X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=b75ecb9a8308707b63049a81299e0776ebcda228;hb=a212c7275fb6052e882a981534b966c09ecc1d4e;hp=c8c76c22d2f12747c805bd1fa1043d47c88423d7;hpb=33b1eec26f02131242fbfdef52184b24763cf4e6;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index c8c76c22..b75ecb9a 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/11/29 17:21:35 $ - Version: $Revision: 1.106 $ + Date: $Date: 2007/09/05 08:22:57 $ + Version: $Revision: 1.122 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -28,10 +28,14 @@ #include #include //for sscanf -namespace gdcm +#if defined(__BORLANDC__) + #include // for memset +#endif + +namespace GDCM_NAME_SPACE { -//bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght); +//bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght); bool gdcm_read_JPEG2000_file (void* raw, char *inputdata, size_t inputlength); //----------------------------------------------------------------------------- @@ -81,8 +85,9 @@ bool PixelReadConvert::IsRawRGB() /** * \brief Gets various usefull informations from the file header * @param file gdcm::File pointer + * @param fileHelper gdcm::FileHelper pointer */ -void PixelReadConvert::GrabInformationsFromFile( File *file, +void PixelReadConvert::GrabInformationsFromFile( File *file, FileHelper *fileHelper ) { // Number of Bits Allocated for storing a Pixel is defaulted to 16 @@ -92,6 +97,10 @@ void PixelReadConvert::GrabInformationsFromFile( File *file, { BitsAllocated = 16; } + else if ( BitsAllocated > 8 && BitsAllocated < 16 && BitsAllocated != 12 ) + { + BitsAllocated = 16; + } // Number of "Bits Stored", defaulted to number of "Bits Allocated" // when absent from the file. @@ -111,16 +120,17 @@ void PixelReadConvert::GrabInformationsFromFile( File *file, XSize = file->GetXSize(); YSize = file->GetYSize(); ZSize = file->GetZSize(); + TSize = file->GetTSize(); SamplesPerPixel = file->GetSamplesPerPixel(); //PixelSize = file->GetPixelSize(); Useless PixelSign = file->IsSignedPixelData(); SwapCode = file->GetSwapCode(); - + IsPrivateGETransferSyntax = IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false; - + if (! file->IsDicomV3() ) // Should be ACR-NEMA file { IsRaw = true; @@ -130,25 +140,27 @@ void PixelReadConvert::GrabInformationsFromFile( File *file, std::string ts = file->GetTransferSyntax(); IsRaw = false; - while (true) // short to write than if elseif elseif elseif ... + while (true) // shorter to write than 'if elseif elseif elseif' ... { // mind the order : check the most usual first. if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian) break; if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) break; if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian) break; if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE) break; - if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian) break; + // DeflatedExplicitVRLittleEndian syntax means the whole Dataset (Header + Pixels) is compressed ! + // Not dealt with ! (Parser hangs) + //if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian) break; break; } // cache whether this is a strange GE transfer syntax (which uses // a little endian transfer syntax for the header and a big endian - // transfer syntax for the pixel data). + // transfer syntax for the pixel data). IsPrivateGETransferSyntax = ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE ); - IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false; + IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false; if (!IsRaw) - { + { while(true) { // mind the order : check the most usual first. @@ -158,6 +170,7 @@ void PixelReadConvert::GrabInformationsFromFile( File *file, if( IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts) ) break; if( IsMPEG = Global::GetTS()->IsMPEG(ts) ) break; if( IsJPEGLS = Global::GetTS()->IsJPEGLS(ts) ) break; + // DeflatedExplicitVRLittleEndian is considered as 'Unexpected' (we don't know yet how to process !) gdcmWarningMacro("Unexpected Transfer Syntax :[" << ts << "]"); break; } @@ -263,7 +276,8 