-/*=========================================================================\r
-\r
- Program: gdcm\r
- Module: $RCSfile: gdcmPixelReadConvert.cxx,v $\r
- Language: C++\r
- Date: $Date: 2004/12/13 06:25:39 $\r
- Version: $Revision: 1.8 $\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
- JPEGFragmentsInfo::JPEGFragmentsList::iterator it;\r
- for( 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( 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: 2004/12/13 14:58:41 $
+ Version: $Revision: 1.9 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+////////////////// TEMPORARY NOTE
+// look for "fixMem" and convert that to a member of this class
+// Removing the prefix fixMem and dealing with allocations should do the trick
+//
+// grep PixelReadConvert everywhere and clean up !
+
+#include "gdcmDebug.h"
+#include "gdcmHeader.h"
+#include "gdcmPixelReadConvert.h"
+#include "gdcmDocEntry.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+
+#include <fstream>
+#include <stdio.h> //for sscanf
+
+namespace gdcm
+{
+#define str2num(str, typeNum) *((typeNum *)(str))
+
+// For JPEG 2000, body in file gdcmJpeg2000.cxx
+bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer);
+
+#define JOCTET uint8_t
+// For JPEG 8 Bits, body in file gdcmJpeg8.cxx
+bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer);
+bool gdcm_read_JPEG_memory8 (const JOCTET* buffer, const size_t buflen,
+ void* image_buffer,
+ size_t *howManyRead, size_t *howManyWritten);
+//
+// For JPEG 12 Bits, body in file gdcmJpeg12.cxx
+bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer);
+bool gdcm_read_JPEG_memory12 (const JOCTET *buffer, const size_t buflen,
+ void* image_buffer,
+ size_t *howManyRead, size_t *howManyWritten);
+
+// For JPEG 16 Bits, body in file gdcmJpeg16.cxx
+// Beware this is misleading there is no 16bits DCT algorithm, only
+// jpeg lossless compression exist in 16bits.
+bool gdcm_read_JPEG_file16 (std::ifstream* fp, void* image_buffer);
+bool gdcm_read_JPEG_memory16 (const JOCTET *buffer, const size_t buflen,
+ void* image_buffer,
+ size_t *howManyRead, size_t *howManyWritten);
+
+
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
+PixelReadConvert::PixelReadConvert()
+{
+ RGB = 0;
+ RGBSize = 0;
+ Raw = 0;
+ RawSize = 0;
+ LutRGBA = 0;
+ LutRedData = 0;
+ LutGreenData = 0;
+ LutBlueData =0;
+}
+
+void PixelReadConvert::Squeeze()
+{
+ if ( RGB )
+ {
+ delete [] RGB;
+ }
+ RGB = 0;
+
+ if ( Raw )
+ {
+ delete [] Raw;
+ }
+ Raw = 0;
+
+ if ( LutRGBA )
+ {
+ delete [] LutRGBA;
+ }
+ LutRGBA = 0;
+}
+
+PixelReadConvert::~PixelReadConvert()
+{
+ Squeeze();
+}
+
+void PixelReadConvert::AllocateRGB()
+{
+ if ( RGB ) {
+ delete [] RGB;
+ }
+ RGB = new uint8_t[ RGBSize ];
+}
+
+void PixelReadConvert::AllocateRaw()
+{
+ if ( Raw ) {
+ delete [] Raw;
+ }
+ Raw = new uint8_t[ RawSize ];
+}
+
+/**
+ * \brief Read from file a 12 bits per pixel image and decompress it
+ * into a 16 bits per pixel image.
+ */
+void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp )
+ throw ( FormatError )
+{
+ int nbPixels = XSize * YSize;
+ uint16_t* localDecompres = (uint16_t*)Raw;
+
+ for( int p = 0; p < nbPixels; p += 2 )
+ {
+ uint8_t b0, b1, b2;
+
+ fp->read( (char*)&b0, 1);
+ if ( fp->fail() || fp->eof() )//Fp->gcount() == 1
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound first block" );
+ }
+
+ fp->read( (char*)&b1, 1 );
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ fp->read( (char*)&b2, 1 );
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ {
+ throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
+ "Unfound second block" );
+ }
+
+ // Two steps are necessary to please VC++
+ //
+ // 2 pixels 12bit = [0xABCDEF]
+ // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
+ // A B D
+ *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ // F C E
+ *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+
+ /// \todo JPR Troubles expected on Big-Endian processors ?
+ }
+}
+
+/**
+ * \brief Try to deal with RLE 16 Bits.
+ * We assume the RLE has allready been parsed and loaded in
+ * Raw (through \ref ReadAndDecompressJPEGFile ).
