-/*=========================================================================\r
-\r
- Program: gdcm\r
- Module: $RCSfile: gdcmPixelReadConvert.cxx,v $\r
- Language: C++\r
- Date: $Date: 2004/12/13 06:22:43 $\r
- Version: $Revision: 1.7 $\r
- \r
- Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de\r
- l'Image). All rights reserved. See Doc/License.txt or\r
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.\r
- \r
- This software is distributed WITHOUT ANY WARRANTY; without even\r
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR\r
- PURPOSE. See the above copyright notices for more information.\r
- \r
-=========================================================================*/\r
-\r
-////////////////// TEMPORARY NOTE\r
-// look for "fixMem" and convert that to a member of this class\r
-// Removing the prefix fixMem and dealing with allocations should do the trick\r
-//\r
-// grep PixelReadConvert everywhere and clean up !\r
-\r
-#include "gdcmDebug.h"\r
-#include "gdcmHeader.h"\r
-#include "gdcmPixelReadConvert.h"\r
-#include "gdcmDocEntry.h"\r
-#include "gdcmRLEFramesInfo.h"\r
-#include "gdcmJPEGFragmentsInfo.h"\r
-\r
-#include <fstream>\r
-#include <stdio.h> //for sscanf\r
-\r
-namespace gdcm\r
-{\r
-#define str2num(str, typeNum) *((typeNum *)(str))\r
-\r
-// For JPEG 2000, body in file gdcmJpeg2000.cxx\r
-bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer);\r
-\r
-#define JOCTET uint8_t\r
-// For JPEG 8 Bits, body in file gdcmJpeg8.cxx\r
-bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer);\r
-bool gdcm_read_JPEG_memory8 (const JOCTET* buffer, const size_t buflen, \r
- void* image_buffer,\r
- size_t *howManyRead, size_t *howManyWritten);\r
-//\r
-// For JPEG 12 Bits, body in file gdcmJpeg12.cxx\r
-bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer);\r
-bool gdcm_read_JPEG_memory12 (const JOCTET *buffer, const size_t buflen, \r
- void* image_buffer,\r
- size_t *howManyRead, size_t *howManyWritten);\r
-\r
-// For JPEG 16 Bits, body in file gdcmJpeg16.cxx\r
-// Beware this is misleading there is no 16bits DCT algorithm, only\r
-// jpeg lossless compression exist in 16bits.\r
-bool gdcm_read_JPEG_file16 (std::ifstream* fp, void* image_buffer);\r
-bool gdcm_read_JPEG_memory16 (const JOCTET *buffer, const size_t buflen, \r
- void* image_buffer,\r
- size_t *howManyRead, size_t *howManyWritten);\r
-\r
-\r
-//-----------------------------------------------------------------------------\r
-// Constructor / Destructor\r
-PixelReadConvert::PixelReadConvert() \r
-{\r
- RGB = 0;\r
- RGBSize = 0;\r
- Raw = 0;\r
- RawSize = 0;\r
- LutRGBA = 0;\r
- LutRedData = 0;\r
- LutGreenData = 0;\r
- LutBlueData =0;\r
-}\r
-\r
-void PixelReadConvert::Squeeze() \r
-{\r
- if ( RGB )\r
- {\r
- delete [] RGB;\r
- } \r
- RGB = 0;\r
-\r
- if ( Raw )\r
- {\r
- delete [] Raw;\r
- }\r
- Raw = 0;\r
-\r
- if ( LutRGBA )\r
- {\r
- delete [] LutRGBA;\r
- }\r
- LutRGBA = 0;\r
-}\r
-\r
-PixelReadConvert::~PixelReadConvert() \r
-{\r
- Squeeze();\r
-}\r
-\r
-void PixelReadConvert::AllocateRGB()\r
-{\r
- if ( RGB ) {\r
- delete [] RGB;\r
- }\r
- RGB = new uint8_t[ RGBSize ];\r
-}\r
-\r
-void PixelReadConvert::AllocateRaw()\r
-{\r
- if ( Raw ) {\r
- delete [] Raw;\r
- }\r
- Raw = new uint8_t[ RawSize ];\r
-}\r
-\r
-/**\r
- * \brief Read from file a 12 bits per pixel image and decompress it\r
- * into a 16 bits per pixel image.\r
- */\r
-void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp )\r
- throw ( FormatError )\r
-{\r
- int nbPixels = XSize * YSize;\r
- uint16_t* localDecompres = (uint16_t*)Raw;\r
-\r
- for( int p = 0; p < nbPixels; p += 2 )\r
- {\r
- uint8_t b0, b1, b2;\r
-\r
- fp->read( (char*)&b0, 1);\r
- if ( fp->fail() || fp->eof() )//Fp->gcount() == 1\r
- {\r
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",\r
- "Unfound first block" );\r
- }\r
-\r
- fp->read( (char*)&b1, 1 );\r
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1\r
- {\r
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",\r
- "Unfound second block" );\r
- }\r
-\r
- fp->read( (char*)&b2, 1 );\r
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1\r
- {\r
- throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",\r
- "Unfound second block" );\r
- }\r
-\r
- // Two steps are necessary to please VC++\r
- //\r
- // 2 pixels 12bit = [0xABCDEF]\r
- // 2 pixels 16bit = [0x0ABD] + [0x0FCE]\r
- // A B D\r
- *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);\r
- // F C E\r
- *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);\r
-\r
- /// \todo JPR Troubles expected on Big-Endian processors ?\r
- }\r
-}\r
-\r
-/**\r
- * \brief Try to deal with RLE 16 Bits. \r
- * We assume the RLE has allready been parsed and loaded in\r
- * Raw (through \ref ReadAndDecompressJPEGFile ).\r
- * We here need to make 16 Bits Pixels from Low Byte and\r
- * High Byte 'Planes'...(for what it may mean)\r
- * @return Boolean\r
- */\r
-bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )\r
-{\r
- size_t PixelNumber = XSize * YSize;\r
- size_t RawSize = XSize * YSize * NumberOfFrames;\r
-\r
- // We assumed Raw contains the decoded RLE pixels but as\r
- // 8 bits per pixel. In order to convert those pixels to 16 bits\r
- // per pixel we cannot work in place within Raw and hence\r
- // we copy it in a safe place, say copyRaw.\r
-\r
- uint8_t* copyRaw = new uint8_t[ RawSize * 2 ];\r
- memmove( copyRaw, Raw, RawSize * 2 );\r
-\r
- uint8_t* x = Raw;\r
- uint8_t* a = copyRaw;\r
- uint8_t* b = a + PixelNumber;\r
-\r
- for ( int i = 0; i < NumberOfFrames; i++ )\r
- {\r
- for ( unsigned int j = 0; j < PixelNumber; j++ )\r
- {\r
- *(x++) = *(b++);\r
- *(x++) = *(a++);\r
- }\r
- }\r
-\r
- delete[] copyRaw;\r
- \r
- /// \todo check that operator new []didn't fail, and sometimes return false\r
- return true;\r
-}\r
-\r
-/**\r
- * \brief Implementation of the RLE decoding algorithm for decompressing\r
- * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86]\r
- * @param subRaw Sub region of \ref Raw where the de\r
- * decoded fragment should be placed.\r
- * @param fragmentSize The length of the binary fragment as found on the disk.\r
- * @param RawSegmentSize The expected length of the fragment ONCE\r
- * Raw.\r
- * @param fp File Pointer: on entry the position should be the one of\r
- * the fragment to be decoded.\r
- */\r
-bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subRaw,\r
- long fragmentSize,\r
- long RawSegmentSize,\r
- std::ifstream* fp )\r
-{\r
- int8_t count;\r
- long numberOfOutputBytes = 0;\r
- long numberOfReadBytes = 0;\r
-\r
- while( numberOfOutputBytes < RawSegmentSize )\r
- {\r
- fp->read( (char*)&count, 1 );\r
- numberOfReadBytes += 1;\r
- if ( count >= 0 )\r
- // Note: count <= 127 comparison is always true due to limited range\r
- // of data type int8_t [since the maximum of an exact width\r
- // signed integer of width N is 2^(N-1) - 1, which for int8_t\r
- // is 127].\r
- {\r
- fp->read( (char*)subRaw, count + 1);\r
- numberOfReadBytes += count + 1;\r
- subRaw += count + 1;\r
- numberOfOutputBytes += count + 1;\r
- }\r
- else\r
- {\r
- if ( ( count <= -1 ) && ( count >= -127 ) )\r
- {\r
- int8_t newByte;\r
- fp->read( (char*)&newByte, 1);\r
- numberOfReadBytes += 1;\r
- for( int i = 0; i < -count + 1; i++ )\r
- {\r
- subRaw[i] = newByte;\r
- }\r
- subRaw += -count + 1;\r
- numberOfOutputBytes += -count + 1;\r
- }\r
- }\r
- // if count = 128 output nothing\r
- \r
- if ( numberOfReadBytes > fragmentSize )\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we "\r
- "read more bytes than the segment size.");\r
- return false;\r
- }\r
- }\r
- return true;\r
-}\r
-\r
-/**\r
- * \brief Reads from disk the Pixel Data of 'Run Length Encoded'\r