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) unsigned int count = 0; unsigned int frameSize; unsigned int bitsAllocated = BitsAllocated; - if(bitsAllocated == 12) + //if(bitsAllocated == 12) + if(bitsAllocated > 8 && bitsAllocated < 16) bitsAllocated = 16; frameSize = XSize*YSize*SamplesPerPixel*bitsAllocated/8; @@ -282,7 +296,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) if ( PixelDataLength != RawSize ) { gdcmWarningMacro( "Mismatch between PixelReadConvert : " - << PixelDataLength << " and RawSize : " << RawSize ); + << PixelDataLength << " and RawSize : " << RawSize ); } //todo : is it the right patch? @@ -301,21 +315,14 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) unsigned int nbFrames = lengthToRead / frameSize; for (i=0;iread( raw, frameSize); raw += frameSize; remainingLength -= frameSize; + count++; } if (remainingLength !=0 ) fp->read( raw, remainingLength); - - //if ( PixelDataLength > RawSize ) - //{ - // fp->read( (char*)Raw, RawSize); // Read all the frames with a single fread - //} - //else - //{ - // fp->read( (char*)Raw, PixelDataLength); // Read all the frames with a single fread - //} if ( fp->fail() || fp->eof()) { @@ -326,7 +333,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) else if ( IsRLELossless ) { if ( ! RLEInfo->DecompressRLEFile - ( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) + ( fp, Raw, XSize, YSize, ZSize, TSize, BitsAllocated ) ) { gdcmWarningMacro( "RLE decompressor failed." ); return false; @@ -448,7 +455,8 @@ bool PixelReadConvert::BuildRGBImage() void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) throw ( FormatError ) { - int nbPixels = XSize * YSize; + /// \todo Fix the 3D, 4D pb + int nbPixels = XSize * YSize * TSize; uint16_t *localDecompres = (uint16_t*)Raw; for( int p = 0; p < nbPixels; p += 2 ) @@ -505,33 +513,60 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) // jpeg2000 stream to use jasper: // I don't think we'll ever be able to deal with multiple fragments properly - unsigned long inputlength = 0; - JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment(); - while( jpegfrag ) - { + if( ZSize == 1 ) + { + unsigned long inputlength = 0; + JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment(); + while( jpegfrag ) + { inputlength += jpegfrag->GetLength(); jpegfrag = JPEGInfo->GetNextFragment(); - } - gdcmAssertMacro( inputlength != 0); - uint8_t *inputdata = new uint8_t[inputlength]; - char *pinputdata = (char*)inputdata; - jpegfrag = JPEGInfo->GetFirstFragment(); - while( jpegfrag ) - { + } + gdcmAssertMacro( inputlength != 0); + uint8_t *inputdata = new uint8_t[inputlength]; + char *pinputdata = (char*)inputdata; + jpegfrag = JPEGInfo->GetFirstFragment(); + while( jpegfrag ) + { fp->seekg( jpegfrag->GetOffset(), std::ios::beg); fp->read(pinputdata, jpegfrag->GetLength()); pinputdata += jpegfrag->GetLength(); jpegfrag = JPEGInfo->GetNextFragment(); - } - // Warning the inputdata buffer is delete in the function - if ( ! gdcm_read_JPEG2000_file( Raw, - (char*)inputdata, inputlength ) ) - { + } + // Warning the inputdata buffer is deleted in the function + if ( gdcm_read_JPEG2000_file( Raw, + (char*)inputdata, inputlength ) ) + { return true; - } - // wow what happen, must be an error - gdcmWarningMacro( "gdcm_read_JPEG2000_file() failed "); - return false; + } + // wow what happen, must be an error + gdcmWarningMacro( "gdcm_read_JPEG2000_file() failed "); + return false; + } + else + { + if( (unsigned int)ZSize != JPEGInfo->GetFragmentCount() ) + { + gdcmErrorMacro( "Sorry GDCM does not handle this type of fragments" ); + return false; + } + // Hopefully every dicom fragment is *exactly* the j2k stream + JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment(); + char *praw = (char*)Raw; + while( jpegfrag ) + { + unsigned long inputlength = jpegfrag->GetLength(); + char *inputdata = new char[inputlength]; + fp->seekg( jpegfrag->GetOffset(), std::ios::beg); + fp->read(inputdata, jpegfrag->GetLength()); + // Warning the inputdata buffer is deleted in the function + gdcm_read_JPEG2000_file( praw, + inputdata, inputlength) ; + praw += XSize*YSize*SamplesPerPixel*(BitsAllocated/8); + jpegfrag = JPEGInfo->GetNextFragment(); + } + return true; + } } else if ( IsJPEGLS ) { @@ -584,10 +619,16 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) // make sure this is the right JPEG compression assert( !IsJPEGLS || !IsJPEG2000 ); // Precompute the offset localRaw will be shifted with - int length = XSize * YSize * SamplesPerPixel; + int length = XSize * YSize * ZSize * SamplesPerPixel; int numberBytes = BitsAllocated / 8; - JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length ); + // to avoid major troubles when BitsStored == 8 && BitsAllocated==16 ! + int dummy; + if (BitsStored == 8 && BitsAllocated==16) + dummy = 16; + else + dummy = BitsStored; + JPEGInfo->DecompressFromFile(fp, Raw, dummy, numberBytes, length ); return true; } } @@ -598,7 +639,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) * and * - (0028,1101),(0028,1102),(0028,1102) * xxx Palette Color Lookup Table Descriptor are found - * and + * and * - (0028,1201),(0028,1202),(0028,1202) * xxx Palette Color Lookup Table Data - are found * \warning does NOT deal with : @@ -835,7 +876,7 @@ void PixelReadConvert::BuildLUTRGBA() void PixelReadConvert::ConvertSwapZone() { unsigned int i; - + // If this file is 'ImplicitVR BigEndian PrivateGE Transfer Syntax', // then the header is in little endian format and the pixel data is in // big endian format. When reading the header, GDCM has already established @@ -1057,27 +1098,38 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) { // pmask : to mask the 'unused bits' (may contain overlays) uint16_t pmask = 0xffff; - pmask = pmask >> ( BitsAllocated - BitsStored ); + + // It's up to the user to decide if he wants to ignore overlays (if any), + // not to gdcm, without asking. + // default is NOT TO LOAD, in order not to confuse ITK users (and others!). + + if ( !FH->GetKeepOverlays() ) // mask spurious bits ! (overlay are NOT loaded!) + { + pmask = pmask >> ( BitsAllocated - BitsStored ); + } + // else : it's up to the user to manage the 'pixels + overlays' he just loaded! uint16_t *deb = (uint16_t*)Raw; if ( !PixelSign ) // Pixels are unsigned { for(int i = 0; i> (BitsStored - HighBitPosition - 1)) & pmask; deb++; } } else // Pixels are signed { + // Hope there is never ACR-NEMA-like overlays within signed pixels (?!?) + // smask : to check the 'sign' when BitsStored != BitsAllocated uint16_t smask = 0x0001; smask = smask << ( 16 - (BitsAllocated - BitsStored + 1) ); // nmask : to propagate sign bit on negative values int16_t nmask = (int16_t)0x8000; nmask = nmask >> ( BitsAllocated - BitsStored - 1 ); - + for(int i = 0; i> (BitsStored - HighBitPosition - 1); @@ -1179,9 +1231,9 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() // except for the few patches of color on the image. // On such images, RLE achieves a compression ratio that is much better // than the compression ratio on an equivalent RGB image. - + gdcmWarningMacro("--> ConvertYcBcRPlanesToRGBPixels"); - + uint8_t *localRaw = Raw; uint8_t *copyRaw = new uint8_t[ RawSize ]; memmove( copyRaw, localRaw, RawSize ); @@ -1191,7 +1243,9 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf // and be *very* affraid // - int l = XSize * YSize; + + /// \todo : find an example to see how 3rd dim and 4th dim work together + int l = XSize * YSize * TSize; int nbFrames = ZSize; uint8_t *a = copyRaw + 0; @@ -1331,7 +1385,7 @@ void PixelReadConvert::ComputeRawAndRGBSizes() bitsAllocated = 16; } - RawSize = XSize * YSize * ZSize + RawSize = XSize * YSize * ZSize * TSize * ( bitsAllocated / 8 ) * SamplesPerPixel; if ( HasLUT ) @@ -1342,6 +1396,8 @@ void PixelReadConvert::ComputeRawAndRGBSizes() { RGBSize = RawSize; } + RawSize += RawSize%2; + RGBSize += RGBSize%2; } /// Allocates room for RGB Pixels @@ -1431,7 +1487,6 @@ void PixelReadConvert::CallEndMethod() CommandManager::ExecuteCommand(FH,CMD_ENDPROGRESS); } - //----------------------------------------------------------------------------- } // end namespace gdcm