+ * We here need to make 16 Bits Pixels from Low Byte and
+ * High Byte 'Planes'...(for what it may mean)
+ * @return Boolean
+ */
+bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )
+{
+ size_t PixelNumber = XSize * YSize;
+ size_t RawSize = XSize * YSize * NumberOfFrames;
+
+ // We assumed Raw contains the decoded RLE pixels but as
+ // 8 bits per pixel. In order to convert those pixels to 16 bits
+ // per pixel we cannot work in place within Raw and hence
+ // we copy it in a safe place, say copyRaw.
+
+ uint8_t* copyRaw = new uint8_t[ RawSize * 2 ];
+ memmove( copyRaw, Raw, RawSize * 2 );
+
+ uint8_t* x = Raw;
+ uint8_t* a = copyRaw;
+ uint8_t* b = a + PixelNumber;
+
+ for ( int i = 0; i < NumberOfFrames; i++ )
+ {
+ for ( unsigned int j = 0; j < PixelNumber; j++ )
+ {
+ *(x++) = *(b++);
+ *(x++) = *(a++);
+ }
+ }
+
+ delete[] copyRaw;
+
+ /// \todo check that operator new []didn't fail, and sometimes return false
+ return true;
+}
+
+/**
+ * \brief Implementation of the RLE decoding algorithm for decompressing
+ * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86]
+ * @param subRaw Sub region of \ref Raw where the de
+ * decoded fragment should be placed.
+ * @param fragmentSize The length of the binary fragment as found on the disk.
+ * @param RawSegmentSize The expected length of the fragment ONCE
+ * Raw.
+ * @param fp File Pointer: on entry the position should be the one of
+ * the fragment to be decoded.
+ */
+bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subRaw,
+ long fragmentSize,
+ long RawSegmentSize,
+ std::ifstream* fp )
+{
+ int8_t count;
+ long numberOfOutputBytes = 0;
+ long numberOfReadBytes = 0;
+
+ while( numberOfOutputBytes < RawSegmentSize )
+ {
+ fp->read( (char*)&count, 1 );
+ numberOfReadBytes += 1;
+ if ( count >= 0 )
+ // Note: count <= 127 comparison is always true due to limited range
+ // of data type int8_t [since the maximum of an exact width
+ // signed integer of width N is 2^(N-1) - 1, which for int8_t
+ // is 127].
+ {
+ fp->read( (char*)subRaw, count + 1);
+ numberOfReadBytes += count + 1;
+ subRaw += count + 1;
+ numberOfOutputBytes += count + 1;
+ }
+ else
+ {
+ if ( ( count <= -1 ) && ( count >= -127 ) )
+ {
+ int8_t newByte;
+ fp->read( (char*)&newByte, 1);
+ numberOfReadBytes += 1;
+ for( int i = 0; i < -count + 1; i++ )
+ {
+ subRaw[i] = newByte;
+ }
+ subRaw += -count + 1;
+ numberOfOutputBytes += -count + 1;
+ }
+ }
+ // if count = 128 output nothing
+
+ if ( numberOfReadBytes > fragmentSize )
+ {
+ dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we "
+ "read more bytes than the segment size.");
+ return false;
+ }
+ }
+ return true;
+}
+
+/**
+ * \brief Reads from disk the Pixel Data of 'Run Length Encoded'
+ * Dicom encapsulated file and decompress it.
+ * @param fp already open File Pointer
+ * at which the pixel data should be copied
+ * @return Boolean
+ */
+bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp )
+{
+ uint8_t* subRaw = Raw;
+ long RawSegmentSize = XSize * YSize;
+
+ // Loop on the frame[s]
+ for( RLEFramesInfo::RLEFrameList::iterator
+ it = RLEInfo->Frames.begin();
+ it != RLEInfo->Frames.end();
+ ++it )
+ {
+ // Loop on the fragments
+ for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ )
+ {
+ fp->seekg( (*it)->Offset[k] , std::ios::beg );
+ (void)ReadAndDecompressRLEFragment( subRaw,
+ (*it)->Length[k],
+ RawSegmentSize,
+ fp );
+ subRaw += RawSegmentSize;
+ }
+ }
+
+ if ( BitsAllocated == 16 )
+ {
+ // Try to deal with RLE 16 Bits
+ (void)DecompressRLE16BitsFromRLE8Bits( ZSize );
+ }
+
+ return true;
+}
+
+/**
+ * \brief Swap the bytes, according to \ref SwapCode.