- * Dicom encapsulated file and decompress it.\r
- * @param fp already open File Pointer\r
- * at which the pixel data should be copied\r
- * @return Boolean\r
- */\r
-bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp )\r
-{\r
- uint8_t* subRaw = Raw;\r
- long RawSegmentSize = XSize * YSize;\r
-\r
- // Loop on the frame[s]\r
- for( RLEFramesInfo::RLEFrameList::iterator\r
- it = RLEInfo->Frames.begin();\r
- it != RLEInfo->Frames.end();\r
- ++it )\r
- {\r
- // Loop on the fragments\r
- for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ )\r
- {\r
- fp->seekg( (*it)->Offset[k] , std::ios::beg );\r
- (void)ReadAndDecompressRLEFragment( subRaw,\r
- (*it)->Length[k],\r
- RawSegmentSize, \r
- fp );\r
- subRaw += RawSegmentSize;\r
- }\r
- }\r
-\r
- if ( BitsAllocated == 16 )\r
- {\r
- // Try to deal with RLE 16 Bits\r
- (void)DecompressRLE16BitsFromRLE8Bits( ZSize );\r
- }\r
-\r
- return true;\r
-}\r
-\r
-/**\r
- * \brief Swap the bytes, according to \ref SwapCode.\r
- */\r
-void PixelReadConvert::ConvertSwapZone()\r
-{\r
- unsigned int i;\r
-\r
- if( BitsAllocated == 16 )\r
- {\r
- uint16_t* im16 = (uint16_t*)Raw;\r
- switch( SwapCode )\r
- {\r
- case 0:\r
- case 12:\r
- case 1234:\r
- break;\r
- case 21:\r
- case 3412:\r
- case 2143:\r
- case 4321:\r
- for( i = 0; i < RawSize / 2; i++ )\r
- {\r
- im16[i]= (im16[i] >> 8) | (im16[i] << 8 );\r
- }\r
- break;\r
- default:\r
- dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "\r
- "(16 bits) not allowed." );\r
- }\r
- }\r
- else if( BitsAllocated == 32 )\r
- {\r
- uint32_t s32;\r
- uint16_t high;\r
- uint16_t low;\r
- uint32_t* im32 = (uint32_t*)Raw;\r
- switch ( SwapCode )\r
- {\r
- case 0:\r
- case 1234:\r
- break;\r
- case 4321:\r
- for( i = 0; i < RawSize / 4; i++ )\r
- {\r
- low = im32[i] & 0x0000ffff; // 4321\r
- high = im32[i] >> 16;\r
- high = ( high >> 8 ) | ( high << 8 );\r
- low = ( low >> 8 ) | ( low << 8 );\r
- s32 = low;\r
- im32[i] = ( s32 << 16 ) | high;\r
- }\r
- break;\r
- case 2143:\r
- for( i = 0; i < RawSize / 4; i++ )\r
- {\r
- low = im32[i] & 0x0000ffff; // 2143\r
- high = im32[i] >> 16;\r
- high = ( high >> 8 ) | ( high << 8 );\r
- low = ( low >> 8 ) | ( low << 8 );\r
- s32 = high;\r
- im32[i] = ( s32 << 16 ) | low;\r
- }\r
- break;\r
- case 3412:\r
- for( i = 0; i < RawSize / 4; i++ )\r
- {\r
- low = im32[i] & 0x0000ffff; // 3412\r
- high = im32[i] >> 16;\r
- s32 = low;\r
- im32[i] = ( s32 << 16 ) | high;\r
- }\r
- break;\r
- default:\r
- dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "\r
- "(32 bits) not allowed." );\r
- }\r
- }\r
-}\r
-\r
-/**\r
- * \brief Deal with endianity i.e. re-arange bytes inside the integer\r
- */\r
-void PixelReadConvert::ConvertReorderEndianity()\r
-{\r
- if ( BitsAllocated != 8 )\r
- {\r
- ConvertSwapZone();\r
- }\r
-\r
- // Special kludge in order to deal with xmedcon broken images:\r
- if ( ( BitsAllocated == 16 )\r
- && ( BitsStored < BitsAllocated )\r
- && ( ! PixelSign ) )\r
- {\r
- int l = (int)( RawSize / ( BitsAllocated / 8 ) );\r
- uint16_t *deb = (uint16_t *)Raw;\r
- for(int i = 0; i<l; i++)\r
- {\r
- if( *deb == 0xffff )\r
- {\r
- *deb = 0;\r
- }\r
- deb++;\r
- }\r
- }\r
-}\r
-\r
-\r
-/**\r
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated\r
- * file and decompress it. This funciton assumes that each\r
- * jpeg fragment contains a whole frame (jpeg file).\r
- * @param fp File Pointer\r
- * @return Boolean\r
- */\r
-bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream* fp )\r
-{\r
- uint8_t* localRaw = Raw;\r
- // Loop on the fragment[s]\r
- for( JPEGFragmentsInfo::JPEGFragmentsList::iterator\r
- it = JPEGInfo->Fragments.begin();\r
- it != JPEGInfo->Fragments.end();\r
- ++it )\r
- {\r
- fp->seekg( (*it)->Offset, std::ios::beg);\r
-\r
- if ( BitsStored == 8)\r
- {\r
- // JPEG Lossy : call to IJG 6b\r
- if ( ! gdcm_read_JPEG_file8( fp, localRaw ) )\r
- {\r
- return false;\r
- }\r
- }\r
- else if ( BitsStored <= 12)\r
- {\r
- // Reading Fragment pixels\r
- if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) )\r
- {\r
- return false;\r
- }\r
- }\r
- else if ( BitsStored <= 16)\r
- {\r
- // Reading Fragment pixels\r
- if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) )\r
- {\r
- return false;\r
- }\r
- //assert( IsJPEGLossless );\r
- }\r
- else\r
- {\r
- // other JPEG lossy not supported\r
- dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown "\r
- "jpeg lossy compression ");\r
- return false;\r
- }\r
-\r
- // Advance to next free location in Raw \r
- // for next fragment decompression (if any)\r
- int length = XSize * YSize * SamplesPerPixel;\r
- int numberBytes = BitsAllocated / 8;\r
-\r
- localRaw += length * numberBytes;\r
- }\r
- return true;\r
-}\r
-\r
-/**\r
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated\r
- * file and decompress it. This function assumes that the dicom\r
- * image is a single frame split into several JPEG fragments.\r
- * Those fragments will be glued together into a memory buffer\r
- * before being read.\r
- * @param fp File Pointer\r
- * @return Boolean\r
- */\r
-bool PixelReadConvert::\r
-ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream* fp )\r
-{\r
- // Loop on the fragment[s] to get total length\r
- size_t totalLength = 0;\r
- for( JPEGFragmentsInfo::JPEGFragmentsList::iterator\r
- it = JPEGInfo->Fragments.begin();\r
- it != JPEGInfo->Fragments.end();\r
- ++it )\r
- {\r
- totalLength += (*it)->Length;\r
- }\r
-\r
- // Concatenate the jpeg fragments into a local buffer\r
- JOCTET *buffer = new JOCTET [totalLength];\r
- JOCTET *p = buffer;\r
-\r
- uint8_t* localRaw = Raw;\r
- // Loop on the fragment[s]\r
- for( JPEGFragmentsInfo::JPEGFragmentsList::iterator\r
- it = JPEGInfo->Fragments.begin();\r
- it != JPEGInfo->Fragments.end();\r
- ++it )\r
- {\r
- fp->seekg( (*it)->Offset, std::ios::beg);\r
- size_t len = (*it)->Length;\r
- fp->read((char *)p,len);\r
- p+=len;\r
- }\r
-\r
- size_t howManyRead = 0;\r
- size_t howManyWritten = 0;\r
- size_t fragmentLength = 0;\r
- \r
- if ( BitsStored == 8)\r
- {\r
- if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw,\r
- &howManyRead, &howManyWritten ) ) \r
- {\r
- dbg.Error(\r
- "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 "\r
- );\r
- delete [] buffer;\r
- return false;\r
- }\r
- }\r
- else if ( BitsStored <= 12)\r
- {\r
- if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw,\r
- &howManyRead, &howManyWritten ) ) \r
- {\r
- dbg.Error(\r
- "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 "\r
- );\r
- delete [] buffer;\r
- return false;\r
- }\r
- }\r
- else if ( BitsStored <= 16)\r
- {\r
- \r
- if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw,\r
- &howManyRead, &howManyWritten ) ) \r
- {\r
- dbg.Error(\r
- "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 "\r
- );\r
- delete [] buffer;\r
- return false;\r
- }\r
- }\r
- else\r
- {\r
- // other JPEG lossy not supported\r
- dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "\r
- "jpeg lossy compression ");\r
- delete [] buffer;\r
- return false;\r
- } \r
-\r
- // free local buffer\r
- delete [] buffer;\r
- \r
- return true; \r
-}\r
-\r
-/**\r
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated\r
- * file and decompress it. This function handles the generic \r
- * and complex case where the DICOM contains several frames,\r
- * and some of the frames are possibly split into several JPEG\r
- * fragments. \r
- * @param fp File Pointer\r
- * @return Boolean\r
- */\r
-bool PixelReadConvert::\r
-ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream* fp )\r
-{\r
- // Loop on the fragment[s] to get total length\r
- size_t totalLength = 0;\r
