\r
1161 // Not so easy : see
\r
1162 // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
\r
1164 if ( ! IsPaletteColor )
\r
1169 if ( LutRedDescriptor == GDCM_UNFOUND
\r
1170 || LutGreenDescriptor == GDCM_UNFOUND
\r
1171 || LutBlueDescriptor == GDCM_UNFOUND )
\r
1176 ////////////////////////////////////////////
\r
1177 // Extract the info from the LUT descriptors
\r
1178 int lengthR; // Red LUT length in Bytes
\r
1179 int debR; // Subscript of the first Lut Value
\r
1180 int nbitsR; // Lut item size (in Bits)
\r
1181 int nbRead = sscanf( LutRedDescriptor.c_str(),
\r
1183 &lengthR, &debR, &nbitsR );
\r
1186 dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor");
\r
1189 int lengthG; // Green LUT length in Bytes
\r
1190 int debG; // Subscript of the first Lut Value
\r
1191 int nbitsG; // Lut item size (in Bits)
\r
1192 nbRead = sscanf( LutGreenDescriptor.c_str(),
\r
1194 &lengthG, &debG, &nbitsG );
\r
1197 dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor");
\r
1200 int lengthB; // Blue LUT length in Bytes
\r
1201 int debB; // Subscript of the first Lut Value
\r
1202 int nbitsB; // Lut item size (in Bits)
\r
1203 nbRead = sscanf( LutRedDescriptor.c_str(),
\r
1205 &lengthB, &debB, &nbitsB );
\r
1208 dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor");
\r
1211 ////////////////////////////////////////////////////////
\r
1212 if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
\r
1217 ////////////////////////////////////////////////
\r
1218 // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
\r
1219 LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
\r
1224 memset( LutRGBA, 0, 1024 );
\r
1227 if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) )
\r
1229 // when LUT item size is different than pixel size
\r
1230 mult = 2; // high byte must be = low byte
\r
1234 // See PS 3.3-2003 C.11.1.1.2 p 619
\r
1238 // if we get a black image, let's just remove the '+1'
\r
1239 // from 'i*mult+1' and check again
\r
1240 // if it works, we shall have to check the 3 Palettes
\r
1241 // to see which byte is ==0 (first one, or second one)
\r
1242 // and fix the code
\r
1243 // We give up the checking to avoid some (useless ?)overhead
\r
1244 // (optimistic asumption)
\r
1246 uint8_t* a = LutRGBA + 0;
\r
1247 for( i=0; i < lengthR; ++i )
\r
1249 *a = LutRedData[i*mult+1];
\r
1254 for( i=0; i < lengthG; ++i)
\r
1256 *a = LutGreenData[i*mult+1];
\r
1261 for(i=0; i < lengthB; ++i)
\r
1263 *a = LutBlueData[i*mult+1];
\r
1268 for(i=0; i < 256; ++i)
\r
1270 *a = 1; // Alpha component
\r
1276 * \brief Build the RGB image from the Raw imagage and the LUTs.
\r
1278 bool PixelReadConvert::BuildRGBImage()
\r
1282 // The job is already done.
\r
1288 // The job can't be done
\r
1295 // The job can't be done
\r
1299 // Build RGB Pixels
\r
1301 uint8_t* localRGB = RGB;
\r
1302 for (size_t i = 0; i < RawSize; ++i )
\r
1304 int j = Raw[i] * 4;
\r
1305 *localRGB++ = LutRGBA[j];
\r
1306 *localRGB++ = LutRGBA[j+1];
\r
1307 *localRGB++ = LutRGBA[j+2];
\r
1313 * \brief Print self.
\r
1314 * @param indent Indentation string to be prepended during printing.
\r
1315 * @param os Stream to print to.
\r
1317 void PixelReadConvert::Print( std::string indent, std::ostream &os )
\r
1320 << "--- Pixel information -------------------------"
\r
1323 << "Pixel Data: offset " << PixelOffset
\r
1324 << " x" << std::hex << PixelOffset << std::dec
\r
1325 << " length " << PixelDataLength
\r
1326 << " x" << std::hex << PixelDataLength << std::dec
\r
1329 if ( IsRLELossless )
\r
1333 RLEInfo->Print( indent, os );
\r
1337 dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file "
\r
1338 "but NO RLEinfo present.");
\r
1342 if ( IsJPEG2000 || IsJPEGLossless )
\r
1346 JPEGInfo->Print( indent, os );
\r
1350 dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file "
\r
1351 "but NO JPEGinfo present.");
\r
1356 } // end namespace gdcm
\r
1358 // NOTES on File internal calls
\r
1360 // ---> GetImageData
\r
1361 // ---> GetImageDataIntoVector
\r
1362 // |---> GetImageDataIntoVectorRaw
\r
1363 // | lut intervention
\r
1365 // ---> GetImageDataRaw
\r
1366 // ---> GetImageDataIntoVectorRaw
\r