X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmPixelReadConvert.cxx;h=ee0eb6cff9a46c2b42bd60fedb78dff3bb8315ed;hb=f55ad21e7872cc4a4b0a37da859650e538d14075;hp=54f8310ac323c6ac2bc00cdb8c041de673c77d1f;hpb=2d70532c1ec0203f5c893310a2d32d573cb0a712;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 54f8310a..ee0eb6cf 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/11/10 13:39:55 $ - Version: $Revision: 1.101 $ + Date: $Date: 2007/08/29 08:10:14 $ + Version: $Revision: 1.117 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -28,7 +28,11 @@ #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); @@ -81,8 +85,10 @@ 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 // when absent from the file. @@ -92,6 +98,10 @@ 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. BitsStored = file->GetBitsStored(); @@ -110,41 +120,45 @@ 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(); - - if (! file->IsDicomV3() ) // Should be ACR-NEMA file - { - IsRaw = true; - // Don't loose time checking unexistant Transfer Syntax ! - IsPrivateGETransferSyntax = IsMPEG + + IsPrivateGETransferSyntax = IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false; + + if (! file->IsDicomV3() ) // Should be ACR-NEMA file + { + IsRaw = true; } else { std::string ts = file->GetTransferSyntax(); IsRaw = false; - while (true) + 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). IsPrivateGETransferSyntax = ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE ); IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false; - if (!IsRaw) { while(true) @@ -156,7 +170,8 @@ 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; - gdcmWarningMacro("Unexepected Transfer Syntax :[" << ts << "]"); + // DeflatedExplicitVRLittleEndian is considered as 'Unexpected' (we don't know yet how to process !) + gdcmWarningMacro("Unexpected Transfer Syntax :[" << ts << "]"); break; } } @@ -226,7 +241,7 @@ void PixelReadConvert::GrabInformationsFromFile( File *file ) } } FileInternal = file; - + FH = fileHelper; ComputeRawAndRGBSizes(); } @@ -256,8 +271,19 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) AllocateRaw(); ////////////////////////////////////////////////// + + CallStartMethod(); // for progress bar + unsigned int count = 0; + unsigned int frameSize; + unsigned int bitsAllocated = BitsAllocated; + //if(bitsAllocated == 12) + if(bitsAllocated > 8 && bitsAllocated < 16) + bitsAllocated = 16; + frameSize = XSize*YSize*SamplesPerPixel*bitsAllocated/8; + //// Second stage: read from disk and decompress. - if ( BitsAllocated == 12 ) + + if ( BitsAllocated == 12 ) // We suppose 'BitsAllocated' = 12 only exist for uncompressed files { ReadAndDecompress12BitsTo16Bits( fp); } @@ -270,17 +296,34 @@ 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? + char *raw = (char*)Raw; + uint32_t remainingLength; + unsigned int i; + unsigned int lengthToRead; + if ( PixelDataLength > RawSize ) - { - fp->read( (char*)Raw, RawSize); - } + lengthToRead = RawSize; else + lengthToRead = PixelDataLength; + + // perform a frame by frame reading + remainingLength = lengthToRead; + unsigned int nbFrames = lengthToRead / frameSize; + for (i=0;iread( (char*)Raw, PixelDataLength); + Progress = (float)(count+1)/(float)nbFrames; + fp->read( raw, frameSize); + raw += frameSize; + remainingLength -= frameSize; + count++; } - + if (remainingLength !