+ */
+void PixelReadConvert::ConvertSwapZone()
+{
+ unsigned int i;
+
+ if( BitsAllocated == 16 )
+ {
+ uint16_t* im16 = (uint16_t*)Raw;
+ switch( SwapCode )
+ {
+ case 0:
+ case 12:
+ case 1234:
+ break;
+ case 21:
+ case 3412:
+ case 2143:
+ case 4321:
+ for( i = 0; i < RawSize / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
+ break;
+ default:
+ dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "
+ "(16 bits) not allowed." );
+ }
+ }
+ else if( BitsAllocated == 32 )
+ {
+ uint32_t s32;
+ uint16_t high;
+ uint16_t low;
+ uint32_t* im32 = (uint32_t*)Raw;
+ switch ( SwapCode )
+ {
+ case 0:
+ case 1234:
+ break;
+ case 4321:
+ for( i = 0; i < RawSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 4321
+ high = im32[i] >> 16;
+ high = ( high >> 8 ) | ( high << 8 );
+ low = ( low >> 8 ) | ( low << 8 );
+ s32 = low;
+ im32[i] = ( s32 << 16 ) | high;
+ }
+ break;
+ case 2143:
+ for( i = 0; i < RawSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 2143
+ high = im32[i] >> 16;
+ high = ( high >> 8 ) | ( high << 8 );
+ low = ( low >> 8 ) | ( low << 8 );
+ s32 = high;
+ im32[i] = ( s32 << 16 ) | low;
+ }
+ break;
+ case 3412:
+ for( i = 0; i < RawSize / 4; i++ )
+ {
+ low = im32[i] & 0x0000ffff; // 3412
+ high = im32[i] >> 16;
+ s32 = low;
+ im32[i] = ( s32 << 16 ) | high;
+ }
+ break;
+ default:
+ dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "
+ "(32 bits) not allowed." );
+ }
+ }
+}
+
+/**
+ * \brief Deal with endianity i.e. re-arange bytes inside the integer
+ */
+void PixelReadConvert::ConvertReorderEndianity()
+{
+ if ( BitsAllocated != 8 )
+ {
+ ConvertSwapZone();
+ }
+
+ // Special kludge in order to deal with xmedcon broken images:
+ if ( ( BitsAllocated == 16 )
+ && ( BitsStored < BitsAllocated )
+ && ( ! PixelSign ) )
+ {
+ int l = (int)( RawSize / ( BitsAllocated / 8 ) );
+ uint16_t *deb = (uint16_t *)Raw;
+ for(int i = 0; i<l; i++)
+ {
+ if( *deb == 0xffff )
+ {
+ *deb = 0;
+ }
+ deb++;
+ }
+ }
+}
+
+
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it. This funciton assumes that each
+ * jpeg fragment contains a whole frame (jpeg file).
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream* fp )
+{
+ uint8_t* localRaw = Raw;
+ // Loop on the fragment[s]
+ for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
+ it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ fp->seekg( (*it)->Offset, std::ios::beg);
+
+ if ( BitsStored == 8)
+ {
+ // JPEG Lossy : call to IJG 6b
+ if ( ! gdcm_read_JPEG_file8( fp, localRaw ) )
+ {
+ return false;
+ }
+ }
+ else if ( BitsStored <= 12)
+ {
+ // Reading Fragment pixels
+ if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) )
+ {
+ return false;
+ }
+ }
+ else if ( BitsStored <= 16)
+ {
+ // Reading Fragment pixels
+ if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) )
+ {
+ return false;
+ }
+ //assert( IsJPEGLossless );
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown "
+ "jpeg lossy compression ");
+ return false;
+ }
+
+ // Advance to next free location in Raw
+ // for next fragment decompression (if any)
+ int length = XSize * YSize * SamplesPerPixel;
+ int numberBytes = BitsAllocated / 8;
+
+ localRaw += length * numberBytes;
+ }
+ return true;
+}
+
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it. This function assumes that the dicom
+ * image is a single frame split into several JPEG fragments.
+ * Those fragments will be glued together into a memory buffer
+ * before being read.
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelReadConvert::
+ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream* fp )
+{
+ // Loop on the fragment[s] to get total length
+ size_t totalLength = 0;
+ JPEGFragmentsInfo::JPEGFragmentsList::iterator it;
+ for( it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ totalLength += (*it)->Length;
+ }
+
+ // Concatenate the jpeg fragments into a local buffer
+ JOCTET *buffer = new JOCTET [totalLength];
+ JOCTET *p = buffer;
+
+ uint8_t* localRaw = Raw;
+ // Loop on the fragment[s]
+ for( it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ fp->seekg( (*it)->Offset, std::ios::beg);
+ size_t len = (*it)->Length;
+ fp->read((char *)p,len);
+ p += len;
+ }
+
+ size_t howManyRead = 0;
+ size_t howManyWritten = 0;
+ size_t fragmentLength = 0;
+
+ if ( BitsStored == 8)
+ {
+ if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error(
+ "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 "
+ );
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 12)
+ {
+ if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error(
+ "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 "
+ );
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 16)
+ {
+
+ if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error(
+ "PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 "
+ );
+ delete [] buffer;
+ return false;
+ }
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "
+ "jpeg lossy compression ");
+ delete [] buffer;
+ return false;
+ }
+
+ // free local buffer
+ delete [] buffer;
+
+ return true;
+}
+
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it. This function handles the generic
+ * and complex case where the DICOM contains several frames,
+ * and some of the frames are possibly split into several JPEG
+ * fragments.
