X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmPixelReadConvert.cxx;h=ee0eb6cff9a46c2b42bd60fedb78dff3bb8315ed;hb=f58d0f1e0e1680554dcd631817b7f81968fdb950;hp=c98ffa17f632c49770815037bb06820321c00056;hpb=01a09cfd14749a3536a0787893dc895d402f40b5;p=gdcm.git diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index c98ffa17..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: 2005/11/30 11:44:38 $ - Version: $Revision: 1.107 $ + 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 +85,9 @@ 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 @@ -93,6 +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(); @@ -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; @@ -130,14 +140,16 @@ 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 @@ -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? @@ -310,15 +324,6 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) 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()) { gdcmWarningMacro( "Reading of Raw pixel data failed." ); @@ -328,7 +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; @@ -450,7 +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 ) @@ -586,9 +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; } @@ -600,7 +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 : @@ -837,7 +843,7 @@ 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 @@ -1193,7 +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; @@ -1333,7 +1341,7 @@ void PixelReadConvert::ComputeRawAndRGBSizes() bitsAllocated = 16; } - RawSize = XSize * YSize * ZSize + RawSize = XSize * YSize * ZSize * TSize * ( bitsAllocated / 8 ) * SamplesPerPixel; if ( HasLUT ) @@ -1343,7 +1351,10 @@ void PixelReadConvert::ComputeRawAndRGBSizes() else { RGBSize = RawSize; + } + RawSize += RawSize%2; + RGBSize += RGBSize%2; } /// Allocates room for RGB Pixels