=0 ) + fp->read( raw, remainingLength); + if ( fp->fail() || fp->eof()) { gdcmWarningMacro( "Reading of Raw pixel data failed." ); @@ -290,7 +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; @@ -310,7 +353,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) if ( ! ReadAndDecompressJPEGFile( fp ) ) { gdcmWarningMacro( "JPEG decompressor ( ReadAndDecompressJPEGFile()" - << " method ) failed." ); + << " method ) failed." ); return false; } } @@ -412,7 +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 ) @@ -548,9 +592,9 @@ 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 ); return true; } @@ -562,7 +606,7 @@ 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 : @@ -639,11 +683,11 @@ void PixelReadConvert::BuildLUTRGBA() } gdcmDebugMacro(" lengthR " << lengthR << " debR " - << debR << " nbitsR " << nbitsR); + << debR << " nbitsR " << nbitsR); gdcmDebugMacro(" lengthG " << lengthG << " debG " - << debG << " nbitsG " << nbitsG); + << debG << " nbitsG " << nbitsG); gdcmDebugMacro(" lengthB " << lengthB << " debB " - << debB << " nbitsB " << nbitsB); + << debB << " nbitsB " << nbitsB); if ( !lengthR ) // if = 2^16, this shall be 0 see : CP-143 lengthR=65536; @@ -799,8 +843,7 @@ void PixelReadConvert::BuildLUTRGBA() void PixelReadConvert::ConvertSwapZone() { unsigned int i; - uint16_t localSwapCode = SwapCode; - + // 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 @@ -827,26 +870,27 @@ void PixelReadConvert::ConvertSwapZone() // Therefore, in either case, if the file is in // 'ImplicitVR BigEndian PrivateGE Transfer Syntax', then GDCM needs to switch // the byte swapping code when entering the pixel data. - + + int tempSwapCode = SwapCode; if ( IsPrivateGETransferSyntax ) { + gdcmWarningMacro(" IsPrivateGETransferSyntax found; turn the SwapCode"); // PrivateGETransferSyntax only exists for 'true' Dicom images // we assume there is no 'exotic' 32 bits endianess! - switch (localSwapCode) + if (SwapCode == 1234) { - case 1234: - localSwapCode = 4321; - break; - case 4321: - localSwapCode = 1234; - break; - } + tempSwapCode = 4321; + } + else if (SwapCode == 4321) + { + tempSwapCode = 1234; + } } - + if ( BitsAllocated == 16 ) { uint16_t *im16 = (uint16_t*)Raw; - switch( localSwapCode ) + switch( tempSwapCode ) { case 1234: break; @@ -859,7 +903,8 @@ void PixelReadConvert::ConvertSwapZone() } break; default: - gdcmWarningMacro("SwapCode value (16 bits) not allowed."); + gdcmWarningMacro("SwapCode value (16 bits) not allowed." + << tempSwapCode); } } else if ( BitsAllocated == 32 ) @@ -868,7 +913,7 @@ void PixelReadConvert::ConvertSwapZone() uint16_t high; uint16_t low; uint32_t *im32 = (uint32_t*)Raw; - switch ( localSwapCode ) + switch ( tempSwapCode ) { case 1234: break; @@ -904,7 +949,7 @@ void PixelReadConvert::ConvertSwapZone() } break; default: - gdcmWarningMacro("SwapCode value (32 bits) not allowed." ); + gdcmWarningMacro("SwapCode value (32 bits) not allowed." << tempSwapCode ); } } } @@ -1154,7 +1199,9 @@ 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; @@ -1244,7 +1291,7 @@ void PixelReadConvert::ConvertHandleColor() // - [Planar 2] OR [Photo D] requires LUT intervention. gdcmDebugMacro("--> ConvertHandleColor " - << "Planar Configuration " << PlanarConfiguration ); + << "Planar Configuration " << PlanarConfiguration ); if ( ! IsRawRGB() ) { @@ -1294,7 +1341,7 @@ void PixelReadConvert::ComputeRawAndRGBSizes() bitsAllocated = 16; } - RawSize = XSize * YSize * ZSize + RawSize = XSize * YSize * ZSize * TSize * ( bitsAllocated / 8 ) * SamplesPerPixel; if ( HasLUT ) @@ -1304,7 +1351,10 @@ void PixelReadConvert::ComputeRawAndRGBSizes() else { RGBSize = RawSize; + } + RawSize += RawSize%2; + RGBSize += RGBSize%2; } /// Allocates room for RGB Pixels @@ -1367,6 +1417,34 @@ void PixelReadConvert::Print( std::ostream &os, std::string const &indent ) } } +/** + * \brief CallStartMethod + */ +void PixelReadConvert::CallStartMethod() +{ + Progress = 0.0f; + Abort = false; + CommandManager::ExecuteCommand(FH,CMD_STARTPROGRESS); +} + +/** + * \brief CallProgressMethod + */ +void PixelReadConvert::CallProgressMethod() +{ + CommandManager::ExecuteCommand(FH,CMD_PROGRESS); +} + +/** + * \brief CallEndMethod + */ +void PixelReadConvert::CallEndMethod() +{ + Progress = 1.0f; + CommandManager::ExecuteCommand(FH,CMD_ENDPROGRESS); +} + + //----------------------------------------------------------------------------- } // end namespace gdcm