From: rouet Date: Sun, 12 Dec 2004 17:21:07 +0000 (+0000) Subject: * FIX: new handling of JPEG decompression, especially when dicom X-Git-Tag: Version1.0.bp~504 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=dd4e6402f3542ddd5e1cc14a29ca3f84a9f063b6;p=gdcm.git * FIX: new handling of JPEG decompression, especially when dicom frames are split into several JPEG Fragments. This makes use of jpeg decompression from memory buffer. This solves reading for example gdcm-JPEG-Lossless_Thoravision.dcm. --- diff --git a/ChangeLog b/ChangeLog index 4d6c4c1d..537849cf 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,9 @@ +2004-12-12 Jean-Michel Rouet + * src/gdcmPixelReadConvert.[h|cxx], src/gdcmJpeg*.cxx : new handling of + JPEG decompression, especially when dicom frames are split into several + JPEG Fragments. This makes use of jpeg decompression from memory buffer. + This solves reading for example gdcm-JPEG-Lossless_Thoravision.dcm. + 2004-12-10 Benoit Regrain * src/gdcmHeader.cxx : change the initialisation of default header. Now, this header is readable by gdm, e-film, DicomWorks diff --git a/src/gdcmJpeg.cxx b/src/gdcmJpeg.cxx index 86403c62..d7579773 100644 --- a/src/gdcmJpeg.cxx +++ b/src/gdcmJpeg.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmJpeg.cxx,v $ Language: C++ - Date: $Date: 2004/10/22 03:05:42 $ - Version: $Revision: 1.28 $ + Date: $Date: 2004/12/12 17:21:08 $ + Version: $Revision: 1.29 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -610,4 +610,253 @@ bool gdcm_read_JPEG_file ( std::ifstream* fp, void* image_buffer ) //---------------------------------------------------------------------------- + +/** + * \brief routine for JPEG decompression from a memory buffer. + * routine for JPEG decompression from a memory buffer. This routine + * only reads one JPEG image at a time, but returns information about + * how many bytes have been consumed from the \c input_buffer, and + * how many bytes have been written into the output \c image_buffer. + * + * @param input_buffer pointer to a memory buffer containing the jpeg + * compressed data. + * @param buflen length of the memory buffer. + * @param image_buffer pointer to the location where the decompressed + * image will be filled. + * @param howManyRead returns how many bytes have been consumed from the + * input_buffer. + * @param howManyWritten returns how many bytes have been written into + * the output image_buffer. + * @return 1 on success, 0 on error + */ + +bool gdcm_read_JPEG_memory ( const JOCTET* input_buffer, const size_t buflen, + void* image_buffer, + size_t *howManyRead, size_t *howManyWritten) +{ + char* pimage=(char *)image_buffer; + JOCTET* input = (JOCTET*) input_buffer; + + /* This struct contains the JPEG decompression parameters and pointers to + * working space (which is allocated as needed by the JPEG library). + */ + struct jpeg_decompress_struct cinfo; + + /* -------------- inside, we found : + * JDIMENSION image_width; // input image width + * JDIMENSION image_height; // input image height + * int input_components; // nb of color components in input image + * J_COLOR_SPACE in_color_space; // colorspace of input image + * double input_gamma; // image gamma of input image + * -------------- */ + + /* We use our private extension JPEG error handler. + * Note that this struct must live as long as the main JPEG parameter + * struct, to avoid dangling-pointer problems. + */ + struct my_error_mgr jerr; + /* More stuff */ + + JSAMPARRAY buffer;/* Output row buffer */ + + // rappel : + // ------ + // typedef unsigned char JSAMPLE; + // typedef JSAMPLE FAR *JSAMPROW;/* ptr to one image row of pixel samples. */ + // typedef JSAMPROW *JSAMPARRAY;/* ptr to some rows (a 2-D sample array) */ + // typedef JSAMPARRAY *JSAMPIMAGE;/* a 3-D sample array: top index is color */ + + int row_stride;/* physical row width in output buffer */ + +#ifdef GDCM_JPG_DEBUG + printf("entree dans File::gdcm_read_JPEG_file (i.e. 8), depuis gdcmJpeg\n"); +#endif //GDCM_JPG_DEBUG + + /* In this example we want to open the input file before doing anything else, + * so that the setjmp() error recovery below can assume the file is open. + * VERY IMPORTANT: use "b" option to fopen() if you are on a machine that + * requires it in order to read binary files. + */ + + /* Step 1: allocate and initialize JPEG decompression object */ +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 1\n"); +#endif //GDCM_JPG_DEBUG + + /* We set up the normal JPEG error routines, then override error_exit. */ + + cinfo.err = jpeg_std_error(&jerr.pub); + jerr.pub.error_exit = my_error_exit; + + /* Establish the setjmp return context for my_error_exit to use. */ + if (setjmp(jerr.setjmp_buffer)) + { + /* If we get here, the JPEG code has signaled an error. + * We need to clean up the JPEG object, close the input file, and return. + */ + jpeg_destroy_decompress(&cinfo); + + *howManyRead += input - input_buffer; + *howManyWritten += pimage - (char *)image_buffer; + return 0; + } + + /* Now we can initialize the JPEG decompression object. */ + jpeg_create_decompress(&cinfo); + + /* Step 2: specify data source (eg, a file) */ +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 2\n"); +#endif //GDCM_JPG_DEBUG + + jpeg_memory_src(&cinfo, input, buflen); + + /* Step 3: read file parameters with jpeg_read_header() */ +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 3\n"); +#endif //GDCM_JPG_DEBUG + + (void) jpeg_read_header(&cinfo, TRUE); + + /* We can ignore the return value from jpeg_read_header since + * (a) suspension is not possible with the stdio data source, and + * (b) we passed TRUE to reject a tables-only JPEG file as an error. + * See libjpeg.doc for more info. + */ + + // prevent the library from performing any color space conversion + if( cinfo.process == JPROC_LOSSLESS ) + { + cinfo.jpeg_color_space = JCS_UNKNOWN; + cinfo.out_color_space = JCS_UNKNOWN; + } + +#ifdef GDCM_JPG_DEBUG + printf("--------------Header contents :----------------\n"); + printf("image_width %d image_height %d\n", + cinfo.image_width , cinfo.image_height); + printf("bits of precision in image data %d \n", + cinfo.output_components); + printf("nb of color components returned %d \n", + cinfo.data_precision); +#endif //GDCM_JPG_DEBUG + + + /* + * JDIMENSION image_width; // input image width + * JDIMENSION image_height; // input image height + * int output_components; // # of color components returned + * J_COLOR_SPACE in_color_space; // colorspace of input image + * double input_gamma; // image gamma of input image + * int data_precision; // bits of precision in image data + */ + + /* Step 4: set parameters for decompression */ +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 4\n"); +#endif //GDCM_JPG_DEBUG + /* In this example, we don't need to change any of the defaults set by + * jpeg_read_header(), so we do nothing here. + */ + + /* Step 5: Start decompressor */ +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 5\n"); +#endif //GDCM_JPG_DEBUG + + (void) jpeg_start_decompress(&cinfo); + /* We can ignore the return value since suspension is not possible + * with the stdio data source. + */ + + /* We may need to do some setup of our own at this point before reading + * the data. After jpeg_start_decompress() we have the correct scaled + * output image dimensions available, as well as the output colormap + * if we asked for color quantization. + * In this example, we need to make an output work buffer of the right size. + */ + + /* JSAMPLEs per row in output buffer */ + row_stride = cinfo.output_width * cinfo.output_components*2; + +#ifdef GDCM_JPG_DEBUG + printf ("cinfo.output_width %d cinfo.output_components %d row_stride %d\n", + cinfo.output_width, cinfo.output_components,row_stride); +#endif //GDCM_JPG_DEBUG + + /* Make a one-row-high sample array that will go away when done with image */ + buffer = (*cinfo.mem->alloc_sarray) + ((j_common_ptr) &cinfo, JPOOL_IMAGE, row_stride, 1); + + + /* Step 6: while (scan lines remain to be read) */ +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 6\n"); +#endif //GDCM_JPG_DEBUG + /* jpeg_read_scanlines(...); */ + + /* Here we use the library's state variable cinfo.output_scanline as the + * loop counter, so that we don't have to keep track ourselves. + */ +#ifdef GDCM_JPG_DEBUG + printf ("cinfo.output_height %d cinfo.output_width %d\n", + cinfo.output_height,cinfo.output_width); +#endif //GDCM_JPG_DEBUG + + int bufsize = cinfo.output_width * cinfo.output_components; + size_t rowsize = bufsize * sizeof(JSAMPLE); + + while (cinfo.output_scanline < cinfo.output_height) { + /* jpeg_read_scanlines