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelReadConvert::
+ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream* fp )
+{
+ // Loop on the fragment[s] to get total length
+ size_t totalLength = 0;
+ for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
+ it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ totalLength += (*it)->Length;
+ }
+
+ // Concatenate the jpeg fragments into a local buffer
+ JOCTET *buffer = new JOCTET [totalLength];
+ JOCTET *p = buffer;
+
+ uint8_t* localRaw = Raw;
+ // Loop on the fragment[s]
+ for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
+ it = JPEGInfo->Fragments.begin();
+ it != JPEGInfo->Fragments.end();
+ ++it )
+ {
+ fp->seekg( (*it)->Offset, std::ios::beg);
+ size_t len = (*it)->Length;
+ fp->read((char *)p,len);
+ p+=len;
+ }
+
+ size_t howManyRead = 0;
+ size_t howManyWritten = 0;
+ size_t fragmentLength = 0;
+
+ for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
+ it = JPEGInfo->Fragments.begin() ;
+ (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength);
+ ++it )
+ {
+ fragmentLength += (*it)->Length;
+
+ if (howManyRead > fragmentLength) continue;
+
+ if ( BitsStored == 8)
+ {
+ if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead,
+ Raw+howManyWritten,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg8 ");
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 12)
+ {
+
+ if ( ! gdcm_read_JPEG_memory12( buffer+howManyRead, totalLength-howManyRead,
+ Raw+howManyWritten,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg12 ");
+ delete [] buffer;
+ return false;
+ }
+ }
+ else if ( BitsStored <= 16)
+ {
+
+ if ( ! gdcm_read_JPEG_memory16( buffer+howManyRead, totalLength-howManyRead,
+ Raw+howManyWritten,
+ &howManyRead, &howManyWritten ) )
+ {
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: failed to read jpeg16 ");
+ delete [] buffer;
+ return false;
+ }
+ }
+ else
+ {
+ // other JPEG lossy not supported
+ dbg.Error("PixelConvert::ReadAndDecompressJPEGFile: unknown "
+ "jpeg lossy compression ");
+ delete [] buffer;
+ return false;
+ }
+
+ if (howManyRead < fragmentLength)
+ howManyRead = fragmentLength;
+ }
+
+ // free local buffer
+ delete [] buffer;
+
+ return true;
+}
+
+/**
+ * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
+ * file and decompress it.
+ * @param fp File Pointer
+ * @return Boolean
+ */
+bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp )
+{
+ if ( IsJPEG2000 )
+ {
+ fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg);
+ if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
+ return false;
+ }
+
+ if ( ( ZSize == 1 ) && ( JPEGInfo->Fragments.size() > 1 ) )
+ {
+ // we have one frame split into several fragments
+ // we will pack those fragments into a single buffer and
+ // read from it
+ return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp );
+ }
+ else if (JPEGInfo->Fragments.size() == ZSize)
+ {
+ // suppose each fragment is a frame
+ return ReadAndDecompressJPEGFramesFromFile( fp );
+ }
+ else
+ {
+ // The dicom image contains frames containing fragments of images
+ // a more complex algorithm :-)
+ return ReadAndDecompressJPEGFragmentedFramesFromFile( fp );
+ }
+}
+
+/**
+ * \brief Re-arrange the bits within the bytes.