- for( JPEGFragmentsInfo::JPEGFragmentsList::iterator\r
- it = JPEGInfo->Fragments.begin();\r
- it != JPEGInfo->Fragments.end();\r
- ++it )\r
- {\r
- totalLength += (*it)->Length;\r
- }\r
-\r
- // Concatenate the jpeg fragments into a local buffer\r
- JOCTET *buffer = new JOCTET [totalLength];\r
- JOCTET *p = buffer;\r
-\r
- uint8_t* localRaw = Raw;\r
- // Loop on the fragment[s]\r
- for( JPEGFragmentsInfo::JPEGFragmentsList::iterator\r
- it = JPEGInfo->Fragments.begin();\r
- it != JPEGInfo->Fragments.end();\r
- ++it )\r
- {\r
- fp->seekg( (*it)->Offset, std::ios::beg);\r
- size_t len = (*it)->Length;\r
- fp->read((char *)p,len);\r
- p+=len;\r
- }\r
-\r
- size_t howManyRead = 0;\r
- size_t howManyWritten = 0;\r
- size_t fragmentLength = 0;\r
- \r
- for( JPEGFragmentsInfo::JPEGFragmentsList::iterator\r
- it = JPEGInfo->Fragments.begin() ;\r
- (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength);\r
- ++it )\r
- {\r
- fragmentLength += (*it)->Length;\r
- \r
- if (howManyRead > fragmentLength) continue;\r
-\r
- if ( BitsStored == 8)\r
- {\r
- if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead,\r
- Raw+howManyWritten,\r
- &howManyRead, &howManyWritten ) ) \r
- {\r
- dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 ");\r
- delete [] buffer;\r
- return false;\r
- }\r
- }\r
- else if ( BitsStored <= 12)\r
- {\r
- \r
- if ( ! gdcm_read_JPEG_memory12( buffer+howManyRead, totalLength-howManyRead,\r
- Raw+howManyWritten,\r
- &howManyRead, &howManyWritten ) ) \r
- {\r
- dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 ");\r
- delete [] buffer;\r
- return false;\r
- }\r
- }\r
- else if ( BitsStored <= 16)\r
- {\r
- \r
- if ( ! gdcm_read_JPEG_memory16( buffer+howManyRead, totalLength-howManyRead,\r
- Raw+howManyWritten,\r
- &howManyRead, &howManyWritten ) ) \r
- {\r
- dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 ");\r
- delete [] buffer;\r
- return false;\r
- }\r
- }\r
- else\r
- {\r
- // other JPEG lossy not supported\r
- dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "\r
- "jpeg lossy compression ");\r
- delete [] buffer;\r
- return false;\r
- }\r
- \r
- if (howManyRead < fragmentLength)\r
- howManyRead = fragmentLength;\r
- }\r
-\r
- // free local buffer\r
- delete [] buffer;\r
- \r
- return true;\r
-}\r
-\r
-/**\r
- * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated\r
- * file and decompress it.\r
- * @param fp File Pointer\r
- * @return Boolean\r
- */\r
-bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp )\r
-{\r
- if ( IsJPEG2000 )\r
- {\r
- fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg);\r
- if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )\r
- return false;\r
- }\r
-\r
- if ( ( ZSize == 1 ) && ( JPEGInfo->Fragments.size() > 1 ) )\r
- {\r
- // we have one frame split into several fragments\r
- // we will pack those fragments into a single buffer and \r
- // read from it\r
- return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp );\r
- }\r
- else if (JPEGInfo->Fragments.size() == ZSize)\r
- {\r
- // suppose each fragment is a frame\r
- return ReadAndDecompressJPEGFramesFromFile( fp );\r
- }\r
- else \r
- {\r
- // The dicom image contains frames containing fragments of images\r
- // a more complex algorithm :-)\r
- return ReadAndDecompressJPEGFragmentedFramesFromFile( fp );\r
- } \r
-}\r
-\r
-/**\r
- * \brief Re-arrange the bits within the bytes.\r
- * @return Boolean\r
- */\r
-bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )\r
-{\r
- if ( BitsStored != BitsAllocated )\r
- {\r
- int l = (int)( RawSize / ( BitsAllocated / 8 ) );\r
- if ( BitsAllocated == 16 )\r
- {\r
- uint16_t mask = 0xffff;\r
- mask = mask >> ( BitsAllocated - BitsStored );\r
- uint16_t* deb = (uint16_t*)Raw;\r
- for(int i = 0; i<l; i++)\r
- {\r
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;\r
- deb++;\r
- }\r
- }\r
- else if ( BitsAllocated == 32 )\r
- {\r
- uint32_t mask = 0xffffffff;\r
- mask = mask >> ( BitsAllocated - BitsStored );\r
- uint32_t* deb = (uint32_t*)Raw;\r
- for(int i = 0; i<l; i++)\r
- {\r
- *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;\r
- deb++;\r
- }\r
- }\r
- else\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image");\r
- throw FormatError( "PixelReadConvert::ConvertReArrangeBits()",\r
- "weird image !?" );\r
- }\r
- }\r
- return true;\r
-}\r
-\r
-/**\r
- * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels\r
- * \warning Works on all the frames at a time\r
- */\r
-void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()\r
-{\r
- uint8_t* localRaw = Raw;\r
- uint8_t* copyRaw = new uint8_t[ RawSize ];\r
- memmove( copyRaw, localRaw, RawSize );\r
-\r
- // to see the tricks about YBR_FULL, YBR_FULL_422,\r
- // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :\r
- // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf\r
- // and be *very* affraid\r
- //\r
- int l = XSize * YSize;\r
- int nbFrames = ZSize;\r
-\r
- uint8_t* a = copyRaw;\r
- uint8_t* b = copyRaw + l;\r
- uint8_t* c = copyRaw + l + l;\r
- double R, G, B;\r
-\r
- /// \todo : Replace by the 'well known' integer computation\r
- /// counterpart. Refer to\r
- /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf\r
- /// for code optimisation.\r
-\r
- for ( int i = 0; i < nbFrames; i++ )\r
- {\r
- for ( int j = 0; j < l; j++ )\r
- {\r
- R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;\r
- G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;\r
- B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;\r
-\r
- if (R < 0.0) R = 0.0;\r
- if (G < 0.0) G = 0.0;\r
- if (B < 0.0) B = 0.0;\r
- if (R > 255.0) R = 255.0;\r
- if (G > 255.0) G = 255.0;\r
- if (B > 255.0) B = 255.0;\r
-\r
- *(localRaw++) = (uint8_t)R;\r
- *(localRaw++) = (uint8_t)G;\r
- *(localRaw++) = (uint8_t)B;\r
- a++;\r
- b++;\r
- c++;\r
- }\r
- }\r
- delete[] copyRaw;\r
-}\r
-\r
-/**\r
- * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels\r
- * \warning Works on all the frames at a time\r
- */\r
-void PixelReadConvert::ConvertRGBPlanesToRGBPixels()\r
-{\r
- uint8_t* localRaw = Raw;\r
- uint8_t* copyRaw = new uint8_t[ RawSize ];\r
- memmove( copyRaw, localRaw, RawSize );\r
-\r
- int l = XSize * YSize * ZSize;\r
-\r
- uint8_t* a = copyRaw;\r
- uint8_t* b = copyRaw + l;\r
- uint8_t* c = copyRaw + l + l;\r
-\r
- for (int j = 0; j < l; j++)\r
- {\r
- *(localRaw++) = *(a++);\r
- *(localRaw++) = *(b++);\r
- *(localRaw++) = *(c++);\r
- }\r
- delete[] copyRaw;\r
-}\r
-\r
-bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp )\r
-{\r
- // ComputeRawAndRGBSizes is already made by \r
- // ::GrabInformationsFromHeader. So, the structure sizes are\r
- // correct\r
- Squeeze();\r
-\r
- //////////////////////////////////////////////////\r
- //// First stage: get our hands on the Pixel Data.\r
- if ( !fp )\r
- {\r
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "\r
- "unavailable file pointer." );\r
- return false;\r
- }\r
-\r
- fp->seekg( PixelOffset, std::ios::beg );\r
- if( fp->fail() || fp->eof()) //Fp->gcount() == 1\r
- {\r
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "\r
- "unable to find PixelOffset in file." );\r
- return false;\r
- }\r
-\r
- AllocateRaw();\r
-\r
- //////////////////////////////////////////////////\r
- //// Second stage: read from disk dans decompress.\r
- if ( BitsAllocated == 12 )\r
- {\r
- ReadAndDecompress12BitsTo16Bits( fp);\r
- }\r
- else if ( IsRaw )\r
- {\r
- // This problem can be found when some obvious informations are found\r
- // after the field containing the image datas. In this case, these\r
- // bad datas are added to the size of the image (in the PixelDataLength\r
- // variable). But RawSize is the right size of the image !\r
- if( PixelDataLength != RawSize)\r