expects an array of pointers to scanlines. + * Here the array is only one element long, but you could ask for + * more than one scanline at a time if that's more convenient. + */ + + //printf( "scanlines: %d\n",cinfo.output_scanline); + (void) jpeg_read_scanlines(&cinfo, buffer, 1); + memcpy( pimage, *buffer,rowsize); + pimage+=rowsize; + } + + /* Step 7: Finish decompression */ +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 7\n"); +#endif //GDCM_JPG_DEBUG + + input = (JOCTET *)cinfo.src->next_input_byte; + + (void) jpeg_finish_decompress(&cinfo); + + /* We can ignore the return value since suspension is not possible + * with the stdio data source. + */ + + /* Step 8: Release JPEG decompression object */ + +#ifdef GDCM_JPG_DEBUG + printf("Entree Step 8\n"); +#endif //GDCM_JPG_DEBUG + + /* This is an important step since it will release a good deal of memory. */ + + jpeg_destroy_decompress(&cinfo); + + + /* After finish_decompress, we can close the input file. + * Here we postpone it until after no more JPEG errors are possible, + * so as to simplify the setjmp error logic above. (Actually, I don't + * think that jpeg_destroy can do an error exit, but why assume anything...) + */ + + /* At this point you may want to check to see whether any corrupt-data + * warnings occurred (test whether jerr.pub.num_warnings is nonzero). + */ + + /* And we're done! */ + *howManyRead += input - input_buffer; + *howManyWritten += pimage - (char *)image_buffer; + + return true; +} + } // end namespace gdcm diff --git a/src/gdcmJpeg12.cxx b/src/gdcmJpeg12.cxx index 9e2dc35c..d4069cb5 100644 --- a/src/gdcmJpeg12.cxx +++ b/src/gdcmJpeg12.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmJpeg12.cxx,v $ Language: C++ - Date: $Date: 2004/11/09 21:55:56 $ - Version: $Revision: 1.27 $ + Date: $Date: 2004/12/12 17:21:08 $ + Version: $Revision: 1.28 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -25,8 +25,9 @@ extern "C" { #include "gdcmjpeg/12/jerror.h" } -#define gdcm_write_JPEG_file gdcm_write_JPEG_file12 -#define gdcm_read_JPEG_file gdcm_read_JPEG_file12 +#define gdcm_write_JPEG_file gdcm_write_JPEG_file12 +#define gdcm_read_JPEG_file gdcm_read_JPEG_file12 +#define gdcm_read_JPEG_memory gdcm_read_JPEG_memory12 #include "gdcmJpeg.cxx" diff --git a/src/gdcmJpeg16.cxx b/src/gdcmJpeg16.cxx index 08575f8c..f820bdca 100644 --- a/src/gdcmJpeg16.cxx +++ b/src/gdcmJpeg16.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmJpeg16.cxx,v $ Language: C++ - Date: $Date: 2004/11/09 21:55:56 $ - Version: $Revision: 1.6 $ + Date: $Date: 2004/12/12 17:21:07 $ + Version: $Revision: 1.7 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -25,8 +25,9 @@ extern "C" { #include "gdcmjpeg/16/jerror.h" } -#define gdcm_write_JPEG_file gdcm_write_JPEG_file16 -#define gdcm_read_JPEG_file gdcm_read_JPEG_file16 +#define gdcm_write_JPEG_file gdcm_write_JPEG_file16 +#define gdcm_read_JPEG_file gdcm_read_JPEG_file16 +#define gdcm_read_JPEG_memory gdcm_read_JPEG_memory16 #include "gdcmJpeg.cxx" diff --git a/src/gdcmJpeg8.cxx b/src/gdcmJpeg8.cxx index e96a6d38..4591c675 100644 --- a/src/gdcmJpeg8.cxx +++ b/src/gdcmJpeg8.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmJpeg8.cxx,v $ Language: C++ - Date: $Date: 2004/11/09 21:55:56 $ - Version: $Revision: 1.12 $ + Date: $Date: 2004/12/12 17:21:07 $ + Version: $Revision: 1.13 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -25,8 +25,9 @@ extern "C" { #include "gdcmjpeg/8/jerror.h" } -#define gdcm_write_JPEG_file gdcm_write_JPEG_file8 -#define gdcm_read_JPEG_file gdcm_read_JPEG_file8 +#define gdcm_write_JPEG_file gdcm_write_JPEG_file8 +#define gdcm_read_JPEG_file gdcm_read_JPEG_file8 +#define gdcm_read_JPEG_memory gdcm_read_JPEG_memory8 #include "gdcmJpeg.cxx" diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 79ab4e44..a3f172f8 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -1,1125 +1,1367 @@ -/*========================================================================= - - Program: gdcm - Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ - Language: C++ - Date: $Date: 2004/12/10 13:49:07 $ - Version: $Revision: 1.5 $ - - Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de - l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. - - This software is distributed WITHOUT ANY WARRANTY; without even - the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR - PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ - -////////////////// TEMPORARY NOTE -// look for "fixMem" and convert that to a member of this class -// Removing the prefix fixMem and dealing with allocations should do the trick -// -// grep PixelReadConvert everywhere and clean up ! - -#include "gdcmDebug.h" -#include "gdcmHeader.h" -#include "gdcmPixelReadConvert.h" -#include "gdcmDocEntry.h" -#include "gdcmRLEFramesInfo.h" -#include "gdcmJPEGFragmentsInfo.h" - -#include -#include //for sscanf - -namespace gdcm -{ -#define str2num(str, typeNum) *((typeNum *)(str)) - -// For JPEG 2000, body in file gdcmJpeg2000.cxx -bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer); - -// For JPEG 8 Bits, body in file gdcmJpeg8.cxx -bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer); - -// For JPEG 12 Bits, body in file gdcmJpeg12.cxx -bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer); - -// 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); - - -//----------------------------------------------------------------------------- -// Constructor / Destructor -PixelReadConvert::PixelReadConvert() -{ - RGB = 0; - RGBSize = 0; - Raw = 0; - RawSize = 0; - LutRGBA = 0; - LutRedData = 0; - LutGreenData = 0; - LutBlueData =0; -} - -void PixelReadConvert::Squeeze() -{ - if ( RGB ) - { - delete [] RGB; - } - RGB = 0; - - if ( Raw ) - { - delete [] Raw; - } - Raw = 0; - - if ( LutRGBA ) - { - delete [] LutRGBA; - } - LutRGBA = 0; -} - -PixelReadConvert::~PixelReadConvert() -{ - Squeeze(); -} - -void PixelReadConvert::AllocateRGB() -{ - if ( RGB ) { - delete [] RGB; - } - RGB = new uint8_t[ RGBSize ]; -} - -void PixelReadConvert::AllocateRaw() -{ - if ( Raw ) { - delete [] Raw; - } - Raw = new uint8_t[ RawSize ]; -} - -/** - * \brief Read from file a 12 bits per pixel image and decompress it - * into a 16 bits per pixel image. - */ -void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp ) - throw ( FormatError ) -{ - int nbPixels = XSize * YSize; - uint16_t* localDecompres = (uint16_t*)Raw; - - for( int p = 0; p < nbPixels; p += 2 ) - { - uint8_t b0, b1, b2; - - fp->read( (char*)&b0, 1); - if ( fp->fail() || fp->eof() )//Fp->gcount() == 1 - { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound first block" ); - } - - fp->read( (char*)&b1, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound second block" ); - } - - fp->read( (char*)&b2, 1 ); - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", - "Unfound second block" ); - } - - // Two steps are necessary to please VC++ - // - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - // A B D - *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // F C E - *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - - /// \todo JPR Troubles expected on Big-Endian processors ? - } -} - -/** - * \brief Try to deal with RLE 16 Bits. - * We assume the RLE has allready been parsed and loaded in - * Raw (through \ref ReadAndDecompressJPEGFile ). - * We here need to make 16 Bits Pixels from Low Byte and - * High Byte 'Planes'...