+ * @return Boolean
+ */
+bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
+{
+ if ( BitsStored != BitsAllocated )
+ {
+ int l = (int)( RawSize / ( BitsAllocated / 8 ) );
+ if ( BitsAllocated == 16 )
+ {
+ uint16_t mask = 0xffff;
+ mask = mask >> ( BitsAllocated - BitsStored );
+ uint16_t* deb = (uint16_t*)Raw;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else if ( BitsAllocated == 32 )
+ {
+ uint32_t mask = 0xffffffff;
+ mask = mask >> ( BitsAllocated - BitsStored );
+ uint32_t* deb = (uint32_t*)Raw;
+ for(int i = 0; i<l; i++)
+ {
+ *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
+ deb++;
+ }
+ }
+ else
+ {
+ dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image");
+ throw FormatError( "PixelReadConvert::ConvertReArrangeBits()",
+ "weird image !?" );
+ }
+ }
+ return true;
+}
+
+/**
+ * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
+{
+ uint8_t* localRaw = Raw;
+ uint8_t* copyRaw = new uint8_t[ RawSize ];
+ memmove( copyRaw, localRaw, RawSize );
+
+ // to see the tricks about YBR_FULL, YBR_FULL_422,
+ // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
+ // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
+ // and be *very* affraid
+ //
+ int l = XSize * YSize;
+ int nbFrames = ZSize;
+
+ uint8_t* a = copyRaw;
+ uint8_t* b = copyRaw + l;
+ uint8_t* c = copyRaw + l + l;
+ double R, G, B;
+
+ /// \todo : Replace by the 'well known' integer computation
+ /// counterpart. Refer to
+ /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ /// for code optimisation.
+
+ for ( int i = 0; i < nbFrames; i++ )
+ {
+ for ( int j = 0; j < l; j++ )
+ {
+ R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
+ G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5;
+ B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5;
+
+ if (R < 0.0) R = 0.0;
+ if (G < 0.0) G = 0.0;
+ if (B < 0.0) B = 0.0;
+ if (R > 255.0) R = 255.0;
+ if (G > 255.0) G = 255.0;
+ if (B > 255.0) B = 255.0;
+
+ *(localRaw++) = (uint8_t)R;
+ *(localRaw++) = (uint8_t)G;
+ *(localRaw++) = (uint8_t)B;
+ a++;
+ b++;
+ c++;
+ }
+ }
+ delete[] copyRaw;
+}
+
+/**
+ * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
+ * \warning Works on all the frames at a time
+ */
+void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
+{
+ uint8_t* localRaw = Raw;
+ uint8_t* copyRaw = new uint8_t[ RawSize ];
+ memmove( copyRaw, localRaw, RawSize );
+
+ int l = XSize * YSize * ZSize;
+
+ uint8_t* a = copyRaw;
+ uint8_t* b = copyRaw + l;
+ uint8_t* c = copyRaw + l + l;
+
+ for (int j = 0; j < l; j++)
+ {
+ *(localRaw++) = *(a++);
+ *(localRaw++) = *(b++);
+ *(localRaw++) = *(c++);
+ }
+ delete[] copyRaw;
+}
+
+bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp )
+{
+ // ComputeRawAndRGBSizes is already made by
+ // ::GrabInformationsFromHeader. So, the structure sizes are
+ // correct
+ Squeeze();
+
+ //////////////////////////////////////////////////
+ //// First stage: get our hands on the Pixel Data.
+ if ( !fp )
+ {
+ dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
+ "unavailable file pointer." );
+ return false;
+ }
+
+ fp->seekg( PixelOffset, std::ios::beg );
+ if( fp->fail() || fp->eof()) //Fp->gcount() == 1
+ {
+ dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
+ "unable to find PixelOffset in file." );
+ return false;
+ }
+
+ AllocateRaw();
+
+ //////////////////////////////////////////////////
+ //// Second stage: read from disk dans decompress.
+ if ( BitsAllocated == 12 )
+ {
+ ReadAndDecompress12BitsTo16Bits( fp);
+ }
+ else if ( IsRaw )
+ {
+ // This problem can be found when some obvious informations are found
+ // after the field containing the image datas. In this case, these
+ // bad datas are added to the size of the image (in the PixelDataLength
+ // variable). But RawSize is the right size of the image !
+ if( PixelDataLength != RawSize)
+ {
+ dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
+ "Mismatch between PixelReadConvert and RawSize." );
+ }
+ if( PixelDataLength > RawSize)
+ {
+ fp->read( (char*)Raw, RawSize);
+ }
+ else
+ {
+ fp->read( (char*)Raw, PixelDataLength);
+ }
+
+ if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ {
+ dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
+ "reading of Raw pixel data failed." );
+ return false;
+ }
+ }
+ else if ( IsRLELossless )
+ {
+ if ( ! ReadAndDecompressRLEFile( fp ) )
+ {
+ dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
+ "RLE decompressor failed." );
+ return false;
+ }
+ }
+ else
+ {
+ // Default case concerns JPEG family
+ if ( ! ReadAndDecompressJPEGFile( fp ) )
+ {
+ dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
+ "JPEG decompressor failed." );
+ return false;
+ }
+ }
+
+ ////////////////////////////////////////////
+ //// Third stage: twigle the bytes and bits.