- {\r
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "\r
- "Mismatch between PixelReadConvert and RawSize." );\r
- }\r
- if( PixelDataLength > RawSize)\r
- {\r
- fp->read( (char*)Raw, RawSize);\r
- }\r
- else\r
- {\r
- fp->read( (char*)Raw, PixelDataLength);\r
- }\r
-\r
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1\r
- {\r
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "\r
- "reading of Raw pixel data failed." );\r
- return false;\r
- }\r
- } \r
- else if ( IsRLELossless )\r
- {\r
- if ( ! ReadAndDecompressRLEFile( fp ) )\r
- {\r
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "\r
- "RLE decompressor failed." );\r
- return false;\r
- }\r
- }\r
- else\r
- {\r
- // Default case concerns JPEG family\r
- if ( ! ReadAndDecompressJPEGFile( fp ) )\r
- {\r
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "\r
- "JPEG decompressor failed." );\r
- return false;\r
- }\r
- }\r
-\r
- ////////////////////////////////////////////\r
- //// Third stage: twigle the bytes and bits.\r
- ConvertReorderEndianity();\r
- ConvertReArrangeBits();\r
- ConvertHandleColor();\r
-\r
- return true;\r
-}\r
-\r
-void PixelReadConvert::ConvertHandleColor()\r
-{\r
- //////////////////////////////////\r
- // Deal with the color decoding i.e. handle:\r
- // - R, G, B planes (as opposed to RGB pixels)\r
- // - YBR (various) encodings.\r
- // - LUT[s] (or "PALETTE COLOR").\r
- //\r
- // The classification in the color decoding schema is based on the blending\r
- // of two Dicom tags values:\r
- // * "Photometric Interpretation" for which we have the cases:\r
- // - [Photo A] MONOCHROME[1|2] pictures,\r
- // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB),\r
- // - [Photo C] YBR_* (with the above exception of YBR_FULL_422)\r
- // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s].\r
- // * "Planar Configuration" for which we have the cases:\r
- // - [Planar 0] 0 then Pixels are already RGB\r
- // - [Planar 1] 1 then we have 3 planes : R, G, B,\r
- // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs\r
- //\r
- // Now in theory, one could expect some coherence when blending the above\r
- // cases. For example we should not encounter files belonging at the\r
- // time to case [Planar 0] and case [Photo D].\r
- // Alas, this was only theory ! Because in practice some odd (read ill\r
- // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:\r
- // - "Planar Configuration" = 0,\r
- // - "Photometric Interpretation" = "PALETTE COLOR".\r
- // Hence gdcm shall use the folowing "heuristic" in order to be tolerant\r
- // towards Dicom-non-conformance files:\r
- // << whatever the "Planar Configuration" value might be, a\r
- // "Photometric Interpretation" set to "PALETTE COLOR" forces\r
- // a LUT intervention >>\r
- //\r
- // Now we are left with the following handling of the cases:\r
- // - [Planar 0] OR [Photo A] no color decoding (since respectively\r
- // Pixels are already RGB and monochrome pictures have no color :),\r
- // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels()\r
- // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()\r
- // - [Planar 2] OR [Photo D] requires LUT intervention.\r
-\r
- if ( ! IsRawRGB() )\r
- {\r
- // [Planar 2] OR [Photo D]: LUT intervention done outside\r
- return;\r
- }\r
- \r
- if ( PlanarConfiguration == 1 )\r
- {\r
- if ( IsYBRFull )\r
- {\r
- // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)\r
- ConvertYcBcRPlanesToRGBPixels();\r
- }\r
- else\r
- {\r
- // [Planar 1] AND [Photo C]\r
- ConvertRGBPlanesToRGBPixels();\r
- }\r
- return;\r
- }\r
- \r
- // When planarConf is 0, and RLELossless (forbidden by Dicom norm)\r
- // pixels need to be RGB-fied anyway\r
- if (IsRLELossless)\r
- {\r
- ConvertRGBPlanesToRGBPixels();\r
- }\r
- // In *normal *case, when planarConf is 0, pixels are already in RGB\r
-}\r
-\r
-/**\r
- * \brief Predicate to know wether the image[s] (once Raw) is RGB.\r
- * \note See comments of \ref ConvertHandleColor\r
- */\r
-bool PixelReadConvert::IsRawRGB()\r
-{\r
- if ( IsMonochrome\r
- || PlanarConfiguration == 2\r
- || IsPaletteColor )\r
- {\r
- return false;\r
- }\r
- return true;\r
-}\r
-\r
-void PixelReadConvert::ComputeRawAndRGBSizes()\r
-{\r
- int bitsAllocated = BitsAllocated;\r
- // Number of "Bits Allocated" is fixed to 16 when it's 12, since\r
- // in this case we will expand the image to 16 bits (see\r
- // \ref ReadAndDecompress12BitsTo16Bits() )\r
- if ( BitsAllocated == 12 )\r
- {\r
- bitsAllocated = 16;\r
- }\r
- \r
- RawSize = XSize * YSize * ZSize\r
- * ( bitsAllocated / 8 )\r
- * SamplesPerPixel;\r
- if ( HasLUT )\r
- {\r
- RGBSize = 3 * RawSize;\r
- }\r
- else\r
- {\r
- RGBSize = RawSize;\r
- }\r
-}\r
-\r
-void PixelReadConvert::GrabInformationsFromHeader( Header* header )\r
-{\r
- // Number of Bits Allocated for storing a Pixel is defaulted to 16\r
- // when absent from the header.\r
- BitsAllocated = header->GetBitsAllocated();\r
- if ( BitsAllocated == 0 )\r
- {\r
- BitsAllocated = 16;\r
- }\r
-\r
- // Number of "Bits Stored" defaulted to number of "Bits Allocated"\r
- // when absent from the header.\r
- BitsStored = header->GetBitsStored();\r
- if ( BitsStored == 0 )\r
- {\r
- BitsStored = BitsAllocated;\r
- }\r
-\r
- // High Bit Position\r
- HighBitPosition = header->GetHighBitPosition();\r
- if ( HighBitPosition == 0 )\r
- {\r
- HighBitPosition = BitsAllocated - 1;\r
- }\r
-\r
- XSize = header->GetXSize();\r
- YSize = header->GetYSize();\r
- ZSize = header->GetZSize();\r
- SamplesPerPixel = header->GetSamplesPerPixel();\r
- PixelSize = header->GetPixelSize();\r
- PixelSign = header->IsSignedPixelData();\r
- SwapCode = header->GetSwapCode();\r
- TransferSyntaxType ts = header->GetTransferSyntax();\r
- IsRaw =\r
- ( ! header->IsDicomV3() )\r
- || ts == ImplicitVRLittleEndian\r
- || ts == ImplicitVRLittleEndianDLXGE\r
- || ts == ExplicitVRLittleEndian\r
- || ts == ExplicitVRBigEndian\r
- || ts == DeflatedExplicitVRLittleEndian;\r
- IsJPEG2000 = header->IsJPEG2000();\r
- IsJPEGLossless = header->IsJPEGLossless();\r
- IsRLELossless = ( ts == RLELossless );\r
- PixelOffset = header->GetPixelOffset();\r
- PixelDataLength = header->GetPixelAreaLength();\r
- RLEInfo = header->GetRLEInfo();\r
- JPEGInfo = header->GetJPEGInfo();\r
- \r
- PlanarConfiguration = header->GetPlanarConfiguration();\r
- IsMonochrome = header->IsMonochrome();\r
- IsPaletteColor = header->IsPaletteColor();\r
- IsYBRFull = header->IsYBRFull();\r
-\r
- /////////////////////////////////////////////////////////////////\r
- // LUT section:\r
- HasLUT = header->HasLUT();\r
- if ( HasLUT )\r
- {\r
- // Just in case some access to a Header element requires disk access.\r
- // Note: gdcmDocument::Fp is leaved open after OpenFile.\r
- LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 );\r
- LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 );\r
- LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 );\r
- \r
- // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE\r
- // [ refer to invocation of Document::SetMaxSizeLoadEntry() in\r
- // Document::Document() ], the loading of the value (content) of a\r
- // [Bin|Val]Entry occurence migth have been hindered (read simply NOT\r
- // loaded). Hence, we first try to obtain the LUTs data from the header\r
- // and when this fails we read the LUTs data directely from disk.\r
- /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge.\r
- /// We should NOT bypass the [Bin|Val]Entry class. Instead\r
- /// an access to an UNLOADED content of a [Bin|Val]Entry occurence\r
- /// (e.g. BinEntry::GetBinArea()) should force disk access from\r
- /// within the [Bin|Val]Entry class itself. The only problem\r
