X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=b94a76a82cb57149e26450a1673bafd2d0dd37bb;hb=ab3dc69a71af640fa49cbd917272d9ff7d1651b6;hp=53c636b4037c1925eb369de293b31ecec48836d1;hpb=e6054327de356b91d8e47d61e4c295536faed707;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 53c636b4..b94a76a8 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/01/13 09:24:08 $ - Version: $Revision: 1.26 $ + Date: $Date: 2005/01/26 11:42:02 $ + Version: $Revision: 1.35 $ 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 @@ -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. @@ -287,11 +257,11 @@ bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream *fp ) ++it ) { // Loop on the fragments - for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ ) + for( unsigned int k = 1; k <= (*it)->GetNumberOfFragments(); k++ ) { - fp->seekg( (*it)->Offset[k] , std::ios::beg ); + fp->seekg( (*it)->GetOffset(k) , std::ios::beg ); (void)ReadAndDecompressRLEFragment( subRaw, - (*it)->Length[k], + (*it)->GetLength(k), RawSegmentSize, fp ); subRaw += RawSegmentSize; @@ -381,7 +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() { @@ -391,9 +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; @@ -411,61 +381,34 @@ 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 ) { - uint8_t *localRaw = Raw; - // Loop on the fragment[s] - for( JPEGFragmentsInfo::JPEGFragmentsList::iterator - it = JPEGInfo->Fragments.begin(); - it != JPEGInfo->Fragments.end(); - ++it ) - { - fp->seekg( (*it)->Offset, std::ios::beg); - - if ( BitsStored == 8) - { - // JPEG Lossy : call to IJG 6b - if ( ! gdcm_read_JPEG_file8( fp, localRaw ) ) - { - return false; - } - } - else if ( BitsStored <= 12) - { - // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) ) - { - return false; - } - } - else if ( BitsStored <= 16) - { - // Reading Fragment pixels - if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) ) - { - return false; - } - //gdcmAssertMacro( IsJPEGLossless ); - } - else - { - // other JPEG lossy not supported - gdcmErrorMacro( "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; - } + // 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 ) +// { +// (*it)->DecompressJPEGFramesFromFile(fp, localRaw, BitsStored ); +// +// // Advance to next free location in Raw +// // for next fragment decompression (if any) +// +// localRaw += length * numberBytes; +// } + JPEGInfo->DecompressJPEGFramesFromFile(fp, Raw, BitsStored, numberBytes, length ); return true; } @@ -482,71 +425,16 @@ 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; @@ -567,84 +455,27 @@ 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 ) { - fragmentLength += (*it)->Length; + fragmentLength += (*it)->GetLength(); 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; @@ -666,8 +497,18 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) { if ( IsJPEG2000 ) { - fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg); - if ( ! gdcm_read_JPEG2000_file( fp,Raw ) ) + gdcmVerboseMacro( "Sorry, JPEG2000 not yet taken into account" ); + fp->seekg( (*JPEGInfo->Fragments.begin())->GetOffset(), std::ios::beg); +// if ( ! gdcm_read_JPEG2000_file( fp,Raw ) ) + gdcmVerboseMacro( "Wrong Blue LUT descriptor" ); + return false; + } + + if ( IsJPEGLS ) + { + gdcmVerboseMacro( "Sorry, JPEG-LS not yet taken into account" ); + fp->seekg( (*JPEGInfo->Fragments.begin())->GetOffset(), std::ios::beg); +// if ( ! gdcm_read_JPEGLS_file( fp,Raw ) ) return false; } @@ -680,15 +521,25 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) } else if (JPEGInfo->Fragments.size() == (size_t)ZSize) { + } +// 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() == (size_t)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 ); - } +// } +// else +// { +// // The dicom image contains frames containing fragments of images +// // a more complex algorithm :-) +// return ReadAndDecompressJPEGFragmentedFramesFromFile( fp ); +// } } /** @@ -732,7 +583,7 @@ 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() @@ -843,8 +694,8 @@ 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) { @@ -1001,7 +852,7 @@ 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. @@ -1011,7 +862,7 @@ 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 ) @@ -1019,7 +870,7 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) BitsStored = BitsAllocated; } - // High Bit Position + // High Bit Position, defaulted to "Bits Allocated" - 1 HighBitPosition = header->GetHighBitPosition(); if ( HighBitPosition == 0 ) { @@ -1041,9 +892,13 @@ 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(); @@ -1059,18 +914,18 @@ void PixelReadConvert::GrabInformationsFromHeader( Header *header ) HasLUT = header->HasLUT(); if ( HasLUT ) { - // Just in case some access to a Header element requires disk access. - LutRedDescriptor = header->GetEntry( 0x0028, 0x1101 ); - LutGreenDescriptor = header->GetEntry( 0x0028, 0x1102 ); - LutBlueDescriptor = header->GetEntry( 0x0028, 0x1103 ); + // Just in case some access to a File element requires disk access. + LutRedDescriptor = header->GetEntryValue( 0x0028, 0x1101 ); + LutGreenDescriptor = header->GetEntryValue( 0x0028, 0x1102 ); + LutBlueDescriptor = header->GetEntryValue( 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. + // 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 @@ -1083,7 +938,7 @@ 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: @@ -1091,7 +946,7 @@ 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: @@ -1099,7 +954,7 @@ 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" ); } } @@ -1107,7 +962,7 @@ 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 @@ -1152,7 +1007,7 @@ 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 @@ -1163,7 +1018,7 @@ 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 @@ -1174,7 +1029,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthB, &debB, &nbitsB ); if( nbRead != 3 ) { - gdcmVerboseMacro( "Wrong blue LUT descriptor" ); + gdcmVerboseMacro( "Wrong Blue LUT descriptor" ); } //////////////////////////////////////////////////////// @@ -1209,7 +1064,7 @@ 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; @@ -1278,21 +1133,12 @@ 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 -------------------------" @@ -1308,7 +1154,7 @@ void PixelReadConvert::Print( std::string indent, std::ostream &os ) { if ( RLEInfo ) { - RLEInfo->Print( indent, os ); + RLEInfo->Print( os, indent ); } else { @@ -1316,11 +1162,11 @@ 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 {