+ ConvertReorderEndianity();
+ ConvertReArrangeBits();
+ ConvertHandleColor();
+
+ return true;
+}
+
+void PixelReadConvert::ConvertHandleColor()
+{
+ //////////////////////////////////
+ // Deal with the color decoding i.e. handle:
+ // - R, G, B planes (as opposed to RGB pixels)
+ // - YBR (various) encodings.
+ // - LUT[s] (or "PALETTE COLOR").
+ //
+ // The classification in the color decoding schema is based on the blending
+ // of two Dicom tags values:
+ // * "Photometric Interpretation" for which we have the cases:
+ // - [Photo A] MONOCHROME[1|2] pictures,
+ // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB),
+ // - [Photo C] YBR_* (with the above exception of YBR_FULL_422)
+ // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s].
+ // * "Planar Configuration" for which we have the cases:
+ // - [Planar 0] 0 then Pixels are already RGB
+ // - [Planar 1] 1 then we have 3 planes : R, G, B,
+ // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs
+ //
+ // Now in theory, one could expect some coherence when blending the above
+ // cases. For example we should not encounter files belonging at the
+ // time to case [Planar 0] and case [Photo D].
+ // Alas, this was only theory ! Because in practice some odd (read ill
+ // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:
+ // - "Planar Configuration" = 0,
+ // - "Photometric Interpretation" = "PALETTE COLOR".
+ // Hence gdcm shall use the folowing "heuristic" in order to be tolerant
+ // towards Dicom-non-conformance files:
+ // << whatever the "Planar Configuration" value might be, a
+ // "Photometric Interpretation" set to "PALETTE COLOR" forces
+ // a LUT intervention >>
+ //
+ // Now we are left with the following handling of the cases:
+ // - [Planar 0] OR [Photo A] no color decoding (since respectively
+ // Pixels are already RGB and monochrome pictures have no color :),
+ // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels()
+ // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
+ // - [Planar 2] OR [Photo D] requires LUT intervention.
+
+ if ( ! IsRawRGB() )
+ {
+ // [Planar 2] OR [Photo D]: LUT intervention done outside
+ return;
+ }
+
+ if ( PlanarConfiguration == 1 )
+ {
+ if ( IsYBRFull )
+ {
+ // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
+ ConvertYcBcRPlanesToRGBPixels();
+ }
+ else
+ {
+ // [Planar 1] AND [Photo C]
+ ConvertRGBPlanesToRGBPixels();
+ }
+ return;
+ }
+
+ // When planarConf is 0, and RLELossless (forbidden by Dicom norm)
+ // pixels need to be RGB-fied anyway
+ if (IsRLELossless)
+ {
+ ConvertRGBPlanesToRGBPixels();
+ }
+ // In *normal *case, when planarConf is 0, pixels are already in RGB
+}
+
+/**
+ * \brief Predicate to know wether the image[s] (once Raw) is RGB.
+ * \note See comments of \ref ConvertHandleColor
+ */
+bool PixelReadConvert::IsRawRGB()
+{
+ if ( IsMonochrome
+ || PlanarConfiguration == 2
+ || IsPaletteColor )
+ {
+ return false;
+ }
+ return true;
+}
+
+void PixelReadConvert::ComputeRawAndRGBSizes()
+{
+ int bitsAllocated = BitsAllocated;
+ // Number of "Bits Allocated" is fixed to 16 when it's 12, since
+ // in this case we will expand the image to 16 bits (see
+ // \ref ReadAndDecompress12BitsTo16Bits() )
+ if ( BitsAllocated == 12 )
+ {
+ bitsAllocated = 16;
+ }
+
+ RawSize = XSize * YSize * ZSize
+ * ( bitsAllocated / 8 )
+ * SamplesPerPixel;
+ if ( HasLUT )
+ {
+ RGBSize = 3 * RawSize;
+ }
+ else
+ {
+ RGBSize = RawSize;
+ }
+}
+
+void PixelReadConvert::GrabInformationsFromHeader( Header* header )
+{
+ // Number of Bits Allocated for storing a Pixel is defaulted to 16
+ // when absent from the header.
+ BitsAllocated = header->GetBitsAllocated();
+ if ( BitsAllocated == 0 )
+ {
+ BitsAllocated = 16;
+ }
+
+ // Number of "Bits Stored" defaulted to number of "Bits Allocated"
+ // when absent from the header.