- /// is that the [Bin|Val]Entry is unaware of the FILE* is was\r
- /// parsed from. Fix that. FIXME.\r
- \r
- ////// Red round\r
- header->LoadEntryBinArea(0x0028, 0x1201);\r
- LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 );\r
- if ( ! LutRedData )\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "\r
- "unable to read red LUT data" );\r
- }\r
-\r
- ////// Green round:\r
- header->LoadEntryBinArea(0x0028, 0x1202);\r
- LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 );\r
- if ( ! LutGreenData)\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "\r
- "unable to read green LUT data" );\r
- }\r
-\r
- ////// Blue round:\r
- header->LoadEntryBinArea(0x0028, 0x1203);\r
- LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 );\r
- if ( ! LutBlueData )\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "\r
- "unable to read blue LUT data" );\r
- }\r
- }\r
-\r
- ComputeRawAndRGBSizes();\r
-}\r
-\r
-/**\r
- * \brief Build Red/Green/Blue/Alpha LUT from Header\r
- * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]\r
- * and (0028,1101),(0028,1102),(0028,1102)\r
- * - xxx Palette Color Lookup Table Descriptor - are found\r
- * and (0028,1201),(0028,1202),(0028,1202)\r
- * - xxx Palette Color Lookup Table Data - are found\r
- * \warning does NOT deal with :\r
- * 0028 1100 Gray Lookup Table Descriptor (Retired)\r
- * 0028 1221 Segmented Red Palette Color Lookup Table Data\r
- * 0028 1222 Segmented Green Palette Color Lookup Table Data\r
- * 0028 1223 Segmented Blue Palette Color Lookup Table Data\r
- * no known Dicom reader deals with them :-(\r
- * @return a RGBA Lookup Table\r
- */\r
-void PixelReadConvert::BuildLUTRGBA()\r
-{\r
- if ( LutRGBA )\r
- {\r
- return;\r
- }\r
- // Not so easy : see\r
- // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables\r
- \r
- if ( ! IsPaletteColor )\r
- {\r
- return;\r
- }\r
- \r
- if ( LutRedDescriptor == GDCM_UNFOUND\r
- || LutGreenDescriptor == GDCM_UNFOUND\r
- || LutBlueDescriptor == GDCM_UNFOUND )\r
- {\r
- return;\r
- }\r
-\r
- ////////////////////////////////////////////\r
- // Extract the info from the LUT descriptors\r
- int lengthR; // Red LUT length in Bytes\r
- int debR; // Subscript of the first Lut Value\r
- int nbitsR; // Lut item size (in Bits)\r
- int nbRead = sscanf( LutRedDescriptor.c_str(),\r
- "%d\\%d\\%d",\r
- &lengthR, &debR, &nbitsR );\r
- if( nbRead != 3 )\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor");\r
- }\r
- \r
- int lengthG; // Green LUT length in Bytes\r
- int debG; // Subscript of the first Lut Value\r
- int nbitsG; // Lut item size (in Bits)\r
- nbRead = sscanf( LutGreenDescriptor.c_str(),\r
- "%d\\%d\\%d",\r
- &lengthG, &debG, &nbitsG );\r
- if( nbRead != 3 )\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor");\r
- }\r
- \r
- int lengthB; // Blue LUT length in Bytes\r
- int debB; // Subscript of the first Lut Value\r
- int nbitsB; // Lut item size (in Bits)\r
- nbRead = sscanf( LutRedDescriptor.c_str(),\r
- "%d\\%d\\%d",\r
- &lengthB, &debB, &nbitsB );\r
- if( nbRead != 3 )\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor");\r
- }\r
- \r
- ////////////////////////////////////////////////////////\r
- if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )\r
- {\r
- return;\r
- }\r
-\r
- ////////////////////////////////////////////////\r
- // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT\r
- LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)\r
- if ( !LutRGBA )\r
- {\r
- return;\r
- }\r
- memset( LutRGBA, 0, 1024 );\r
- \r
- int mult;\r
- if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) )\r
- {\r
- // when LUT item size is different than pixel size\r
- mult = 2; // high byte must be = low byte\r
- }\r
- else\r
- {\r
- // See PS 3.3-2003 C.11.1.1.2 p 619\r
- mult = 1;\r
- }\r
- \r
- // if we get a black image, let's just remove the '+1'\r
- // from 'i*mult+1' and check again\r
- // if it works, we shall have to check the 3 Palettes\r
- // to see which byte is ==0 (first one, or second one)\r
- // and fix the code\r
- // We give up the checking to avoid some (useless ?)overhead\r
- // (optimistic asumption)\r
- int i;\r
- uint8_t* a = LutRGBA + 0;\r
- for( i=0; i < lengthR; ++i )\r
- {\r
- *a = LutRedData[i*mult+1];\r
- a += 4;\r
- }\r
- \r
- a = LutRGBA + 1;\r
- for( i=0; i < lengthG; ++i)\r
- {\r
- *a = LutGreenData[i*mult+1];\r
- a += 4;\r
- }\r
- \r
- a = LutRGBA + 2;\r
- for(i=0; i < lengthB; ++i)\r
- {\r
- *a = LutBlueData[i*mult+1];\r
- a += 4;\r
- }\r
- \r
- a = LutRGBA + 3;\r
- for(i=0; i < 256; ++i)\r
- {\r
- *a = 1; // Alpha component\r
- a += 4;\r
- }\r
-}\r
-\r
-/**\r
- * \brief Build the RGB image from the Raw imagage and the LUTs.\r
- */\r
-bool PixelReadConvert::BuildRGBImage()\r
-{\r
- if ( RGB )\r
- {\r
- // The job is already done.\r
- return true;\r
- }\r
-\r
- if ( ! Raw )\r
- {\r
- // The job can't be done\r
- return false;\r
- }\r
-\r
- BuildLUTRGBA();\r
- if ( ! LutRGBA )\r
- {\r
- // The job can't be done\r
- return false;\r
- }\r
- \r
- // Build RGB Pixels\r
- AllocateRGB();\r
- uint8_t* localRGB = RGB;\r
- for (size_t i = 0; i < RawSize; ++i )\r
- {\r
- int j = Raw[i] * 4;\r
- *localRGB++ = LutRGBA[j];\r
- *localRGB++ = LutRGBA[j+1];\r
- *localRGB++ = LutRGBA[j+2];\r
- }\r
- return true;\r
-}\r
-\r
-/**\r
- * \brief Print self.\r
- * @param indent Indentation string to be prepended during printing.\r
- * @param os Stream to print to.\r
- */\r
-void PixelReadConvert::Print( std::string indent, std::ostream &os )\r
-{\r
- os << indent\r
- << "--- Pixel information -------------------------"\r
- << std::endl;\r
- os << indent\r
- << "Pixel Data: offset " << PixelOffset\r
- << " x" << std::hex << PixelOffset << std::dec\r
- << " length " << PixelDataLength\r
- << " x" << std::hex << PixelDataLength << std::dec\r
- << std::endl;\r
-\r
- if ( IsRLELossless )\r
- {\r
- if ( RLEInfo )\r
- {\r
- RLEInfo->Print( indent, os );\r
- }\r
- else\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file "\r
- "but NO RLEinfo present.");\r
- }\r
- }\r
-\r
- if ( IsJPEG2000 || IsJPEGLossless )\r
- {\r
- if ( JPEGInfo )\r
- {\r
- JPEGInfo->Print( indent, os );\r
- }\r
- else\r
- {\r
- dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file "\r
- "but NO JPEGinfo present.");\r
- }\r
- }\r
-}\r
-\r
-} // end namespace gdcm\r
-\r
-// NOTES on File internal calls\r
-// User\r
-// ---> GetImageData\r
-// ---> GetImageDataIntoVector\r
-// |---> GetImageDataIntoVectorRaw\r
-// | lut intervention\r
-// User\r
-// ---> GetImageDataRaw\r
-// ---> GetImageDataIntoVectorRaw\r
-\r
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
+ Language: C++
+ Date: $Date: 2005/11/08 16:35:54 $
+ Version: $Revision: 1.97 $
+
+ 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 "gdcmPixelReadConvert.h"
+#include "gdcmDebug.h"
+#include "gdcmFile.h"
+#include "gdcmGlobal.h"
+#include "gdcmTS.h"
+#include "gdcmDocEntry.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+
+#include <fstream>
+#include <stdio.h> //for sscanf
+
+namespace gdcm
+{
+
+bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght);
+bool gdcm_read_JPEG2000_file (void* raw,
+ char *inputdata, size_t inputlength);
+//-----------------------------------------------------------------------------
+#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;
+ RLEInfo = 0;
+ JPEGInfo = 0;
+ UserFunction = 0;
+ FileInternal = 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(); Useless
+ PixelSign = file->IsSignedPixelData();
+ SwapCode = file->GetSwapCode();
+
+ if (! file->IsDicomV3() ) // Should be ACR-NEMA file
+ {
+ IsRaw = true;
+ // Don't loose time checking unexistant Transfer Syntax !
