X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmPixelReadConvert.cxx;h=d505d2832075f5a5d728f619fac682b98c37d7b3;hb=4725aeb3e10e02e1e0ad9ac18baf7cc6a3feed6d;hp=02ee4dd0d50e675ec21c75f7f80fa78b58954ad4;hpb=030b22f65c2933ac680497672f8a236dcf2a460b;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 02ee4dd0..d505d283 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/11/28 15:30:04 $ - Version: $Revision: 1.104 $ + Date: $Date: 2006/06/29 13:27:59 $ + Version: $Revision: 1.112 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -28,6 +28,10 @@ #include #include //for sscanf +#if defined(__BORLANDC__) + #include // for memset +#endif + namespace gdcm { @@ -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. @@ -110,16 +116,17 @@ 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; @@ -129,14 +136,16 @@ 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 @@ -157,7 +166,8 @@ 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; - gdcmStaticWarningMacro("Unexpected Transfer Syntax :[" << ts << "]"); + // DeflatedExplicitVRLittleEndian is considered as 'Unexpected' (we don't know yet haow to process !) + gdcmWarningMacro("Unexpected Transfer Syntax :[" << ts << "]"); break; } } @@ -207,7 +217,7 @@ void PixelReadConvert::GrabInformationsFromFile( File *file ) LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 ); if ( ! LutRedData ) { - gdcmStaticWarningMacro("Unable to read Red Palette Color Lookup Table data"); + gdcmWarningMacro("Unable to read Red Palette Color Lookup Table data"); } // //// Green round: @@ -215,7 +225,7 @@ void PixelReadConvert::GrabInformationsFromFile( File *file ) LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 ); if ( ! LutGreenData) { - gdcmStaticWarningMacro("Unable to read Green Palette Color Lookup Table data"); + gdcmWarningMacro("Unable to read Green Palette Color Lookup Table data"); } // //// Blue round: @@ -223,11 +233,11 @@ void PixelReadConvert::GrabInformationsFromFile( File *file ) LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 ); if ( ! LutBlueData ) { - gdcmStaticWarningMacro("Unable to read Blue Palette Color Lookup Table data"); + gdcmWarningMacro("Unable to read Blue Palette Color Lookup Table data"); } } FileInternal = file; - + FH = fileHelper; ComputeRawAndRGBSizes(); } @@ -243,22 +253,32 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) //// First stage: get our hands on the Pixel Data. if ( !fp ) { - gdcmStaticWarningMacro( "Unavailable file pointer." ); + gdcmWarningMacro( "Unavailable file pointer." ); return false; } fp->seekg( PixelOffset, std::ios::beg ); if ( fp->fail() || fp->eof() ) { - gdcmStaticWarningMacro( "Unable to find PixelOffset in file." ); + gdcmWarningMacro( "Unable to find PixelOffset in file." ); return false; } AllocateRaw(); ////////////////////////////////////////////////// + + CallStartMethod(); // for progress bar + unsigned int count = 0; + unsigned int frameSize; + unsigned int bitsAllocated = BitsAllocated; + if(bitsAllocated == 12) + 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); } @@ -270,36 +290,53 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) // variable). But RawSize is the right size of the image ! if ( PixelDataLength != RawSize ) { - gdcmStaticWarningMacro( "Mismatch between PixelReadConvert : " - << PixelDataLength << " and RawSize : " << RawSize ); + gdcmWarningMacro( "Mismatch between PixelReadConvert : " + << 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()) { - gdcmStaticWarningMacro( "Reading of Raw pixel data failed." ); + gdcmWarningMacro( "Reading of Raw pixel data failed." ); return false; } } else if ( IsRLELossless ) { if ( ! RLEInfo->DecompressRLEFile - ( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) + ( fp, Raw, XSize, YSize, ZSize, TSize, BitsAllocated ) ) { - gdcmStaticWarningMacro( "RLE decompressor failed." ); + gdcmWarningMacro( "RLE decompressor failed." ); return false; } } else if ( IsMPEG ) { - //gdcmStaticWarningMacro( "Sorry, MPEG not yet taken into account" ); + //gdcmWarningMacro( "Sorry, MPEG not yet taken into account" ); //return false; // fp has already been seek to start of mpeg //ReadMPEGFile(fp, (char*)Raw, PixelDataLength); @@ -310,7 +347,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) // Default case concerns JPEG family if ( ! ReadAndDecompressJPEGFile( fp ) ) { - gdcmStaticWarningMacro( "JPEG decompressor ( ReadAndDecompressJPEGFile()" + gdcmWarningMacro( "JPEG decompressor ( ReadAndDecompressJPEGFile()" << " method ) failed." ); return false; } @@ -368,7 +405,7 @@ bool PixelReadConvert::BuildRGBImage() return false; } - gdcmStaticDebugMacro( "--> BuildRGBImage" ); + gdcmDebugMacro( "--> BuildRGBImage" ); // Build RGB Pixels AllocateRGB(); @@ -413,7 +450,8 @@ 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 ) @@ -477,7 +515,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) inputlength += jpegfrag->GetLength(); jpegfrag = JPEGInfo->GetNextFragment(); } - gdcmStaticAssertMacro( inputlength != 0); + gdcmAssertMacro( inputlength != 0); uint8_t *inputdata = new uint8_t[inputlength]; char *pinputdata = (char*)inputdata; jpegfrag = JPEGInfo->GetFirstFragment(); @@ -495,7 +533,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) return true; } // wow what happen, must be an error - gdcmStaticWarningMacro( "gdcm_read_JPEG2000_file() failed "); + gdcmWarningMacro( "gdcm_read_JPEG2000_file() failed "); return false; } else if ( IsJPEGLS ) @@ -519,7 +557,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) inputlength += jpegfrag->GetLength(); jpegfrag = JPEGInfo->GetNextFragment(); } - gdcmStaticAssertMacro( inputlength != 0); + gdcmAssertMacro( inputlength != 0); uint8_t *inputdata = new uint8_t[inputlength]; char *pinputdata = (char*)inputdata; jpegfrag = JPEGInfo->GetFirstFragment(); @@ -539,7 +577,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) delete[] inputdata; #endif - gdcmStaticWarningMacro( "Sorry, JPEG-LS not yet taken into account" ); + gdcmWarningMacro( "Sorry, JPEG-LS not yet taken into account" ); fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg); // if ( ! gdcm_read_JPEGLS_file( fp,Raw ) ) return false; @@ -549,7 +587,7 @@ 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 ); @@ -563,7 +601,7 @@ 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 : @@ -598,7 +636,7 @@ void PixelReadConvert::BuildLUTRGBA() || LutGreenDescriptor == GDCM_UNFOUND || LutBlueDescriptor == GDCM_UNFOUND ) { - gdcmStaticWarningMacro( "(At least) a LUT Descriptor is missing" ); + gdcmWarningMacro( "(At least) a LUT Descriptor is missing" ); return; } @@ -614,7 +652,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthR, &debR, &nbitsR ); if ( nbRead != 3 ) { - gdcmStaticWarningMacro( "Wrong Red LUT descriptor" ); + gdcmWarningMacro( "Wrong Red LUT descriptor" ); } int lengthG; // Green LUT length in Bytes int debG; // Subscript of the first Lut Value @@ -625,7 +663,7 @@ void PixelReadConvert::BuildLUTRGBA() &lengthG, &debG, &nbitsG ); if ( nbRead != 3 ) { - gdcmStaticWarningMacro( "Wrong Green LUT descriptor" ); + gdcmWarningMacro( "Wrong Green LUT descriptor" ); } int lengthB; // Blue LUT length in Bytes @@ -636,15 +674,15 @@ void PixelReadConvert::BuildLUTRGBA() &lengthB, &debB, &nbitsB ); if ( nbRead != 3 ) { - gdcmStaticWarningMacro( "Wrong Blue LUT descriptor" ); + gdcmWarningMacro( "Wrong Blue LUT descriptor" ); } - gdcmStaticDebugMacro(" lengthR " << lengthR << " debR " - << debR << " nbitsR " << nbitsR); - gdcmStaticDebugMacro(" lengthG " << lengthG << " debG " - << debG << " nbitsG " << nbitsG); - gdcmStaticDebugMacro(" lengthB " << lengthB << " debB " - << debB << " nbitsB " << nbitsB); + gdcmDebugMacro(" lengthR " << lengthR << " debR " + << debR << " nbitsR " << nbitsR); + gdcmDebugMacro(" lengthG " << lengthG << " debG " + << debG << " nbitsG " << nbitsG); + gdcmDebugMacro(" lengthB " << lengthB << " debB " + << debB << " nbitsB " << nbitsB); if ( !lengthR ) // if = 2^16, this shall be 0 see : CP-143 lengthR=65536; @@ -657,7 +695,7 @@ void PixelReadConvert::BuildLUTRGBA() if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) ) { - gdcmStaticWarningMacro( "(At least) a LUT is missing" ); + gdcmWarningMacro( "(At least) a LUT is missing" ); return; } @@ -735,7 +773,7 @@ void PixelReadConvert::BuildLUTRGBA() // with 65536 entries LUT ?!? // Still looking for accurate info on the web :-( - gdcmStaticWarningMacro( "Sorry