X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=f2bbb902f79f03458cdc5a25e6edb7b564d9f34d;hb=0ad9dae4659b21bfd5c834c1af724eab4dcdf4f6;hp=17c28603bcf67a5bc08cd0586ef5704cab7defb5;hpb=31c63a6cb25b49a119e0132201c051ade2e17704;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 17c28603..f2bbb902 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/01/11 16:44:43 $ - Version: $Revision: 1.21 $ + Date: $Date: 2005/01/23 10:12:34 $ + Version: $Revision: 1.32 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,14 +16,8 @@ =========================================================================*/ -////////////////// 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 "gdcmFile.h" #include "gdcmGlobal.h" #include "gdcmTS.h" #include "gdcmPixelReadConvert.h" @@ -38,30 +32,6 @@ 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 @@ -169,7 +139,7 @@ void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) /** * \brief Try to deal with RLE 16 Bits. - * We assume the RLE has allready been parsed and loaded in + * We assume the RLE has already 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) @@ -210,8 +180,8 @@ bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) /** * \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 subRaw Sub region of \ref Raw where the 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. @@ -319,11 +289,8 @@ void PixelReadConvert::ConvertSwapZone() uint16_t *im16 = (uint16_t*)Raw; switch( SwapCode ) { - case 0: - case 12: case 1234: break; - case 21: case 3412: case 2143: case 4321: @@ -344,7 +311,6 @@ void PixelReadConvert::ConvertSwapZone() uint32_t* im32 = (uint32_t*)Raw; switch ( SwapCode ) { - case 0: case 1234: break; case 4321: @@ -385,7 +351,7 @@ void PixelReadConvert::ConvertSwapZone() } /** - * \brief Deal with endianity i.e. re-arange bytes inside the integer + * \brief Deal with endianness i.e. re-arange bytes inside the integer */ void PixelReadConvert::ConvertReorderEndianity() { @@ -395,9 +361,9 @@ void PixelReadConvert::ConvertReorderEndianity() } // Special kludge in order to deal with xmedcon broken images: - if ( ( BitsAllocated == 16 ) - && ( BitsStored < BitsAllocated ) - && ( ! PixelSign ) ) + if ( BitsAllocated == 16 + && BitsStored < BitsAllocated + && !PixelSign ) { int l = (int)( RawSize / ( BitsAllocated / 8 ) ); uint16_t *deb = (uint16_t *)Raw; @@ -415,58 +381,30 @@ void PixelReadConvert::ConvertReorderEndianity() /** * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated - * file and decompress it. This funciton assumes that each + * file and decompress it. This function assumes that each * jpeg fragment contains a whole frame (jpeg file). * @param fp File Pointer * @return Boolean */ bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream *fp ) { + // Pointer to the Raw image uint8_t *localRaw = Raw; + + // Precompute the offset localRaw will be shifted with + int length = XSize * YSize * SamplesPerPixel; + int numberBytes = BitsAllocated / 8; + // 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; - } - //gdcmAssertMacro( IsJPEGLossless ); - } - else - { - // other JPEG lossy not supported - gdcmErrorMacro( "Unknown jpeg lossy compression "); - return false; - } + (*it)->DecompressJPEGFramesFromFile(fp, localRaw, BitsStored ); // 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; } @@ -486,71 +424,16 @@ 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; - } + size_t totalLength = JPEGInfo->GetFragmentsLength(); // Concatenate the jpeg fragments into a local buffer JOCTET *buffer = new JOCTET [totalLength]; - JOCTET *p = buffer; + // Fill in the buffer: + JPEGInfo->ReadAllFragments(fp, buffer); - // 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; - - if ( BitsStored == 8) - { - if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw, - &howManyRead, &howManyWritten ) ) - { - gdcmErrorMacro( "Failed to read jpeg8 "); - delete [] buffer; - return false; - } - } - else if ( BitsStored <= 12) - { - if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw, - &howManyRead, &howManyWritten ) ) - { - gdcmErrorMacro( "Failed to read jpeg12 "); - delete [] buffer; - return false; - } - } - else if ( BitsStored <= 16) - { - - if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw, - &howManyRead, &howManyWritten ) ) - { - gdcmErrorMacro( "Failed to read jpeg16 "); - delete [] buffer; - return