+ IsPrivateGETransferSyntax = IsMPEG
+ = IsJPEG2000 = IsJPEGLS = IsJPEGLossy
+ = IsJPEGLossless = IsRLELossless
+ = false;
+ }
+ else
+ {
+ std::string ts = file->GetTransferSyntax();
+
+ IsRaw = false;
+ while (true)
+ {
+ // mind the order : check the most usual first.
+ if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian) break;
+ if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) break;
+ if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian) break;
+ if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE) break;
+ if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian) break;
+ break;
+ }
+
+ IsPrivateGETransferSyntax =
+ ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE );
+
+ IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false;
+
+ if (!IsRaw)
+ {
+ while(true)
+ {
+ // mind the order : check the most usual first.
+ if( IsJPEGLossy = Global::GetTS()->IsJPEGLossy(ts) ) break;
+ if( IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts) ) break;
+ if( IsRLELossless = Global::GetTS()->IsRLELossless(ts) ) break;
+ if( IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts) ) break;
+ if( IsMPEG = Global::GetTS()->IsMPEG(ts) ) break;
+ if( IsJPEGLS = Global::GetTS()->IsJPEGLS(ts) ) break;
+ gdcmWarningMacro("Unexepected Transfer Syntax :[" << ts << "]");
+ break;
+ }
+ }
+ }
+
+ 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->GetEntryString( 0x0028, 0x1101 );
+ LutGreenDescriptor = file->GetEntryString( 0x0028, 0x1102 );
+ LutBlueDescriptor = file->GetEntryString( 0x0028, 0x1103 );
+
+ // FIXME : The following comment is probabely meaningless, since LUT are *always*
+ // loaded at parsing time, whatever their length is.
+
+ // 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. DataEntry::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 Palette Color Lookup Table data");
+ }
+
+ // //// Green round:
+ file->LoadEntryBinArea(0x0028, 0x1202);
+ LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
+ if ( ! LutGreenData)
+ {
+ gdcmWarningMacro("Unable to read Green Palette Color Lookup Table data");
+ }
+
+ // //// Blue round:
+ file->LoadEntryBinArea(0x0028, 0x1203);
+ LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
+ {
+ gdcmWarningMacro("Unable to read Blue Palette Color Lookup Table data");
+ }
+ }
+ FileInternal = file;
+
+ 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 and 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 if ( IsMPEG )
+ {
+ //gdcmWarningMacro( "Sorry, MPEG not yet taken into account" );
+ //return false;
+ // fp has already been seek to start of mpeg
+ ReadMPEGFile(fp, (char*)Raw, PixelDataLength);
+ return true;
+ }
+ 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();
+ if (UserFunction) // user is allowed to Mirror, TopDown, Rotate,...the image
+ UserFunction( Raw, FileInternal);
+ 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 image 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;
+ }
+
+ gdcmWarningMacro( "--> BuildRGBImage" );
+
+ // Build RGB Pixels
+ AllocateRGB();
+
+ int j;
+ if ( BitsAllocated <= 8 )
+ {
+ uint8_t *localRGB = RGB;
+ for (size_t i = 0; i < RawSize; ++i )
+ {
+ j = Raw[i] * 4;
+ *localRGB++ = LutRGBA[j];
+ *localRGB++ = LutRGBA[j+1];
+ *localRGB++ = LutRGBA[j+2];
+ }
+ }
+
+ else // deal with 16 bits pixels and 16 bits Palette color
+ {
+ uint16_t *localRGB = (uint16_t *)RGB;
+ for (size_t i = 0; i < RawSize/2; ++i )
+ {
+ j = ((uint16_t *)Raw)[i] * 4;
+ *localRGB++ = ((uint16_t *)LutRGBA)[j];
+ *localRGB++ = ((uint16_t *)LutRGBA)[j+1];
+ *localRGB++ = ((uint16_t *)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 )
+ {
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEGLS );
+ // FIXME this is really ugly but it seems I have to load the complete
+ // jpeg2000 stream to use jasper:
+ // I don't think we'll ever be able to deal with multiple fragments properly
+
+ unsigned long inputlength = 0;
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ inputlength += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ gdcmAssertMacro( inputlength != 0);
+ uint8_t *inputdata = new uint8_t[inputlength];
+ char *pinputdata = (char*)inputdata;
+ jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
+ fp->read(pinputdata, jpegfrag->GetLength());
+ pinputdata += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ // Warning the inputdata buffer is delete in the function
+ if ( ! gdcm_read_JPEG2000_file( Raw,
+ (char*)inputdata, inputlength ) )
+ {
+ return true;
+ }
+ // wow what happen, must be an error
+ return false;
+ }
+ else if ( IsJPEGLS )
+ {
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEG2000 );
+ // WARNING : JPEG-LS is NOT the 'classical' Jpeg Lossless :
+ // [JPEG-LS is the basis for new lossless/near-lossless compression
+ // standard for continuous-tone images intended for JPEG2000. The standard
+ // is based on the LOCO-I algorithm (LOw COmplexity LOssless COmpression
+ // for Images) developed at Hewlett-Packard Laboratories]
+ //
+ // see http://datacompression.info/JPEGLS.shtml
+ //
+#if 0
+ std::cerr << "count:" << JPEGInfo->GetFragmentCount() << std::endl;
+ unsigned long inputlength = 0;
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ inputlength += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ gdcmAssertMacro( inputlength != 0);
+ uint8_t *inputdata = new uint8_t[inputlength];
+ char *pinputdata = (char*)inputdata;
+ jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
+ fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
+ fp->read(pinputdata, jpegfrag->GetLength());
+ pinputdata += jpegfrag->GetLength();
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+
+ //fp->read((char*)Raw, PixelDataLength);
+
+ std::ofstream out("/tmp/jpegls.jpg");
+ out.write((char*)inputdata, inputlength);
+ out.close();
+ delete[] inputdata;
+#endif
+
+ 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
+ {
+ // make sure this is the right JPEG compression
+ assert( !IsJPEGLS || !IsJPEG2000 );
+ // 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()
+{
+
+ // Note to code reviewers :
+ // The problem is *much more* complicated, since a lot of manufacturers
+ // Don't follow the norm :
+ // have a look at David Clunie's remark at the end of this .cxx file.
+ 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 )
+ {
+ gdcmWarningMacro( "(At least) a LUT Descriptor is missing" );
+ 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; // nb of items in LUT descriptor (must be = 3)
+
+ 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" );
+ }
+
+ gdcmWarningMacro(" lengthR " << lengthR << " debR "
+ << debR << " nbitsR " << nbitsR);
+ gdcmWarningMacro(" lengthG " << lengthG << " debG "
+ << debG << " nbitsG " << nbitsG);
+ gdcmWarningMacro(" lengthB " << lengthB << " debB "
+ << debB << " nbitsB " << nbitsB);
+
+ if ( !lengthR ) // if = 2^16, this shall be 0 see : CP-143
+ lengthR=65536;
+ if ( !lengthG ) // if = 2^16, this shall be 0
+ lengthG=65536;
+ if ( !lengthB ) // if = 2^16, this shall be 0
+ lengthB=65536;
+
+ ////////////////////////////////////////////////////////
+
+ if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
+ {
+ gdcmWarningMacro( "(At least) a LUT is missing" );
+ return;
+ }
+
+ // -------------------------------------------------------------
+
+ if ( BitsAllocated <= 8 )
+ {
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+ LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
+ if ( !LutRGBA )
+ return;
+ LutItemNumber = 256;
+ LutItemSize = 8;
+ 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;
+
+ //take "Subscript of the first Lut Value" (debR,debG,debB) into account!
+
+ //FIXME : +1 : to get 'low value' byte
+ // Trouble expected on Big Endian Processors ?
+ // 16 BIts Per Pixel Palette Color to be swapped?
+
+ a = LutRGBA + 0 + debR;
+ for( i=0; i < lengthR; ++i )
+ {
+ *a = LutRedData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 1 + debG;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a = LutGreenData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 2 + debB;
+ 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;
+ }
+ }
+ else
+ {
+ // Probabely the same stuff is to be done for 16 Bits Pixels
+ // with 65536 entries LUT ?!?