+ BitsStored = header->GetBitsStored();
+ if ( BitsStored == 0 )
+ {
+ BitsStored = BitsAllocated;
+ }
+
+ // High Bit Position
+ HighBitPosition = header->GetHighBitPosition();
+ if ( HighBitPosition == 0 )
+ {
+ HighBitPosition = BitsAllocated - 1;
+ }
+
+ XSize = header->GetXSize();
+ YSize = header->GetYSize();
+ ZSize = header->GetZSize();
+ SamplesPerPixel = header->GetSamplesPerPixel();
+ PixelSize = header->GetPixelSize();
+ PixelSign = header->IsSignedPixelData();
+ SwapCode = header->GetSwapCode();
+ TransferSyntaxType ts = header->GetTransferSyntax();
+ IsRaw =
+ ( ! header->IsDicomV3() )
+ || ts == ImplicitVRLittleEndian
+ || ts == ImplicitVRLittleEndianDLXGE
+ || ts == ExplicitVRLittleEndian
+ || ts == ExplicitVRBigEndian
+ || ts == DeflatedExplicitVRLittleEndian;
+ IsJPEG2000 = header->IsJPEG2000();
+ IsJPEGLossless = header->IsJPEGLossless();
+ IsRLELossless = ( ts == RLELossless );
+ PixelOffset = header->GetPixelOffset();
+ PixelDataLength = header->GetPixelAreaLength();
+ RLEInfo = header->GetRLEInfo();
+ JPEGInfo = header->GetJPEGInfo();
+
+ PlanarConfiguration = header->GetPlanarConfiguration();
+ IsMonochrome = header->IsMonochrome();
+ IsPaletteColor = header->IsPaletteColor();
+ IsYBRFull = header->IsYBRFull();
+
+ /////////////////////////////////////////////////////////////////
+ // LUT section:
+ HasLUT = header->HasLUT();
+ if ( HasLUT )
+ {
+ // Just in case some access to a Header element requires disk access.
+ // Note: gdcmDocument::Fp is leaved open after OpenFile.
+ LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 );
+ LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 );
+ LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 );
+
+ // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE
+ // [ refer to invocation of Document::SetMaxSizeLoadEntry() in
+ // Document::Document() ], the loading of the value (content) of a
+ // [Bin|Val]Entry occurence migth have been hindered (read simply NOT
+ // loaded). Hence, we first try to obtain the LUTs data from the header
+ // and when this fails we read the LUTs data directely from disk.
+ /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge.
+ /// We should NOT bypass the [Bin|Val]Entry class. Instead
+ /// an access to an UNLOADED content of a [Bin|Val]Entry occurence
+ /// (e.g. BinEntry::GetBinArea()) should force disk access from
+ /// within the [Bin|Val]Entry class itself. The only problem
+ /// is that the [Bin|Val]Entry is unaware of the FILE* is was
+ /// parsed from. Fix that. FIXME.
+
+ ////// Red round
+ header->LoadEntryBinArea(0x0028, 0x1201);
+ LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 );
+ if ( ! LutRedData )
+ {
+ dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
+ "unable to read red LUT data" );
+ }
+
+ ////// Green round:
+ header->LoadEntryBinArea(0x0028, 0x1202);
+ LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 );
+ if ( ! LutGreenData)
+ {
+ dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
+ "unable to read green LUT data" );
+ }
+
+ ////// Blue round:
+ header->LoadEntryBinArea(0x0028, 0x1203);
+ LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
+ {
+ dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
+ "unable to read blue LUT data" );
+ }
+ }
+
+ ComputeRawAndRGBSizes();
+}
+
+/**
+ * \brief Build Red/Green/Blue/Alpha LUT from Header
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * and (0028,1101),(0028,1102),(0028,1102)
+ * - xxx Palette Color Lookup Table Descriptor - are found
+ * and (0028,1201),(0028,1202),(0028,1202)
+ * - xxx Palette Color Lookup Table Data - are found
+ * \warning does NOT deal with :
+ * 0028 1100 Gray Lookup Table Descriptor (Retired)
+ * 0028 1221 Segmented Red Palette Color Lookup Table Data
+ * 0028 1222 Segmented Green Palette Color Lookup Table Data
+ * 0028 1223 Segmented Blue Palette Color Lookup Table Data
+ * no known Dicom reader deals with them :-(
+ * @return a RGBA Lookup Table
+ */
+void PixelReadConvert::BuildLUTRGBA()
+{
+ if ( LutRGBA )
+ {
+ return;
+ }
+ // Not so easy : see
+ // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
+
+ if ( ! IsPaletteColor )
+ {
+ return;
+ }
+
+ if ( LutRedDescriptor == GDCM_UNFOUND
+ || LutGreenDescriptor == GDCM_UNFOUND