(for what it may mean) - * @return Boolean - */ -bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) -{ - size_t PixelNumber = XSize * YSize; - size_t RawSize = XSize * YSize * NumberOfFrames; - - // We assumed Raw contains the decoded RLE pixels but as - // 8 bits per pixel. In order to convert those pixels to 16 bits - // per pixel we cannot work in place within Raw and hence - // we copy it in a safe place, say copyRaw. - - uint8_t* copyRaw = new uint8_t[ RawSize * 2 ]; - memmove( copyRaw, Raw, RawSize * 2 ); - - uint8_t* x = Raw; - uint8_t* a = copyRaw; - uint8_t* b = a + PixelNumber; - - for ( int i = 0; i < NumberOfFrames; i++ ) - { - for ( unsigned int j = 0; j < PixelNumber; j++ ) - { - *(x++) = *(b++); - *(x++) = *(a++); - } - } - - delete[] copyRaw; - - /// \todo check that operator new []didn't fail, and sometimes return false - return true; -} - -/** - * \brief Implementation of the RLE decoding algorithm for decompressing - * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86] - * @param subRaw Sub region of \ref Raw where the de - * decoded fragment should be placed. - * @param fragmentSize The length of the binary fragment as found on the disk. - * @param RawSegmentSize The expected length of the fragment ONCE - * Raw. - * @param fp File Pointer: on entry the position should be the one of - * the fragment to be decoded. - */ -bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subRaw, - long fragmentSize, - long RawSegmentSize, - std::ifstream* fp ) -{ - int8_t count; - long numberOfOutputBytes = 0; - long numberOfReadBytes = 0; - - while( numberOfOutputBytes < RawSegmentSize ) - { - fp->read( (char*)&count, 1 ); - numberOfReadBytes += 1; - if ( count >= 0 ) - // Note: count <= 127 comparison is always true due to limited range - // of data type int8_t [since the maximum of an exact width - // signed integer of width N is 2^(N-1) - 1, which for int8_t - // is 127]. - { - fp->read( (char*)subRaw, count + 1); - numberOfReadBytes += count + 1; - subRaw += count + 1; - numberOfOutputBytes += count + 1; - } - else - { - if ( ( count <= -1 ) && ( count >= -127 ) ) - { - int8_t newByte; - fp->read( (char*)&newByte, 1); - numberOfReadBytes += 1; - for( int i = 0; i < -count + 1; i++ ) - { - subRaw[i] = newByte; - } - subRaw += -count + 1; - numberOfOutputBytes += -count + 1; - } - } - // if count = 128 output nothing - - if ( numberOfReadBytes > fragmentSize ) - { - dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we " - "read more bytes than the segment size."); - return false; - } - } - return true; -} - -/** - * \brief Reads from disk the Pixel Data of 'Run Length Encoded' - * Dicom encapsulated file and decompress it. - * @param fp already open File Pointer - * at which the pixel data should be copied - * @return Boolean - */ -bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp ) -{ - uint8_t* subRaw = Raw; - long RawSegmentSize = XSize * YSize; - - // Loop on the frame[s] - for( RLEFramesInfo::RLEFrameList::iterator - it = RLEInfo->Frames.begin(); - it != RLEInfo->Frames.end(); - ++it ) - { - // Loop on the fragments - for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ ) - { - fp->seekg( (*it)->Offset[k] , std::ios::beg ); - (void)ReadAndDecompressRLEFragment( subRaw, - (*it)->Length[k], - RawSegmentSize, - fp ); - subRaw += RawSegmentSize; - } - } - - if ( BitsAllocated == 16 ) - { - // Try to deal with RLE 16 Bits - (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); - } - - return true; -} - -/** - * \brief Swap the bytes, according to \ref SwapCode. - */ -void PixelReadConvert::ConvertSwapZone() -{ - unsigned int i; - - if( BitsAllocated == 16 ) - { - uint16_t* im16 = (uint16_t*)Raw; - switch( SwapCode ) - { - case 0: - case 12: - case 1234: - break; - case 21: - case 3412: - case 2143: - case 4321: - for( i = 0; i < RawSize / 2; i++ ) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - break; - default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(16 bits) not allowed." ); - } - } - else if( BitsAllocated == 32 ) - { - uint32_t s32; - uint16_t high; - uint16_t low; - uint32_t* im32 = (uint32_t*)Raw; - switch ( SwapCode ) - { - case 0: - case 1234: - break; - case 4321: - for( i = 0; i < RawSize / 4; i++ ) - { - low = im32[i] & 0x0000ffff; // 4321 - high = im32[i] >> 16; - high = ( high >> 8 ) | ( high << 8 ); - low = ( low >> 8 ) | ( low << 8 ); - s32 = low; - im32[i] = ( s32 << 16 ) | high; - } - break; - case 2143: - for( i = 0; i < RawSize / 4; i++ ) - { - low = im32[i] & 0x0000ffff; // 2143 - high = im32[i] >> 16; - high = ( high >> 8 ) | ( high << 8 ); - low = ( low >> 8 ) | ( low << 8 ); - s32 = high; - im32[i] = ( s32 << 16 ) | low; - } - break; - case 3412: - for( i = 0; i < RawSize / 4; i++ ) - { - low = im32[i] & 0x0000ffff; // 3412 - high = im32[i] >> 16; - s32 = low; - im32[i] = ( s32 << 16 ) | high; - } - break; - default: - dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " - "(32 bits) not allowed." ); - } - } -} - -/** - * \brief Deal with endianity i.e. re-arange bytes inside the integer - */ -void PixelReadConvert::ConvertReorderEndianity() -{ - if ( BitsAllocated != 8 ) - { - ConvertSwapZone(); - } - - // Special kludge in order to deal with xmedcon broken images: - if ( ( BitsAllocated == 16 ) - && ( BitsStored < BitsAllocated ) - && ( ! PixelSign ) ) - { - int l = (int)( RawSize / ( BitsAllocated / 8 ) ); - uint16_t *deb = (uint16_t *)Raw; - for(int i = 0; iFragments.begin(); - it != JPEGInfo->Fragments.end(); - ++it ) - { - fp->seekg( (*it)->Offset, std::ios::beg); - - if ( IsJPEG2000 ) - { - if ( ! gdcm_read_JPEG2000_file( fp,localRaw ) ) - { - return false; - } - } - else 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 Re-arrange the bits within the bytes. - * @return Boolean - */ -bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) -{ - if ( BitsStored != BitsAllocated ) - { - int l = (int)( RawSize / ( BitsAllocated / 8 ) ); - if ( BitsAllocated == 16 ) - { - uint16_t mask = 0xffff; - mask = mask >> ( BitsAllocated - BitsStored ); - uint16_t* deb = (uint16_t*)Raw; - for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; - deb++; - } - } - else if ( BitsAllocated == 32 ) - { - uint32_t mask = 0xffffffff; - mask = mask >> ( BitsAllocated - BitsStored ); - uint32_t* deb = (uint32_t*)Raw; - for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; - deb++; - } - } - else - { - dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image"); - throw FormatError( "PixelReadConvert::ConvertReArrangeBits()", - "weird image !?" ); - } - } - return true; -} - -/** - * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels - * \warning Works on all the frames at a time - */ -void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() -{ - uint8_t* localRaw = Raw; - uint8_t* copyRaw = new uint8_t[ RawSize ]; - memmove( copyRaw, localRaw, RawSize ); - - // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : - // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf - // and be *very* affraid - // - int l = XSize * YSize; - int nbFrames = ZSize; - - uint8_t* a = copyRaw; - uint8_t* b = copyRaw + l; - uint8_t* c = copyRaw + l + l; - double R, G, B; - - /// \todo : Replace by the 'well known' integer computation - /// counterpart. Refer to - /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - /// for code optimisation. - - for ( int i = 0; i < nbFrames; i++ ) - { - for ( int j = 0; j < l; j++ ) - { - R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; - G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; - B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; - - if (R < 0.0) R = 0.0; - if (G < 0.0) G = 0.0; - if (B < 0.0) B = 0.0; - if (R > 255.0) R = 255.0; - if (G > 255.0) G = 255.0; - if (B > 255.0) B = 255.0; - - *(localRaw++) = (uint8_t)R; - *(localRaw++) = (uint8_t)G; - *(localRaw++) = (uint8_t)B; - a++; - b++; - c++; - } - } - delete[] copyRaw; -} - -/** - * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels - * \warning Works on all the frames at a time - */ -void PixelReadConvert::ConvertRGBPlanesToRGBPixels() -{ - uint8_t* localRaw = Raw; - uint8_t* copyRaw = new uint8_t[ RawSize ]; - memmove( copyRaw, localRaw, RawSize ); - - int l = XSize * YSize * ZSize; - - uint8_t* a = copyRaw; - uint8_t* b = copyRaw + l; - uint8_t* c = copyRaw + l + l; - - for (int j = 0; j < l; j++) - { - *(localRaw++) = *(a++); - *(localRaw++) = *(b++); - *(localRaw++) = *(c++); - } - delete[] copyRaw; -} - -bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) -{ - // ComputeRawAndRGBSizes is already made by - // ::GrabInformationsFromHeader. So, the structure sizes are - // correct - Squeeze(); - - ////////////////////////////////////////////////// - //// First stage: get our hands on the Pixel Data. - if ( !fp ) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "unavailable file pointer." ); - return false; - } - - fp->seekg( PixelOffset, std::ios::beg ); - if( fp->fail() || fp->eof()) //Fp->gcount() == 1 - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "unable to find PixelOffset in file." ); - return false; - } - - AllocateRaw(); - - ////////////////////////////////////////////////// - //// Second stage: read from disk dans decompress. - if ( BitsAllocated == 12 ) - { - ReadAndDecompress12BitsTo16Bits( fp); - } - else if ( IsRaw ) - { - // This problem can be found when some obvious informations are found - // after the field containing the image datas. In this case, these - // bad datas are added to the size of the image (in the PixelDataLength - // variable). But RawSize is the right size of the image ! - if( PixelDataLength != RawSize) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "Mismatch between PixelReadConvert and RawSize." ); - } - if( PixelDataLength > RawSize) - { - fp->read( (char*)Raw, RawSize); - } - else - { - fp->read( (char*)Raw, PixelDataLength); - } - - if ( fp->fail() || fp->eof())//Fp->gcount() == 1 - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "reading of Raw pixel data failed." ); - return false; - } - } - else if ( IsRLELossless ) - { - if ( ! ReadAndDecompressRLEFile( fp ) ) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "RLE decompressor failed." ); - return false; - } - } - else - { - // Default case concerns JPEG family - if ( ! ReadAndDecompressJPEGFile( fp ) ) - { - dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " - "JPEG decompressor failed." ); - return false; - } - } - - //////////////////////////////////////////// - //// Third stage: twigle the bytes and bits. - ConvertReorderEndianity(); - ConvertReArrangeBits(); - ConvertHandleColor(); - - return true; -} - -void PixelReadConvert::ConvertHandleColor() -{ - ////////////////////////////////// - // Deal with the color decoding i.e. handle: - // - R, G, B planes (as opposed to RGB pixels) - // - YBR (various) encodings. - // - LUT[s] (or "PALETTE COLOR"). - // - // The classification in the color decoding schema is based on the blending - // of two Dicom tags values: - // * "Photometric Interpretation" for which we have the cases: - // - [Photo A] MONOCHROME[1|2] pictures, - // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB), - // - [Photo C] YBR_* (with the above exception of YBR_FULL_422) - // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s]. - // * "Planar Configuration" for which we have the cases: - // - [Planar 0] 0 then Pixels are already RGB - // - [Planar 1] 1 then we have 3 planes : R, G, B, - // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs - // - // Now in theory, one could expect some coherence when blending the above - // cases. For example we should not encounter files belonging at the - // time to case [Planar 0] and case [Photo D]. - // Alas, this was only theory ! Because in practice some odd (read ill - // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter: - // - "Planar Configuration" = 0, - // - "Photometric Interpretation" = "PALETTE COLOR". - // Hence gdcm shall use the folowing "heuristic" in order to be tolerant - // towards Dicom-non-conformance files: - // << whatever the "Planar Configuration" value might be, a - // "Photometric Interpretation" set to "PALETTE COLOR" forces - // a LUT intervention >> - // - // Now we are left with the following handling of the cases: - // - [Planar 0] OR [Photo A] no color decoding (since respectively - // Pixels are already RGB and monochrome pictures have no color :), - // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels() - // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels() - // - [Planar 2] OR [Photo D] requires LUT intervention. - - if ( ! IsRawRGB() ) - { - // [Planar 2] OR [Photo D]: LUT intervention done outside - return; - } - - if ( PlanarConfiguration == 1 ) - { - if ( IsYBRFull ) - { - // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB) - ConvertYcBcRPlanesToRGBPixels(); - } - else - { - // [Planar 1] AND [Photo C] - ConvertRGBPlanesToRGBPixels(); - } - return; - } - - // When planarConf is 0, and RLELossless (forbidden by Dicom norm) - // pixels need to be RGB-fied anyway - if (IsRLELossless) - { - ConvertRGBPlanesToRGBPixels(); - } - // In *normal *case, when planarConf is 0, pixels are already in RGB -} - -/** - * \brief Predicate to know wether the image[s] (once Raw) is RGB. - * \note See comments of \ref ConvertHandleColor - */ -bool PixelReadConvert::IsRawRGB() -{ - if ( IsMonochrome - || PlanarConfiguration == 2 - || IsPaletteColor ) - { - return false; - } - return true; -} - -void PixelReadConvert::ComputeRawAndRGBSizes() -{ - int bitsAllocated = BitsAllocated; - // Number of "Bits Allocated" is fixed to 16 when it's 12, since - // in this case we will expand the image to 16 bits (see - // \ref ReadAndDecompress12BitsTo16Bits() ) - if ( BitsAllocated == 12 ) - { - bitsAllocated = 16; - } - - RawSize = XSize * YSize * ZSize - * ( bitsAllocated / 8 ) - * SamplesPerPixel; - if ( HasLUT ) - { - RGBSize = 3 * RawSize; - } - else - { - RGBSize = RawSize; - } -} - -void PixelReadConvert::GrabInformationsFromHeader( Header* header ) -{ - // Number of Bits Allocated for storing a Pixel is defaulted to 16 - // when absent from the header. - BitsAllocated = header->GetBitsAllocated(); - if ( BitsAllocated == 0 ) - { - BitsAllocated = 16; - } - - // Number of "Bits Stored" defaulted to number of "Bits Allocated" - // when absent from the header. - BitsStored = header->GetBitsStored(); - if ( BitsStored == 0 ) - { - BitsStored = BitsAllocated; - } - - // High Bit Position - HighBitPosition = header->GetHighBitPosition(); - if ( HighBitPosition == 0 ) - { - HighBitPosition = BitsAllocated - 1; - } - - XSize = header->GetXSize(); - YSize = header->GetYSize(); - ZSize = header->GetZSize(); - SamplesPerPixel = header->GetSamplesPerPixel(); - PixelSize = header->GetPixelSize(); - PixelSign = header->IsSignedPixelData(); - SwapCode = header->GetSwapCode(); - TransferSyntaxType ts = header->GetTransferSyntax(); - IsRaw = - ( ! header->IsDicomV3() ) - || ts == ImplicitVRLittleEndian - || ts == ImplicitVRLittleEndianDLXGE - || ts == ExplicitVRLittleEndian - || ts == ExplicitVRBigEndian - || ts == DeflatedExplicitVRLittleEndian; - IsJPEG2000 = header->IsJPEG2000(); - IsJPEGLossless = header->IsJPEGLossless(); - IsRLELossless = ( ts == RLELossless ); - PixelOffset = header->GetPixelOffset(); - PixelDataLength = header->GetPixelAreaLength(); - RLEInfo = header->GetRLEInfo(); - JPEGInfo = header->GetJPEGInfo(); - - PlanarConfiguration = header->GetPlanarConfiguration(); - IsMonochrome = header->IsMonochrome(); - IsPaletteColor = header->IsPaletteColor(); - IsYBRFull = header->IsYBRFull(); - - ///////////////////////////////////////////////////////////////// - // LUT section: - HasLUT = header->HasLUT(); - if ( HasLUT ) - { - // Just in case some access to a Header element requires disk access. - // Note: gdcmDocument::Fp is leaved open after OpenFile. - LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 ); - LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 ); - LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 ); - - // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE - // [ refer to invocation of Document::SetMaxSizeLoadEntry() in - // Document::Document() ], the loading of the value (content) of a - // [Bin|Val]Entry occurence migth have been hindered (read simply NOT - // loaded). Hence, we first try to obtain the LUTs data from the header - // and when this fails we read the LUTs data directely from disk. - /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge. - /// We should NOT bypass the [Bin|Val]Entry class. Instead - /// an access to an UNLOADED content of a [Bin|Val]Entry occurence - /// (e.g. BinEntry::GetBinArea()) should force disk access from - /// within the [Bin|Val]Entry class itself. The only problem - /// is that the [Bin|Val]Entry is unaware of the FILE* is was - /// parsed from. Fix that. FIXME. - - ////// Red round - header->LoadEntryBinArea(0x0028, 0x1201); - LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 ); - if ( ! LutRedData ) - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read red LUT data" ); - } - - ////// Green round: - header->LoadEntryBinArea(0x0028, 0x1202); - LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 ); - if ( ! LutGreenData) - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read green LUT data" ); - } - - ////// Blue round: - header->LoadEntryBinArea(0x0028, 0x1203); - LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 ); - if ( ! LutBlueData ) - { - dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " - "unable to read blue LUT data" ); - } - } - - ComputeRawAndRGBSizes(); -} - -/** - * \brief Build Red/Green/Blue/Alpha LUT from Header - * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] - * and (0028,1101),(0028,1102),(0028,1102) - * - xxx Palette Color Lookup Table Descriptor - are found - * and (0028,1201),(0028,1202),(0028,1202) - * - xxx Palette Color Lookup Table Data - are found - * \warning does NOT deal with : - * 0028 1100 Gray Lookup Table Descriptor (Retired) - * 0028 1221 Segmented Red Palette Color Lookup Table Data - * 0028 1222 Segmented Green Palette Color Lookup Table Data - * 0028 1223 Segmented Blue Palette Color Lookup Table Data - * no known Dicom reader deals with them :-( - * @return a RGBA Lookup Table - */ -void PixelReadConvert::BuildLUTRGBA() -{ - if ( LutRGBA ) - { - return; - } - // Not so easy : see - // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables - - if ( ! IsPaletteColor ) - { - return; - } - - if ( LutRedDescriptor == GDCM_UNFOUND - || LutGreenDescriptor == GDCM_UNFOUND - || LutBlueDescriptor == GDCM_UNFOUND ) - { - return; - } - - //////////////////////////////////////////// - // Extract the info from the LUT descriptors - int lengthR; // Red LUT length in Bytes - int debR; // Subscript of the first Lut Value - int nbitsR; // Lut item size (in Bits) - int nbRead = sscanf( LutRedDescriptor.c_str(), - "%d\\%d\\%d", - &lengthR, &debR, &nbitsR ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor"); - } - - int lengthG; // Green LUT length in Bytes - int debG; // Subscript of the first Lut Value - int nbitsG; // Lut item size (in Bits) - nbRead = sscanf( LutGreenDescriptor.c_str(), - "%d\\%d\\%d", - &lengthG, &debG, &nbitsG ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor"); - } - - int lengthB; // Blue LUT length in Bytes - int debB; // Subscript of the first Lut Value - int nbitsB; // Lut item size (in Bits) - nbRead = sscanf( LutRedDescriptor.c_str(), - "%d\\%d\\%d", - &lengthB, &debB, &nbitsB ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor"); - } - - //////////////////////////////////////////////////////// - if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) ) - { - return; - } - - //////////////////////////////////////////////// - // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT - LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha) - if ( !LutRGBA ) - { - return; - } - memset( LutRGBA, 0, 1024 ); - - int mult; - if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) ) - { - // when LUT item size is different than pixel size - mult = 2; // high byte must be = low byte - } - else - { - // See PS 3.3-2003 C.11.1.1.2 p 619 - mult = 1; - } - - // if we get a black image, let's just remove the '+1' - // from 'i*mult+1' and check again - // if it works, we shall have to check the 3 Palettes - // to see which byte is ==0 (first one, or second one) - // and fix the code - // We give up the checking to avoid some (useless ?)overhead - // (optimistic asumption) - int i; - uint8_t* a = LutRGBA + 0; - for( i=0; i < lengthR; ++i ) - { - *a = LutRedData[i*mult+1]; - a += 4; - } - - a = LutRGBA + 1; - for( i=0; i < lengthG; ++i) - { - *a = LutGreenData[i*mult+1]; - a += 4; - } - - a = LutRGBA + 2; - for(i=0; i < lengthB; ++i) - { - *a = LutBlueData[i*mult+1]; - a += 4; - } - - a = LutRGBA + 3; - for(i=0; i < 256; ++i) - { - *a = 1; // Alpha component - a += 4; - } -} - -/** - * \brief Build the RGB image from the Raw imagage and the LUTs. - */ -bool PixelReadConvert::BuildRGBImage() -{ - if ( RGB ) - { - // The job is already done. - return true; - } - - if ( ! Raw ) - { - // The job can't be done - return false; - } - - BuildLUTRGBA(); - if ( ! LutRGBA ) - { - // The job can't be done - return false; - } - - // Build RGB Pixels - AllocateRGB(); - uint8_t* localRGB = RGB; - for (size_t i = 0; i < RawSize; ++i ) - { - int j = Raw[i] * 4; - *localRGB++ = LutRGBA[j]; - *localRGB++ = LutRGBA[j+1]; - *localRGB++ = LutRGBA[j+2]; - } - return true; -} - -/** - * \brief Print self. - * @param indent Indentation string to be prepended during printing. - * @param os Stream to print to. - */ -void PixelReadConvert::Print( std::string indent, std::ostream &os ) -{ - os << indent - << "--- Pixel information -------------------------" - << std::endl; - os << indent - << "Pixel Data: offset " << PixelOffset - << " x" << std::hex << PixelOffset << std::dec - << " length " << PixelDataLength - << " x" << std::hex << PixelDataLength << std::dec - << std::endl; - - if ( IsRLELossless ) - { - if ( RLEInfo ) - { - RLEInfo->Print( indent, os ); - } - else - { - dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file " - "but NO RLEinfo present."); - } - } - - if ( IsJPEG2000 || IsJPEGLossless ) - { - if ( JPEGInfo ) - { - JPEGInfo->Print( indent, os ); - } - else - { - dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file " - "but NO JPEGinfo present."); - } - } -} - -} // end namespace gdcm - -// NOTES on File internal calls -// User -// ---> GetImageData -// ---> GetImageDataIntoVector -// |---> GetImageDataIntoVectorRaw -// | lut intervention -// User -// ---> GetImageDataRaw -// ---> GetImageDataIntoVectorRaw +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ + Language: C++ + Date: $Date: 2004/12/12 17:21:07 $ + Version: $Revision: 1.6 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +////////////////// TEMPORARY NOTE +// look for "fixMem" and convert that to a member of this class +// Removing the prefix fixMem and dealing with allocations should do the trick +// +// grep PixelReadConvert everywhere and clean up ! + +#include "gdcmDebug.h" +#include "gdcmHeader.h" +#include "gdcmPixelReadConvert.h" +#include "gdcmDocEntry.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" + +#include +#include //for sscanf + +namespace gdcm +{ +#define str2num(str, typeNum) *((typeNum *)(str)) + +// For JPEG 2000, body in file gdcmJpeg2000.cxx +bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer); + +#define JOCTET uint8_t +// For JPEG 8 Bits, body in file gdcmJpeg8.cxx +bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer); +bool gdcm_read_JPEG_memory8 (const JOCTET* buffer, const size_t buflen, + void* image_buffer, + size_t *howManyRead, size_t *howManyWritten); +// +// For JPEG 12 Bits, body in file gdcmJpeg12.cxx +bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer); +bool gdcm_read_JPEG_memory12 (const JOCTET *buffer, const size_t buflen, + void* image_buffer, + size_t *howManyRead, size_t *howManyWritten); + +// For JPEG 16 Bits, body in file gdcmJpeg16.cxx +// Beware this is misleading there is no 16bits DCT algorithm, only +// jpeg lossless compression exist in 16bits. +bool gdcm_read_JPEG_file16 (std::ifstream* fp, void* image_buffer); +bool gdcm_read_JPEG_memory16 (const JOCTET *buffer, const size_t buflen, + void* image_buffer, + size_t *howManyRead, size_t *howManyWritten); + + +//----------------------------------------------------------------------------- +// Constructor / Destructor +PixelReadConvert::PixelReadConvert() +{ + RGB = 0; + RGBSize = 0; + Raw = 0; + RawSize = 0; + LutRGBA = 0; + LutRedData = 0; + LutGreenData = 0; + LutBlueData =0; +} + +void PixelReadConvert::Squeeze() +{ + if ( RGB ) + { + delete [] RGB; + } + RGB = 0; + + if ( Raw ) + { + delete [] Raw; + } + Raw = 0; + + if ( LutRGBA ) + { + delete [] LutRGBA; + } + LutRGBA = 0; +} + +PixelReadConvert::~PixelReadConvert() +{ + Squeeze(); +} + +void PixelReadConvert::AllocateRGB() +{ + if ( RGB ) { + delete [] RGB; + } + RGB = new uint8_t[ RGBSize ]; +} + +void PixelReadConvert::AllocateRaw() +{ + if ( Raw ) { + delete [] Raw; + } + Raw = new uint8_t[ RawSize ]; +} + +/** + * \brief Read from file a 12 bits per pixel image and decompress it + * into a 16 bits per pixel image. + */ +void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp ) + throw ( FormatError ) +{ + int nbPixels = XSize * YSize; + uint16_t* localDecompres = (uint16_t*)Raw; + + for( int p = 0; p < nbPixels; p += 2 ) + { + uint8_t b0, b1, b2; + + fp->read( (char*)&b0, 1); + if ( fp->fail() || fp->eof() )//Fp->gcount() == 1 + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound first block" ); + } + + fp->read( (char*)&b1, 1 ); + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); + } + + fp->read( (char*)&b2, 1 ); + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + { + throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()", + "Unfound second block" ); + } + + // Two steps are necessary to please VC++ + // + // 2 pixels 12bit = [0xABCDEF] + // 2 pixels 16bit = [0x0ABD] + [0x0FCE] + // A B D + *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); + // F C E + *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); + + /// \todo JPR Troubles expected on Big-Endian processors ? + } +} + +/** + * \brief Try to deal with RLE 16 Bits. + * We assume the RLE has allready been parsed and loaded in + * Raw (through \ref ReadAndDecompressJPEGFile ). + * We here need to make 16 Bits Pixels from Low Byte and + * High Byte 'Planes'...