+ // Still looking for accurate info on the web :-(
+
+ gdcmWarningMacro( "Sorry Palette Color Lookup Tables not yet dealt with"
+ << " for 16 Bits Per Pixel images" );
+
+ // forge the 4 * 16 Bits Red/Green/Blue/Alpha LUT
+
+ LutRGBA = (uint8_t *)new uint16_t[ 65536*4 ]; // 2^16 * 4 (R, G, B, Alpha)
+ if ( !LutRGBA )
+ return;
+ memset( LutRGBA, 0, 65536*4*2 ); // 16 bits = 2 bytes ;-)
+
+ LutItemNumber = 65536;
+ LutItemSize = 16;
+
+ int i;
+ uint16_t *a16;
+
+ //take "Subscript of the first Lut Value" (debR,debG,debB) into account!
+
+ a16 = (uint16_t*)LutRGBA + 0 + debR;
+ for( i=0; i < lengthR; ++i )
+ {
+ *a16 = ((uint16_t*)LutRedData)[i];
+ a16 += 4;
+ }
+
+ a16 = (uint16_t*)LutRGBA + 1 + debG;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a16 = ((uint16_t*)LutGreenData)[i];
+ a16 += 4;
+ }
+
+ a16 = (uint16_t*)LutRGBA + 2 + debB;
+ for(i=0; i < lengthB; ++i)
+ {
+ *a16 = ((uint16_t*)LutBlueData)[i];
+ a16 += 4;
+ }
+
+ a16 = (uint16_t*)LutRGBA + 3 ;
+ for(i=0; i < 65536; ++i)
+ {
+ *a16 = 1; // Alpha component
+ a16 += 4;
+ }
+/* Just to 'see' the LUT, at debug time
+// Don't remove this commented out code.
+
+ a16=(uint16_t*)LutRGBA;
+ for (int j=0;j<65536;j++)
+ {
+ std::cout << *a16 << " " << *(a16+1) << " "
+ << *(a16+2) << " " << *(a16+3) << std::endl;
+ a16+=4;
+ }
+*/
+ }
+}
+
+/**
+ * \brief Swap the bytes, according to \ref SwapCode.
+ */
+void PixelReadConvert::ConvertSwapZone()
+{
+ unsigned int i;
+ uint16_t localSwapCode = SwapCode;
+
+ // If this file is 'ImplicitVR BigEndian PrivateGE Transfer Syntax',
+ // then the header is in little endian format and the pixel data is in
+ // big endian format. When reading the header, GDCM has already established
+ // a byte swapping code suitable for this machine to read the
+ // header. In TS::ImplicitVRBigEndianPrivateGE, this code will need
+ // to be switched in order to read the pixel data. This must be
+ // done REGARDLESS of the processor endianess!
+ //
+ // Example: Assume we are on a little endian machine. When
+ // GDCM reads the header, the header will match the machine
+ // endianess and the swap code will be established as a no-op.
+ // When GDCM reaches the pixel data, it will need to switch the
+ // swap code to do big endian to little endian conversion.
+ //
+ // Now, assume we are on a big endian machine. When GDCM reads the
+ // header, the header will be recognized as a different endianess
+ // than the machine endianess, and a swap code will be established
+ // to convert from little endian to big endian. When GDCM readers
+ // the pixel data, the pixel data endianess will now match the
+ // machine endianess. But we currently have a swap code that
+ // converts from little endian to big endian. In this case, we
+ // need to switch the swap code to a no-op.
+ //
+ // Therefore, in either case, if the file is in
+ // 'ImplicitVR BigEndian PrivateGE Transfer Syntax', then GDCM needs to switch
+ // the byte swapping code when entering the pixel data.
+
+ if ( IsPrivateGETransferSyntax )
+ {
+ // PrivateGETransferSyntax only exists for 'true' Dicom images
+ // we assume there is no 'exotic' 32 bits endianess!
+ switch (localSwapCode)
+ {
+ case 1234:
+ localSwapCode = 4321;
+ break;
+ case 4321:
+ localSwapCode = 1234;
+ break;
+ }
+ }
+
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t *im16 = (uint16_t*)Raw;
+ switch( localSwapCode )
+ {
+ 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 ( localSwapCode )
+ {
+ 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<l; i++)
+ {
+ if ( *deb == 0xffff )
+ {
+ *deb = 0;
+ }
+ deb++;
+ }
+ }
+}
+
+/**
+ * \brief Deal with Grey levels i.e. re-arange them
+ * to have low values = dark, high values = bright
+ */
+void PixelReadConvert::ConvertFixGreyLevels()
+{
+ if (!IsMonochrome1)
+ return;
+
+ uint32_t i; // to please M$VC6
+ int16_t j;
+
+ if (!PixelSign)
+ {
+ if ( BitsAllocated == 8 )
+ {
+ uint8_t *deb = (uint8_t *)Raw;
+ for (i=0; i<RawSize; i++)
+ {
+ *deb = 255 - *deb;
+ deb++;
+ }
+ return;
+ }
+
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t mask =1;
+ for (j=0; j<BitsStored-1; j++)
+ {
+ mask = (mask << 1) +1; // will be fff when BitsStored=12
+ }
+
+ uint16_t *deb = (uint16_t *)Raw;
+ for (i=0; i<RawSize/2; i++)
+ {
+ *deb = mask - *deb;
+ deb++;
+ }
+ return;
+ }
+ }
+ else
+ {
+ if ( BitsAllocated == 8 )
+ {
+ uint8_t smask8 = 255;
+ uint8_t *deb = (uint8_t *)Raw;
+ for (i=0; i<RawSize; i++)
+ {
+ *deb = smask8 - *deb;
+ deb++;
+ }
+ return;
+ }
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t smask16 = 65535;
+ uint16_t *deb = (uint16_t *)Raw;
+ for (i=0; i<RawSize/2; i++)
+ {
+ *deb = smask16 - *deb;
+ deb++;
+ }
+ return;
+ }
+ }
+}
+
+/**
+ * \brief Re-arrange the bits within the bytes.
+ * @return Boolean always true
+ */
+bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
+{
+
+ if ( BitsStored != BitsAllocated )
+ {
+ int l = (int)( RawSize / ( BitsAllocated / 8 ) );
+ if ( BitsAllocated == 16 )
+ {
+ // pmask : to mask the 'unused bits' (may contain overlays)
+ uint16_t pmask = 0xffff;
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+
+ uint16_t *deb = (uint16_t*)Raw;
+
+ if ( !PixelSign ) // Pixels are unsigned
+ {
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
+ deb++;
+ }
+ }
+ else // Pixels are signed
+ {
+ // smask : to check the 'sign' when BitsStored != BitsAllocated
+ uint16_t smask = 0x0001;
+ smask = smask << ( 16 - (BitsAllocated - BitsStored + 1) );
+ // nmask : to propagate sign bit on negative values
+ int16_t nmask = (int16_t)0x8000;
+ nmask = nmask >> ( BitsAllocated - BitsStored - 1 );
+
+ for(int i = 0; i<l; i++)
+ {
+ *deb = *deb >> (BitsStored - HighBitPosition - 1);
+ if ( *deb & smask )
+ {
+ *deb = *deb | nmask;
+ }
+ else
+ {
+ *deb = *deb & pmask;
+ }
+ deb++;
+ }
+ }
+ }
+ else if ( BitsAllocated == 32 )
+ {
+ // pmask : to mask the 'unused bits' (may contain overlays)
+ uint32_t pmask = 0xffffffff;
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+
+ uint32_t *deb = (uint32_t*)Raw;
+
+ if ( !PixelSign )
+ {
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
+ deb++;
+ }
+ }
+ else
+ {
+ // smask : to check the 'sign' when BitsStored != BitsAllocated
+ uint32_t smask = 0x00000001;
+ smask = smask >> ( 32 - (BitsAllocated - BitsStored +1 ));
+ // nmask : to propagate sign bit on negative values
+ int32_t nmask = 0x80000000;
+ nmask = nmask >> ( BitsAllocated - BitsStored -1 );
+
+ for(int i = 0; i<l; i++)
+ {
+ *deb = *deb >> (BitsStored - HighBitPosition - 1);
+ if ( *deb & smask )
+ *deb = *deb | nmask;
+ else
+ *deb = *deb & pmask;
+ deb++;
+ }
+ }
+ }
+ else
+ {
+ gdcmWarningMacro("Weird image (BitsAllocated !=8, 12, 16, 32)");
+ 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()
+{
+ gdcmWarningMacro("--> 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()
+{
+ // Remarks for YBR newbees :
+ // YBR_FULL works very much like RGB, i.e. three samples per pixel,
+ // just the color space is YCbCr instead of RGB. This is particularly useful
+ // for doppler ultrasound where most of the image is grayscale
+ // (i.e. only populates the Y components) and Cb and Cr are mostly zero,
+ // except for the few patches of color on the image.
+ // On such images, RLE achieves a compression ratio that is much better
+ // than the compression ratio on an equivalent RGB image.