false; - } - } - else - { - // other JPEG lossy not supported - gdcmErrorMacro( "Unknown jpeg lossy compression "); - delete [] buffer; - return false; - } + // kludge: // FIXME + JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it = JPEGInfo->Fragments.begin(); + (*it)->DecompressJPEGSingleFrameFragmentsFromFile(buffer, totalLength, Raw, BitsStored); // free local buffer delete [] buffer; @@ -571,34 +454,18 @@ bool PixelReadConvert:: ReadAndDecompressJPEGFragmentedFramesFromFile( 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; - } + size_t totalLength = JPEGInfo->GetFragmentsLength(); // Concatenate the jpeg fragments into a local buffer JOCTET *buffer = new JOCTET [totalLength]; - JOCTET *p = buffer; - - // 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; - } + // Fill in the buffer: + JPEGInfo->ReadAllFragments(fp, buffer); size_t howManyRead = 0; size_t howManyWritten = 0; size_t fragmentLength = 0; + JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it; for( it = JPEGInfo->Fragments.begin() ; (it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength); ++it ) @@ -606,49 +473,8 @@ ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream *fp ) fragmentLength += (*it)->Length; if (howManyRead > fragmentLength) continue; - - if ( BitsStored == 8) - { - if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead, - Raw+howManyWritten, - &howManyRead, &howManyWritten ) ) - { - gdcmErrorMacro( "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 ) ) - { - gdcmErrorMacro( "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 ) ) - { - gdcmErrorMacro( "Failed to read jpeg16 "); - delete [] buffer; - return false; - } - } - else - { - // other JPEG lossy not supported - gdcmErrorMacro( "Unknown jpeg lossy compression "); - delete [] buffer; - return false; - } + (*it)->DecompressJPEGFragmentedFramesFromFile(buffer, Raw, BitsStored, howManyRead, howManyWritten, totalLength); if (howManyRead < fragmentLength) howManyRead = fragmentLength; @@ -671,7 +497,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) if ( IsJPEG2000 ) { fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg); - if ( ! gdcm_read_JPEG2000_file( fp,Raw ) ) +// if ( ! gdcm_read_JPEG2000_file( fp,Raw ) ) return false; } @@ -736,7 +562,7 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) } /** - * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels + * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels * \warning Works on all the frames at a time */ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() @@ -847,8 +673,8 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *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 + // after the field containing the image data. In this case, these + // bad data are added to the size of the image (in the PixelDataLength // variable). But RawSize is the right size of the image ! if( PixelDataLength != RawSize) { @@ -923,7 +749,7 @@ void PixelReadConvert::ConvertHandleColor() // 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 + // Hence gdcm will 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 @@ -1005,7 +831,7 @@ void PixelReadConvert::ComputeRawAndRGBSizes() } } -void PixelReadConvert::GrabInformationsFromHeader( Header *header ) +void PixelReadConvert::GrabInformationsFromHeader( File *header ) { // Number of Bits Allocated for storing a Pixel is defaulted to 16 // when absent from the header. @@ -1015,7 +841,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) BitsAllocated = 16; } - // Number of "Bits Stored" defaulted to number of "Bits Allocated" + // Number of "Bits Stored", defaulted to number of "Bits Allocated" // when absent from the header. BitsStored = header->GetBitsStored(); if ( BitsStored == 0 ) @@ -1023,7 +849,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) BitsStored = BitsAllocated; } - // High Bit Position + // High Bit Position, defaulted to "Bits Allocated" - 1 HighBitPosition = header->GetHighBitPosition(); if ( HighBitPosition == 0 ) { @@ -1045,9 +871,13 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian; - IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts); - IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts); - IsRLELossless = Global::GetTS()->IsRLELossless(ts); + + IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts); + IsJPEGLS = Global::GetTS()->IsJPEGLS(ts); + IsJPEGLossy = Global::GetTS()->IsJPEGLossy(ts); + IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts); + IsRLELossless = Global::GetTS()->IsRLELossless(ts); + PixelOffset = header->GetPixelOffset(); PixelDataLength = header->GetPixelAreaLength(); RLEInfo = header->GetRLEInfo(); @@ -1063,7 +893,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) HasLUT = header->HasLUT(); if ( HasLUT ) { - // Just in case some access to a Header element requires disk access. + // Just in case some access to a File element requires disk access. LutRedDescriptor = header->GetEntry( 0x0028, 0x1101 ); LutGreenDescriptor = header->GetEntry( 0x0028, 0x1102 ); LutBlueDescriptor = header->GetEntry( 0x0028, 0x1103 ); @@ -1072,9 +902,9 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) // [ 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. + // loaded). Hence, we first try to obtain the LUTs data from the file + // and when this fails we read the LUTs data directly from disk. + /// \TODO Reading a [Bin|Val]Entry directly from disk is a kludge. /// We should NOT bypass the [Bin|Val]Entry class. Instead /// an access to an UNLOADED content of a [Bin|Val]Entry occurence /// (e.g. BinEntry::GetBinArea()) should force disk access from @@ -1087,7 +917,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) LutRedData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1201 ); if ( ! LutRedData ) { - gdcmVerboseMacro( "Unable to read red LUT data" ); + gdcmVerboseMacro( "Unable to read Red LUT data" ); } ////// Green round: @@ -1095,7 +925,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) LutGreenData = (uint8_t*)header->GetEntryBinArea(0x0028, 0x1202 ); if ( ! LutGreenData) { - gdcmVerboseMacro( "Unable to read green LUT data" ); + gdcmVerboseMacro( "Unable to read Green LUT data" ); } ////// Blue round: @@ -1103,7 +933,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) LutBlueData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1203 ); if ( ! LutBlueData ) { - gdcmVerboseMacro( "Unable to read blue LUT data" ); + gdcmVerboseMacro( "Unable to read Blue LUT data" ); } } @@ -1111,7 +941,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) } /** - * \brief Build Red/Green/Blue/Alpha LUT from Header + * \brief Build Red/Green/Blue/Alpha LUT from File * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] * and (0028,1101),(0028,1102),(0028,1102) * - xxx Palette Color Lookup Table Descriptor - are found @@ -1156,7 +986,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthR, &debR, &nbitsR ); if( nbRead != 3 ) { - gdcmVerboseMacro( "Wrong red LUT descriptor" ); + gdcmVerboseMacro( "Wrong Red LUT descriptor" ); } int lengthG; // Green LUT length in Bytes @@ -1167,7 +997,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthG, &debG, &nbitsG ); if( nbRead != 3 ) { - gdcmVerboseMacro( "Wrong green LUT descriptor" ); + gdcmVerboseMacro( "Wrong Green LUT descriptor" ); } int lengthB; // Blue LUT length in Bytes @@ -1178,7 +1008,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthB, &debB, &nbitsB ); if( nbRead != 3 ) { - gdcmVerboseMacro( "Wrong blue LUT descriptor" ); + gdcmVerboseMacro( "Wrong Blue LUT descriptor" ); } //////////////////////////////////////////////////////// @@ -1213,7 +1043,7 @@ void PixelReadConvert::BuildLUTRGBA() // 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 + // We give up the checking to avoid some (useless ?) overhead // (optimistic asumption) int i; uint8_t* a = LutRGBA + 0; @@ -1282,21 +1112,12 @@ bool PixelReadConvert::BuildRGBImage() return true; } -/** - * \brief Print self. - * @param os Stream to print to. - */ -void PixelReadConvert::Print( std::ostream &os ) -{ - Print("",os); -} - /** * \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 ) +void PixelReadConvert::Print( std::ostream &os, std::string const & indent ) { os << indent << "--- Pixel information -------------------------" @@ -1312,7 +1133,7 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) { if ( RLEInfo ) { - RLEInfo->Print( indent, os ); + RLEInfo->Print( os, indent ); } else { @@ -1320,11 +1141,11 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) } } - if ( IsJPEG2000 || IsJPEGLossless ) + if ( IsJPEG2000 || IsJPEGLossless || IsJPEGLossy || IsJPEGLS ) { if ( JPEGInfo ) { - JPEGInfo->Print( indent, os ); + JPEGInfo->Print( os, indent ); } else {