(for what it may mean) + * @return Boolean + */ +bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) +{ + size_t PixelNumber = XSize * YSize; + size_t RawSize = XSize * YSize * NumberOfFrames; + + // We assumed Raw contains the decoded RLE pixels but as + // 8 bits per pixel. In order to convert those pixels to 16 bits + // per pixel we cannot work in place within Raw and hence + // we copy it in a safe place, say copyRaw. + + uint8_t* copyRaw = new uint8_t[ RawSize * 2 ]; + memmove( copyRaw, Raw, RawSize * 2 ); + + uint8_t* x = Raw; + uint8_t* a = copyRaw; + uint8_t* b = a + PixelNumber; + + for ( int i = 0; i < NumberOfFrames; i++ ) + { + for ( unsigned int j = 0; j < PixelNumber; j++ ) + { + *(x++) = *(b++); + *(x++) = *(a++); + } + } + + delete[] copyRaw; + + /// \todo check that operator new []didn't fail, and sometimes return false + return true; +} + +/** + * \brief Implementation of the RLE decoding algorithm for decompressing + * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86] + * @param subRaw Sub region of \ref Raw where the de + * decoded fragment should be placed. + * @param fragmentSize The length of the binary fragment as found on the disk. + * @param RawSegmentSize The expected length of the fragment ONCE + * Raw. + * @param fp File Pointer: on entry the position should be the one of + * the fragment to be decoded. + */ +bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subRaw, + long fragmentSize, + long RawSegmentSize, + std::ifstream* fp ) +{ + int8_t count; + long numberOfOutputBytes = 0; + long numberOfReadBytes = 0; + + while( numberOfOutputBytes < RawSegmentSize ) + { + fp->read( (char*)&count, 1 ); + numberOfReadBytes += 1; + if ( count >= 0 ) + // Note: count <= 127 comparison is always true due to limited range + // of data type int8_t [since the maximum of an exact width + // signed integer of width N is 2^(N-1) - 1, which for int8_t + // is 127]. + { + fp->read( (char*)subRaw, count + 1); + numberOfReadBytes += count + 1; + subRaw += count + 1; + numberOfOutputBytes += count + 1; + } + else + { + if ( ( count <= -1 ) && ( count >= -127 ) ) + { + int8_t newByte; + fp->read( (char*)&newByte, 1); + numberOfReadBytes += 1; + for( int i = 0; i < -count + 1; i++ ) + { + subRaw[i] = newByte; + } + subRaw += -count + 1; + numberOfOutputBytes += -count + 1; + } + } + // if count = 128 output nothing + + if ( numberOfReadBytes > fragmentSize ) + { + dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we " + "read more bytes than the segment size."); + return false; + } + } + return true; +} + +/** + * \brief Reads from disk the Pixel Data of 'Run Length Encoded' + * Dicom encapsulated file and decompress it. + * @param fp already open File Pointer + * at which the pixel data should be copied + * @return Boolean + */ +bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp ) +{ + uint8_t* subRaw = Raw; + long RawSegmentSize = XSize * YSize; + + // Loop on the frame[s] + for( RLEFramesInfo::RLEFrameList::iterator + it = RLEInfo->Frames.begin(); + it != RLEInfo->Frames.end(); + ++it ) + { + // Loop on the fragments + for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ ) + { + fp->seekg( (*it)->Offset[k] , std::ios::beg ); + (void)ReadAndDecompressRLEFragment( subRaw, + (*it)->Length[k], + RawSegmentSize, + fp ); + subRaw += RawSegmentSize; + } + } + + if ( BitsAllocated == 16 ) + { + // Try to deal with RLE 16 Bits + (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); + } + + return true; +} + +/** + * \brief Swap the bytes, according to \ref SwapCode. + */ +void PixelReadConvert::ConvertSwapZone() +{ + unsigned int i; + + if( BitsAllocated == 16 ) + { + uint16_t* im16 = (uint16_t*)Raw; + switch( SwapCode ) + { + case 0: + case 12: + case 1234: + break; + case 21: + case 3412: + case 2143: + case 4321: + for( i = 0; i < RawSize / 2; i++ ) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } + break; + default: + dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " + "(16 bits) not allowed." ); + } + } + else if( BitsAllocated == 32 ) + { + uint32_t s32; + uint16_t high; + uint16_t low; + uint32_t* im32 = (uint32_t*)Raw; + switch ( SwapCode ) + { + case 0: + case 1234: + break; + case 4321: + for( i = 0; i < RawSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 4321 + high = im32[i] >> 16; + high = ( high >> 8 ) | ( high << 8 ); + low = ( low >> 8 ) | ( low << 8 ); + s32 = low; + im32[i] = ( s32 << 16 ) | high; + } + break; + case 2143: + for( i = 0; i < RawSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 2143 + high = im32[i] >> 16; + high = ( high >> 8 ) | ( high << 8 ); + low = ( low >> 8 ) | ( low << 8 ); + s32 = high; + im32[i] = ( s32 << 16 ) | low; + } + break; + case 3412: + for( i = 0; i < RawSize / 4; i++ ) + { + low = im32[i] & 0x0000ffff; // 3412 + high = im32[i] >> 16; + s32 = low; + im32[i] = ( s32 << 16 ) | high; + } + break; + default: + dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value " + "(32 bits) not allowed." ); + } + } +} + +/** + * \brief Deal with endianity i.e. re-arange bytes inside the integer + */ +void PixelReadConvert::ConvertReorderEndianity() +{ + if ( BitsAllocated != 8 ) + { + ConvertSwapZone(); + } + + // Special kludge in order to deal with xmedcon broken images: + if ( ( BitsAllocated == 16 ) + && ( BitsStored < BitsAllocated ) + && ( ! PixelSign ) ) + { + int l = (int)( RawSize / ( BitsAllocated / 8 ) ); + uint16_t *deb = (uint16_t *)Raw; + for(int i = 0; iFragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + fp->seekg( (*it)->Offset, std::ios::beg); + + if ( BitsStored == 8) + { + // JPEG Lossy : call to IJG 6b + if ( ! gdcm_read_JPEG_file8( fp, localRaw ) ) + { + return false; + } + } + else if ( BitsStored <= 12) + { + // Reading Fragment pixels + if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) ) + { + return false; + } + } + else if ( BitsStored <= 16) + { + // Reading Fragment pixels + if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) ) + { + return false; + } + //assert( IsJPEGLossless ); + } + else + { + // other JPEG lossy not supported + dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown " + "jpeg lossy compression "); + return false; + } + + // Advance to next free location in Raw + // for next fragment decompression (if any) + int length = XSize * YSize * SamplesPerPixel; + int numberBytes = BitsAllocated / 8; + + localRaw += length * numberBytes; + } + return true; +} + +/** + * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated + * file and decompress it. This function assumes that the dicom + * image is a single frame split into several JPEG fragments. + * Those fragments will be glued together into a memory buffer + * before being read. + * @param fp File Pointer + * @return Boolean + */ +bool PixelReadConvert:: +ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream* fp ) +{ + // Loop on the fragment[s] to get total length + size_t totalLength = 0; + for( JPEGFragmentsInfo::JPEGFragmentsList::iterator + it = JPEGInfo->Fragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + totalLength += (*it)->Length; + } + + // Concatenate the jpeg fragments into a local buffer + JOCTET *buffer = new JOCTET [totalLength]; + JOCTET *p = buffer; + + uint8_t* localRaw = Raw; + // Loop on the fragment[s] + for( JPEGFragmentsInfo::JPEGFragmentsList::iterator + it = JPEGInfo->Fragments.begin(); + it != JPEGInfo->Fragments.end(); + ++it ) + { + fp->seekg( (*it)->Offset, std::ios_base::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_base::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_base::beg); + if ( ! gdcm_read_JPEG2000_file( fp,Raw ) ) + return false; + } + + if ( ( ZSize == 1 ) && ( JPEGInfo->Fragments.size() > 1 ) ) + { + // we have one frame split into several fragments + // we will pack those fragments into a single buffer and + // read from it + return ReadAndDecompressJPEGSingleFrameFragmentsFromFile( fp ); + } + else if (JPEGInfo->Fragments.size() == ZSize) + { + // suppose each fragment is a frame + return ReadAndDecompressJPEGFramesFromFile( fp ); + } + else + { + // The dicom image contains frames containing fragments of images + // a more complex algorithm :-) + return ReadAndDecompressJPEGFragmentedFramesFromFile( fp ); + } +} + +/** + * \brief Re-arrange the bits within the bytes. + * @return Boolean + */ +bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) +{ + if ( BitsStored != BitsAllocated ) + { + int l = (int)( RawSize / ( BitsAllocated / 8 ) ); + if ( BitsAllocated == 16 ) + { + uint16_t mask = 0xffff; + mask = mask >> ( BitsAllocated - BitsStored ); + uint16_t* deb = (uint16_t*)Raw; + for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; + deb++; + } + } + else if ( BitsAllocated == 32 ) + { + uint32_t mask = 0xffffffff; + mask = mask >> ( BitsAllocated - BitsStored ); + uint32_t* deb = (uint32_t*)Raw; + for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & mask; + deb++; + } + } + else + { + dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image"); + throw FormatError( "PixelReadConvert::ConvertReArrangeBits()", + "weird image !?" ); + } + } + return true; +} + +/** + * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels + * \warning Works on all the frames at a time + */ +void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() +{ + uint8_t* localRaw = Raw; + uint8_t* copyRaw = new uint8_t[ RawSize ]; + memmove( copyRaw, localRaw, RawSize ); + + // to see the tricks about YBR_FULL, YBR_FULL_422, + // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : + // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf + // and be *very* affraid + // + int l = XSize * YSize; + int nbFrames = ZSize; + + uint8_t* a = copyRaw; + uint8_t* b = copyRaw + l; + uint8_t* c = copyRaw + l + l; + double R, G, B; + + /// \todo : Replace by the 'well known' integer computation + /// counterpart. Refer to + /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf + /// for code optimisation. + + for ( int i = 0; i < nbFrames; i++ ) + { + for ( int j = 0; j < l; j++ ) + { + R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; + G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; + B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; + + if (R < 0.0) R = 0.0; + if (G < 0.0) G = 0.0; + if (B < 0.0) B = 0.0; + if (R > 255.0) R = 255.0; + if (G > 255.0) G = 255.0; + if (B > 255.0) B = 255.0; + + *(localRaw++) = (uint8_t)R; + *(localRaw++) = (uint8_t)G; + *(localRaw++) = (uint8_t)B; + a++; + b++; + c++; + } + } + delete[] copyRaw; +} + +/** + * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels + * \warning Works on all the frames at a time + */ +void PixelReadConvert::ConvertRGBPlanesToRGBPixels() +{ + uint8_t* localRaw = Raw; + uint8_t* copyRaw = new uint8_t[ RawSize ]; + memmove( copyRaw, localRaw, RawSize ); + + int l = XSize * YSize * ZSize; + + uint8_t* a = copyRaw; + uint8_t* b = copyRaw + l; + uint8_t* c = copyRaw + l + l; + + for (int j = 0; j < l; j++) + { + *(localRaw++) = *(a++); + *(localRaw++) = *(b++); + *(localRaw++) = *(c++); + } + delete[] copyRaw; +} + +bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp ) +{ + // ComputeRawAndRGBSizes is already made by + // ::GrabInformationsFromHeader. So, the structure sizes are + // correct + Squeeze(); + + ////////////////////////////////////////////////// + //// First stage: get our hands on the Pixel Data. + if ( !fp ) + { + dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " + "unavailable file pointer." ); + return false; + } + + fp->seekg( PixelOffset, std::ios::beg ); + if( fp->fail() || fp->eof()) //Fp->gcount() == 1 + { + dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " + "unable to find PixelOffset in file." ); + return false; + } + + AllocateRaw(); + + ////////////////////////////////////////////////// + //// Second stage: read from disk dans decompress. + if ( BitsAllocated == 12 ) + { + ReadAndDecompress12BitsTo16Bits( fp); + } + else if ( IsRaw ) + { + // This problem can be found when some obvious informations are found + // after the field containing the image datas. In this case, these + // bad datas are added to the size of the image (in the PixelDataLength + // variable). But RawSize is the right size of the image ! + if( PixelDataLength != RawSize) + { + dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " + "Mismatch between PixelReadConvert and RawSize." ); + } + if( PixelDataLength > RawSize) + { + fp->read( (char*)Raw, RawSize); + } + else + { + fp->read( (char*)Raw, PixelDataLength); + } + + if ( fp->fail() || fp->eof())//Fp->gcount() == 1 + { + dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " + "reading of Raw pixel data failed." ); + return false; + } + } + else if ( IsRLELossless ) + { + if ( ! ReadAndDecompressRLEFile( fp ) ) + { + dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " + "RLE decompressor failed." ); + return false; + } + } + else + { + // Default case concerns JPEG family + if ( ! ReadAndDecompressJPEGFile( fp ) ) + { + dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: " + "JPEG decompressor failed." ); + return false; + } + } + + //////////////////////////////////////////// + //// Third stage: twigle the bytes and bits. + ConvertReorderEndianity(); + ConvertReArrangeBits(); + ConvertHandleColor(); + + return true; +} + +void PixelReadConvert::ConvertHandleColor() +{ + ////////////////////////////////// + // Deal with the color decoding i.e. handle: + // - R, G, B planes (as opposed to RGB pixels) + // - YBR (various) encodings. + // - LUT[s] (or "PALETTE COLOR"). + // + // The classification in the color decoding schema is based on the blending + // of two Dicom tags values: + // * "Photometric Interpretation" for which we have the cases: + // - [Photo A] MONOCHROME[1|2] pictures, + // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB), + // - [Photo C] YBR_* (with the above exception of YBR_FULL_422) + // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s]. + // * "Planar Configuration" for which we have the cases: + // - [Planar 0] 0 then Pixels are already RGB + // - [Planar 1] 1 then we have 3 planes : R, G, B, + // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs + // + // Now in theory, one could expect some coherence when blending the above + // cases. For example we should not encounter files belonging at the + // time to case [Planar 0] and case [Photo D]. + // Alas, this was only theory ! Because in practice some odd (read ill + // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter: + // - "Planar Configuration" = 0, + // - "Photometric Interpretation" = "PALETTE COLOR". + // Hence gdcm shall use the folowing "heuristic" in order to be tolerant + // towards Dicom-non-conformance files: + // << whatever the "Planar Configuration" value might be, a + // "Photometric Interpretation" set to "PALETTE COLOR" forces + // a LUT intervention >> + // + // Now we are left with the following handling of the cases: + // - [Planar 0] OR [Photo A] no color decoding (since respectively + // Pixels are already RGB and monochrome pictures have no color :), + // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels() + // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels() + // - [Planar 2] OR [Photo D] requires LUT intervention. + + if ( ! IsRawRGB() ) + { + // [Planar 2] OR [Photo D]: LUT intervention done outside + return; + } + + if ( PlanarConfiguration == 1 ) + { + if ( IsYBRFull ) + { + // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB) + ConvertYcBcRPlanesToRGBPixels(); + } + else + { + // [Planar 1] AND [Photo C] + ConvertRGBPlanesToRGBPixels(); + } + return; + } + + // When planarConf is 0, and RLELossless (forbidden by Dicom norm) + // pixels need to be RGB-fied anyway + if (IsRLELossless) + { + ConvertRGBPlanesToRGBPixels(); + } + // In *normal *case, when planarConf is 0, pixels are already in RGB +} + +/** + * \brief Predicate to know wether the image[s] (once Raw) is RGB. + * \note See comments of \ref ConvertHandleColor + */ +bool PixelReadConvert::IsRawRGB() +{ + if ( IsMonochrome + || PlanarConfiguration == 2 + || IsPaletteColor ) + { + return false; + } + return true; +} + +void PixelReadConvert::ComputeRawAndRGBSizes() +{ + int bitsAllocated = BitsAllocated; + // Number of "Bits Allocated" is fixed to 16 when it's 12, since + // in this case we will expand the image to 16 bits (see + // \ref ReadAndDecompress12BitsTo16Bits() ) + if ( BitsAllocated == 12 ) + { + bitsAllocated = 16; + } + + RawSize = XSize * YSize * ZSize + * ( bitsAllocated / 8 ) + * SamplesPerPixel; + if ( HasLUT ) + { + RGBSize = 3 * RawSize; + } + else + { + RGBSize = RawSize; + } +} + +void PixelReadConvert::GrabInformationsFromHeader( Header* header ) +{ + // Number of Bits Allocated for storing a Pixel is defaulted to 16 + // when absent from the header. + BitsAllocated = header->GetBitsAllocated(); + if ( BitsAllocated == 0 ) + { + BitsAllocated = 16; + } + + // Number of "Bits Stored" defaulted to number of "Bits Allocated" + // when absent from the header. + BitsStored = header->GetBitsStored(); + if ( BitsStored == 0 ) + { + BitsStored = BitsAllocated; + } + + // High Bit Position + HighBitPosition = header->GetHighBitPosition(); + if ( HighBitPosition == 0 ) + { + HighBitPosition = BitsAllocated - 1; + } + + XSize = header->GetXSize(); + YSize = header->GetYSize(); + ZSize = header->GetZSize(); + SamplesPerPixel = header->GetSamplesPerPixel(); + PixelSize = header->GetPixelSize(); + PixelSign = header->IsSignedPixelData(); + SwapCode = header->GetSwapCode(); + TransferSyntaxType ts = header->GetTransferSyntax(); + IsRaw = + ( ! header->IsDicomV3() ) + || ts == ImplicitVRLittleEndian + || ts == ImplicitVRLittleEndianDLXGE + || ts == ExplicitVRLittleEndian + || ts == ExplicitVRBigEndian + || ts == DeflatedExplicitVRLittleEndian; + IsJPEG2000 = header->IsJPEG2000(); + IsJPEGLossless = header->IsJPEGLossless(); + IsRLELossless = ( ts == RLELossless ); + PixelOffset = header->GetPixelOffset(); + PixelDataLength = header->GetPixelAreaLength(); + RLEInfo = header->GetRLEInfo(); + JPEGInfo = header->GetJPEGInfo(); + + PlanarConfiguration = header->GetPlanarConfiguration(); + IsMonochrome = header->IsMonochrome(); + IsPaletteColor = header->IsPaletteColor(); + IsYBRFull = header->IsYBRFull(); + + ///////////////////////////////////////////////////////////////// + // LUT section: + HasLUT = header->HasLUT(); + if ( HasLUT ) + { + // Just in case some access to a Header element requires disk access. + // Note: gdcmDocument::Fp is leaved open after OpenFile. + LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 ); + LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 ); + LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 ); + + // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE + // [ refer to invocation of Document::SetMaxSizeLoadEntry() in + // Document::Document() ], the loading of the value (content) of a + // [Bin|Val]Entry occurence migth have been hindered (read simply NOT + // loaded). Hence, we first try to obtain the LUTs data from the header + // and when this fails we read the LUTs data directely from disk. + /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge. + /// We should NOT bypass the [Bin|Val]Entry class. Instead + /// an access to an UNLOADED content of a [Bin|Val]Entry occurence + /// (e.g. BinEntry::GetBinArea()) should force disk access from + /// within the [Bin|Val]Entry class itself. The only problem + /// is that the [Bin|Val]Entry is unaware of the FILE* is was + /// parsed from. Fix that. FIXME. + + ////// Red round + header->LoadEntryBinArea(0x0028, 0x1201); + LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 ); + if ( ! LutRedData ) + { + dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " + "unable to read red LUT data" ); + } + + ////// Green round: + header->LoadEntryBinArea(0x0028, 0x1202); + LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 ); + if ( ! LutGreenData) + { + dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " + "unable to read green LUT data" ); + } + + ////// Blue round: + header->LoadEntryBinArea(0x0028, 0x1203); + LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 ); + if ( ! LutBlueData ) + { + dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: " + "unable to read blue LUT data" ); + } + } + + ComputeRawAndRGBSizes(); +} + +/** + * \brief Build Red/Green/Blue/Alpha LUT from Header + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * and (0028,1101),(0028,1102),(0028,1102) + * - xxx Palette Color Lookup Table Descriptor - are found + * and (0028,1201),(0028,1202),(0028,1202) + * - xxx Palette Color Lookup Table Data - are found + * \warning does NOT deal with : + * 0028 1100 Gray Lookup Table Descriptor (Retired) + * 0028 1221 Segmented Red Palette Color Lookup Table Data + * 0028 1222 Segmented Green Palette Color Lookup Table Data + * 0028 1223 Segmented Blue Palette Color Lookup Table Data + * no known Dicom reader deals with them :-( + * @return a RGBA Lookup Table + */ +void PixelReadConvert::BuildLUTRGBA() +{ + if ( LutRGBA ) + { + return; + } + // Not so easy : see + // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables + + if ( ! IsPaletteColor ) + { + return; + } + + if ( LutRedDescriptor == GDCM_UNFOUND + || LutGreenDescriptor == GDCM_UNFOUND + || LutBlueDescriptor == GDCM_UNFOUND ) + { + return; + } + + //////////////////////////////////////////// + // Extract the info from the LUT descriptors + int lengthR; // Red LUT length in Bytes + int debR; // Subscript of the first Lut Value + int nbitsR; // Lut item size (in Bits) + int nbRead = sscanf( LutRedDescriptor.c_str(), + "%d\\%d\\%d", + &lengthR, &debR, &nbitsR ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor"); + } + + int lengthG; // Green LUT length in Bytes + int debG; // Subscript of the first Lut Value + int nbitsG; // Lut item size (in Bits) + nbRead = sscanf( LutGreenDescriptor.c_str(), + "%d\\%d\\%d", + &lengthG, &debG, &nbitsG ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor"); + } + + int lengthB; // Blue LUT length in Bytes + int debB; // Subscript of the first Lut Value + int nbitsB; // Lut item size (in Bits) + nbRead = sscanf( LutRedDescriptor.c_str(), + "%d\\%d\\%d", + &lengthB, &debB, &nbitsB ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor"); + } + + //////////////////////////////////////////////////////// + if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) ) + { + return; + } + + //////////////////////////////////////////////// + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha) + if ( !LutRGBA ) + { + return; + } + memset( LutRGBA, 0, 1024 ); + + int mult; + if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) ) + { + // when LUT item size is different than pixel size + mult = 2; // high byte must be = low byte + } + else + { + // See PS 3.3-2003 C.11.1.1.2 p 619 + mult = 1; + } + + // if we get a black image, let's just remove the '+1' + // from 'i*mult+1' and check again + // if it works, we shall have to check the 3 Palettes + // to see which byte is ==0 (first one, or second one) + // and fix the code + // We give up the checking to avoid some (useless ?)overhead + // (optimistic asumption) + int i; + uint8_t* a = LutRGBA + 0; + for( i=0; i < lengthR; ++i ) + { + *a = LutRedData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 1; + for( i=0; i < lengthG; ++i) + { + *a = LutGreenData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 2; + for(i=0; i < lengthB; ++i) + { + *a = LutBlueData[i*mult+1]; + a += 4; + } + + a = LutRGBA + 3; + for(i=0; i < 256; ++i) + { + *a = 1; // Alpha component + a += 4; + } +} + +/** + * \brief Build the RGB image from the Raw imagage and the LUTs. + */ +bool PixelReadConvert::BuildRGBImage() +{ + if ( RGB ) + { + // The job is already done. + return true; + } + + if ( ! Raw ) + { + // The job can't be done + return false; + } + + BuildLUTRGBA(); + if ( ! LutRGBA ) + { + // The job can't be done + return false; + } + + // Build RGB Pixels + AllocateRGB(); + uint8_t* localRGB = RGB; + for (size_t i = 0; i < RawSize; ++i ) + { + int j = Raw[i] * 4; + *localRGB++ = LutRGBA[j]; + *localRGB++ = LutRGBA[j+1]; + *localRGB++ = LutRGBA[j+2]; + } + return true; +} + +/** + * \brief Print self. + * @param indent Indentation string to be prepended during printing. + * @param os Stream to print to. + */ +void PixelReadConvert::Print( std::string indent, std::ostream &os ) +{ + os << indent + << "--- Pixel information -------------------------" + << std::endl; + os << indent + << "Pixel Data: offset " << PixelOffset + << " x" << std::hex << PixelOffset << std::dec + << " length " << PixelDataLength + << " x" << std::hex << PixelDataLength << std::dec + << std::endl; + + if ( IsRLELossless ) + { + if ( RLEInfo ) + { + RLEInfo->Print( indent, os ); + } + else + { + dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file " + "but NO RLEinfo present."); + } + } + + if ( IsJPEG2000 || IsJPEGLossless ) + { + if ( JPEGInfo ) + { + JPEGInfo->Print( indent, os ); + } + else + { + dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file " + "but NO JPEGinfo present."); + } + } +} + +} // end namespace gdcm + +// NOTES on File internal calls +// User +// ---> GetImageData +// ---> GetImageDataIntoVector +// |---> GetImageDataIntoVectorRaw +// | lut intervention +// User +// ---> GetImageDataRaw +// ---> GetImageDataIntoVectorRaw + diff --git a/src/gdcmPixelReadConvert.h b/src/gdcmPixelReadConvert.h index 29d895d1..af5e4bbd 100644 --- a/src/gdcmPixelReadConvert.h +++ b/src/gdcmPixelReadConvert.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.h,v $ Language: C++ - Date: $Date: 2004/12/10 13:49:07 $ - Version: $Revision: 1.4 $ + Date: $Date: 2004/12/12 17:21:07 $ + Version: $Revision: 1.5 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -66,6 +66,11 @@ private: void ReadAndDecompress12BitsTo16Bits( std::ifstream* fp ) throw ( FormatError ); bool ReadAndDecompressRLEFile( std::ifstream* fp ); bool ReadAndDecompressJPEGFile( std::ifstream* fp ); + bool ReadAndDecompressJPEGFramesFromFile( std::ifstream* fp ); + bool ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream* fp ); + bool ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream* fp ); + + void BuildLUTRGBA( std::ifstream* fp ); // In place (within Decompressed and with no fp access) decompression