+
+ gdcmWarningMacro("--> 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 + 0;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l+ l;
+ int32_t R, G, B;
+
+ /// We replaced easy to understand but time consuming floating point
+ /// computations 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 = 38142 *(*a-16) + 52298 *(*c -128);
+ G = 38142 *(*a-16) - 26640 *(*c -128) - 12845 *(*b -128);
+ B = 38142 *(*a-16) + 66093 *(*b -128);
+
+ R = (R+16384)>>15;
+ G = (G+16384)>>15;
+ B = (B+16384)>>15;
+
+ if (R < 0) R = 0;
+ if (G < 0) G = 0;
+ if (B < 0) B = 0;
+ if (R > 255) R = 255;
+ if (G > 255) G = 255;
+ if (B > 255) B = 255;
+
+ *(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-conformant 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.
+
+ gdcmDebugMacro("--> ConvertHandleColor "
+ << "Planar Configuration " << PlanarConfiguration );
+
+ if ( ! IsRawRGB() )
+ {
+ // [Planar 2] OR [Photo D]: LUT intervention done outside
+ gdcmDebugMacro("--> RawRGB : LUT intervention done outside");
+ return;
+ }
+
+ if ( PlanarConfiguration == 1 )
+ {
+ if ( IsYBRFull )
+ {
+ // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ gdcmWarningMacro("--> YBRFull");
+ ConvertYcBcRPlanesToRGBPixels();
+ }
+ else
+ {
+ // [Planar 1] AND [Photo C]
+ gdcmWarningMacro("--> YBRFull");
+ ConvertRGBPlanesToRGBPixels();
+ }
+ return;
+ }
+
+ // When planarConf is 0, and RLELossless (forbidden by Dicom norm)
+ // pixels need to be RGB-fyied anyway
+
+ if (IsRLELossless)
+ {
+ gdcmWarningMacro("--> RLE Lossless");
+ 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; // works for 8 and 16 bits per Pixel
+ }
+ 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
+
+// Note to developpers :
+// Here is a very detailled post from David Clunie, on the troubles caused
+// 'non standard' LUT and LUT description
+// We shall have to take it into accound in our code.
+// Some day ...
+
+
+/*
+Subject: Problem with VOI LUTs in Agfa and Fuji CR and GE DX images, was Re: VOI LUT issues
+Date: Sun, 06 Feb 2005 17:13:40 GMT
+From: David Clunie <dclunie@dclunie.com>
+Reply-To: dclunie@dclunie.com
+Newsgroups: comp.protocols.dicom
+References: <1107553502.040221.189550@o13g2000cwo.googlegroups.com>
+
+> THE LUT that comes with [my] image claims to be 16-bit, but none of the
+> values goes higher than 4095. That being said, though, none of my
+> original pixel values goes higher than that, either. I have read
+> elsewhere on this group that when that happens you are supposed to
+> adjust the LUT. Can someone be more specific? There was a thread from
+> 2002 where Marco and David were mentioning doing precisely that.
+>
+> Thanks
+>
+> -carlos rodriguez
+
+
+You have encountered the well known "we know what the standard says but
+we are going to ignore it and do what we have been doing for almost
+a decade regardless" CR vendor bug. Agfa started this, but they are not
+the only vendor doing this now; GE and Fuji may have joined the club.
+
+Sadly, one needs to look at the LUT Data, figure out what the maximum
+value actually encoded is, and find the next highest power of 2 (e.g.
+212 in this case), to figure out what the range of the data is
+supposed to be. I have assumed that if the maximum value in the LUT
+data is less than a power of 2 minus 1 (e.g. 0xebc) then the intent
+of the vendor was not to use the maximum available grayscale range
+of the display (e.g. the maximum is 0xfff in this case). An alternative
+would be to scale to the actual maximum rather than a power of two.
+
+Very irritating, and in theory not totally reliable if one really
+intended the full 16 bits and only used, say 15, but that is extremely
+unlikely since everything would be too dark, and this heuristic
+seems to work OK.
+
+There has never been anything in the standard that describes having
+to go through these convolutions. Since the only value in the
+standard that describes the bit depth of the LUT values is LUT
+Descriptor value 3 and that is (usually) always required to be
+either 8 or 16, it mystifies me how the creators' of these images
+imagine that the receiver is going to divine the range that is intended. Further, the standard is quite explicit that this 3rd
+value defines the range of LUT values, but as far as I am aware, all
+the vendors are ignoring the standard and indeed sending a third value
+of 16 in all cases.
+
+This problem is not confined to CR, and is also seen with DX products.
+
+Typically I have seen:
+
+- Agfa CR, which usually (always ?) sends LUTs, values up to 0x0fff
+- Fuji CR, which occasionally send LUTs, values up to 0x03ff
+- GE DX, for presentation, which always have LUTs, up to 0x3fff
+
+Swissray, Siemens, Philips, Canon and Kodak never seem to send VOI LUTs
+at this point (which is a whole other problem). Note that the presence
+or absence of a VOI LUT as opposed to window values may be configurable
+on the modality in some cases, and I have just looked at what I happen
+to have received from a myriad of sites over whose configuration I have
+no control. This may be why the majority of Fuji images have no VOI LUTs,
+but a few do (or it may be the Siemens system that these Fuji images went
+through that perhaps added it). I do have some test Hologic DX images that
+are not from a clinical site that do actually get this right (a value
+of 12 for the third value and a max of 0xfff).
+
+Since almost every vendor that I have encountered that encodes LUTs
+makes this mistake, perhaps it is time to amend the standard to warn
+implementor's of receivers and/or sanction this bad behavior. We have
+talked about this in the past in WG 6 but so far everyone has been
+reluctant to write into the standard such a comment. Maybe it is time
+to try again, since if one is not aware of this problem, one cannot
+effectively implement display using VOI LUTs, and there is a vast
+installed base to contend with.
+
+I did not check presentation states, in which VOI LUTs could also be
+encountered, for the prevalence of this mistake, nor did I look at the
+encoding of Modality LUT's, which are unusual. Nor did I check digital
+mammography images. I would be interested to hear from anyone who has.
+
+David
+
+PS. The following older thread in this newsgroup discusses this:
+
+"http://groups-beta.google.com/group/comp.protocols.dicom/browse_frm/t hread/6a033444802a35fc/0f0a9a1e35c1468e?q=voi+lut&_done=%2Fgroup%2Fcom p.protocols.dicom%2Fsearch%3Fgroup%3Dcomp.protocols.dicom%26q%3Dvoi+lu t%26qt_g%3D1%26searchnow%3DSearch+this+group%26&_doneTitle=Back+to+Sea rch&&d#0f0a9a1e35c1468e"
+
+PPS. From a historical perspective, the following may be of interest.
+
+In the original standard in 1993, all that was said about this was a
+reference to the corresponding such where Modality LUTs are described
+that said:
+
+"The third value specifies the number of bits for each entry in the
+LUT Data. It shall take the value 8 or 16. The LUT Data shall be stored
+in a format equivalent to 8 or 16 bits allocated and high bit equal
+1-bits allocated."
+
+Since the high bit hint was not apparently explicit enough, a very
+early CP, CP 15 (submitted by Agfa as it happens), replaced this with:
+
+"The third value conveys the range of LUT entry values. It shall take
+the value 8 or 16, corresponding with the LUT entry value range of
+256 or 65536.
+
+Note: The third value is not required for describing the
+ LUT data and is only included for informational usage
+ and for maintaining compatibility with ACRNEMA 2.0.
+
+The LUT Data contains the LUT entry values."
+
+That is how it read in the 1996, 1998 and 1999 editions.
+
+By the 2000 edition, Supplement 33 that introduced presentation states
+extensively reworked this entire section and tried to explain this in
+different words:
+
+"The output range is from 0 to 2^n-1 where n is the third value of LUT
+Descriptor. This range is always unsigned."
+
+and also added a note to spell out what the output range meant in the
+VOI LUT section:
+
+"9. The output of the Window Center/Width or VOI LUT transformation
+is either implicitly scaled to the full range of the display device
+if there is no succeeding transformation defined, or implicitly scaled
+to the full input range of the succeeding transformation step (such as
+the Presentation LUT), if present. See C.11.6.1."
+
+It still reads this way in the 2004 edition.
+
+Note that LUTs in other applications than the general VOI LUT allow for
+values other than 8 or 16 in the third value of LUT descriptor to permit
+ranges other than 0 to 255 or 65535.
+
+In addition, the DX Image Module specializes the VOI LUT
+attributes as follows, in PS 3.3 section C.8.11.3.1.5 (added in Sup 32):
+
+"The third value specifies the number of bits for each entry in the LUT
+Data (analogous to ìbits storedî). It shall be between 10-16. The LUT
+Data shall be stored in a format equivalent to 16 ìbits allocatedî and
+ìhigh bitî equal to ìbits storedî - 1. The third value conveys the range
+of LUT entry values. These unsigned LUT entry values shall range between
+0 and 2^n-1, where n is the third value of the LUT Descriptor."
+
+So in the case of the GE DX for presentation images, the third value of
+LUT descriptor is allowed to be and probably should be 14 rather than 16.
+
+*/
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