+ || LutBlueDescriptor == GDCM_UNFOUND )
+ {
+ return;
+ }
+
+ ////////////////////////////////////////////
+ // Extract the info from the LUT descriptors
+ int lengthR; // Red LUT length in Bytes
+ int debR; // Subscript of the first Lut Value
+ int nbitsR; // Lut item size (in Bits)
+ int nbRead = sscanf( LutRedDescriptor.c_str(),
+ "%d\\%d\\%d",
+ &lengthR, &debR, &nbitsR );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor");
+ }
+
+ int lengthG; // Green LUT length in Bytes
+ int debG; // Subscript of the first Lut Value
+ int nbitsG; // Lut item size (in Bits)
+ nbRead = sscanf( LutGreenDescriptor.c_str(),
+ "%d\\%d\\%d",
+ &lengthG, &debG, &nbitsG );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor");
+ }
+
+ int lengthB; // Blue LUT length in Bytes
+ int debB; // Subscript of the first Lut Value
+ int nbitsB; // Lut item size (in Bits)
+ nbRead = sscanf( LutRedDescriptor.c_str(),
+ "%d\\%d\\%d",
+ &lengthB, &debB, &nbitsB );
+ if( nbRead != 3 )
+ {
+ dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor");
+ }
+
+ ////////////////////////////////////////////////////////
+ if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
+ {
+ return;
+ }
+
+ ////////////////////////////////////////////////
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+ LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
+ if ( !LutRGBA )
+ {
+ return;
+ }
+ memset( LutRGBA, 0, 1024 );
+
+ int mult;
+ if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) )
+ {
+ // when LUT item size is different than pixel size
+ mult = 2; // high byte must be = low byte
+ }
+ else
+ {
+ // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult = 1;
+ }
+
+ // if we get a black image, let's just remove the '+1'
+ // from 'i*mult+1' and check again
+ // if it works, we shall have to check the 3 Palettes
+ // to see which byte is ==0 (first one, or second one)
+ // and fix the code
+ // We give up the checking to avoid some (useless ?)overhead
+ // (optimistic asumption)
+ int i;
+ uint8_t* a = LutRGBA + 0;
+ for( i=0; i < lengthR; ++i )
+ {
+ *a = LutRedData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 1;
+ for( i=0; i < lengthG; ++i)
+ {
+ *a = LutGreenData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 2;
+ for(i=0; i < lengthB; ++i)
+ {
+ *a = LutBlueData[i*mult+1];
+ a += 4;
+ }
+
+ a = LutRGBA + 3;
+ for(i=0; i < 256; ++i)
+ {
+ *a = 1; // Alpha component
+ a += 4;
+ }
+}
+
+/**
+ * \brief Build the RGB image from the Raw imagage and the LUTs.
+ */
+bool PixelReadConvert::BuildRGBImage()
+{
+ if ( RGB )
+ {
+ // The job is already done.
+ return true;
+ }
+
+ if ( ! Raw )
+ {
+ // The job can't be done
+ return false;
+ }
+
+ BuildLUTRGBA();
+ if ( ! LutRGBA )
+ {
+ // The job can't be done
+ return false;
+ }
+
+ // Build RGB Pixels
+ AllocateRGB();
+ uint8_t* localRGB = RGB;
+ for (size_t i = 0; i < RawSize; ++i )
+ {
+ int j = Raw[i] * 4;
+ *localRGB++ = LutRGBA[j];
+ *localRGB++ = LutRGBA[j+1];
+ *localRGB++ = LutRGBA[j+2];
+ }
+ return true;
+}
+
+/**
+ * \brief Print self.
+ * @param indent Indentation string to be prepended during printing.
+ * @param os Stream to print to.
+ */
+void PixelReadConvert::Print( std::string indent, std::ostream &os )
+{
+ os << indent
+ << "--- Pixel information -------------------------"
+ << std::endl;
+ os << indent
+ << "Pixel Data: offset " << PixelOffset
+ << " x" << std::hex << PixelOffset << std::dec
+ << " length " << PixelDataLength
+ << " x" << std::hex << PixelDataLength << std::dec
+ << std::endl;
+
+ if ( IsRLELossless )
+ {
+ if ( RLEInfo )
+ {
+ RLEInfo->Print( indent, os );
+ }
+ else
+ {
+ dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file "
+ "but NO RLEinfo present.");
+ }
+ }
+
+ if ( IsJPEG2000 || IsJPEGLossless )
+ {
+ if ( JPEGInfo )
+ {
+ JPEGInfo->Print( indent, os );
+ }
+ else
+ {
+ dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file "
+ "but NO JPEGinfo present.");
+ }
+ }
+}
+
+} // end namespace gdcm
+
+// NOTES on File internal calls
+// User
+// ---> GetImageData
+// ---> GetImageDataIntoVector
+// |---> GetImageDataIntoVectorRaw
+// | lut intervention
+// User
+// ---> GetImageDataRaw
+// ---> GetImageDataIntoVectorRaw
+
projects / gdcm.git / commitdiff