Palette Color Lookup Tables not yet dealt with" + gdcmWarningMacro( "Sorry Palette Color Lookup Tables not yet dealt with" << " for 16 Bits Per Pixel images" ); // forge the 4 * 16 Bits Red/Green/Blue/Alpha LUT @@ -800,7 +838,7 @@ 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 @@ -831,7 +869,7 @@ void PixelReadConvert::ConvertSwapZone() int tempSwapCode = SwapCode; if ( IsPrivateGETransferSyntax ) { - gdcmStaticWarningMacro(" IsPrivateGETransferSyntax found; turn the SwapCode"); + gdcmWarningMacro(" IsPrivateGETransferSyntax found; turn the SwapCode"); // PrivateGETransferSyntax only exists for 'true' Dicom images // we assume there is no 'exotic' 32 bits endianess! if (SwapCode == 1234) @@ -860,7 +898,7 @@ void PixelReadConvert::ConvertSwapZone() } break; default: - gdcmStaticWarningMacro("SwapCode value (16 bits) not allowed." + gdcmWarningMacro("SwapCode value (16 bits) not allowed." << tempSwapCode); } } @@ -906,7 +944,7 @@ void PixelReadConvert::ConvertSwapZone() } break; default: - gdcmStaticWarningMacro("SwapCode value (32 bits) not allowed." << tempSwapCode ); + gdcmWarningMacro("SwapCode value (32 bits) not allowed." << tempSwapCode ); } } } @@ -1096,7 +1134,7 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) } else { - gdcmStaticWarningMacro("Weird image (BitsAllocated !=8, 12, 16, 32)"); + gdcmWarningMacro("Weird image (BitsAllocated !=8, 12, 16, 32)"); throw FormatError( "Weird image !?" ); } } @@ -1109,7 +1147,7 @@ bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError ) */ void PixelReadConvert::ConvertRGBPlanesToRGBPixels() { - gdcmStaticWarningMacro("--> ConvertRGBPlanesToRGBPixels"); + gdcmWarningMacro("--> ConvertRGBPlanesToRGBPixels"); uint8_t *localRaw = Raw; uint8_t *copyRaw = new uint8_t[ RawSize ]; @@ -1145,7 +1183,7 @@ void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels() // On such images, RLE achieves a compression ratio that is much better // than the compression ratio on an equivalent RGB image. - gdcmStaticWarningMacro("--> ConvertYcBcRPlanesToRGBPixels"); + gdcmWarningMacro("--> ConvertYcBcRPlanesToRGBPixels"); uint8_t *localRaw = Raw; uint8_t *copyRaw = new uint8_t[ RawSize ]; @@ -1156,7 +1194,9 @@ 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; @@ -1245,13 +1285,13 @@ void PixelReadConvert::ConvertHandleColor() // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels() // - [Planar 2] OR [Photo D] requires LUT intervention. - gdcmStaticDebugMacro("--> ConvertHandleColor " + gdcmDebugMacro("--> ConvertHandleColor " << "Planar Configuration " << PlanarConfiguration ); if ( ! IsRawRGB() ) { // [Planar 2] OR [Photo D]: LUT intervention done outside - gdcmStaticDebugMacro("--> RawRGB : LUT intervention done outside"); + gdcmDebugMacro("--> RawRGB : LUT intervention done outside"); return; } @@ -1260,13 +1300,13 @@ void PixelReadConvert::ConvertHandleColor() if ( IsYBRFull ) { // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB) - gdcmStaticDebugMacro("--> YBRFull"); + gdcmDebugMacro("--> YBRFull"); ConvertYcBcRPlanesToRGBPixels(); } else { // [Planar 1] AND [Photo C] - gdcmStaticDebugMacro("--> YBRFull"); + gdcmDebugMacro("--> YBRFull"); ConvertRGBPlanesToRGBPixels(); } return; @@ -1277,7 +1317,7 @@ void PixelReadConvert::ConvertHandleColor() if (IsRLELossless) { - gdcmStaticDebugMacro("--> RLE Lossless"); + gdcmDebugMacro("--> RLE Lossless"); ConvertRGBPlanesToRGBPixels(); } @@ -1296,7 +1336,7 @@ void PixelReadConvert::ComputeRawAndRGBSizes() bitsAllocated = 16; } - RawSize = XSize * YSize * ZSize + RawSize = XSize * YSize * ZSize * TSize * ( bitsAllocated / 8 ) * SamplesPerPixel; if ( HasLUT ) @@ -1352,7 +1392,7 @@ void PixelReadConvert::Print( std::ostream &os, std::string const &indent ) } else { - gdcmStaticWarningMacro("Set as RLE file but NO RLEinfo present."); + gdcmWarningMacro("Set as RLE file but NO RLEinfo present."); } } @@ -1364,11 +1404,39 @@ void PixelReadConvert::Print( std::ostream &os, std::string const &indent ) } else { - gdcmStaticWarningMacro("Set as JPEG file but NO JPEGinfo present."); + gdcmWarningMacro("Set as JPEG file but NO JPEGinfo present."); } } } +/** + * \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