X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=2faa65533b97252e4ae16041817351300ac834e9;hb=eb427dc05df82e0d814ea43533e7711ba35d189a;hp=02e6a08ad5618281327011bdc88f1b7c2a48a6de;hpb=c132b43ebda61490fe85f62a88969b6cfb9e400d;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 02e6a08a..2faa6553 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/10/15 10:43:27 $ - Version: $Revision: 1.144 $ + Date: $Date: 2004/11/15 15:29:04 $ + Version: $Revision: 1.154 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -18,6 +18,7 @@ #include "gdcmFile.h" #include "gdcmDebug.h" +#include namespace gdcm { @@ -72,6 +73,7 @@ File::File(std::string const & filename ) */ void File::Initialise() { + PixelConverter = NULL; //just in case if ( HeaderInternal->IsReadable() ) { ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); @@ -84,70 +86,8 @@ void File::Initialise() ImageDataSize = ImageDataSizeRaw; } - - - - // Just in case some access to a Header element requires disk access. - // Note: gdcmDocument::Fp is leaved open after OpenFile. - (void)HeaderInternal->OpenFile(); - // Number of Bits Allocated for storing a Pixel is defaulted to 16 - // when absent from the header. - int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); - if ( numberBitsAllocated == 0 ) - { - numberBitsAllocated = 16; - } - PixelConverter.SetBitsAllocated( numberBitsAllocated ); - - // Number of "Bits Stored" defaulted to number of "Bits Allocated" - // when absent from the header. - int numberBitsStored = HeaderInternal->GetBitsStored(); - if ( numberBitsStored == 0 ) - { - numberBitsStored = numberBitsAllocated; - } - PixelConverter.SetBitsStored( numberBitsStored ); - - // High Bit Position - int highBitPosition = HeaderInternal->GetHighBitPosition(); - if ( highBitPosition == 0 ) - { - highBitPosition = numberBitsAllocated - 1; - } - PixelConverter.SetHighBitPosition( highBitPosition ); - - - PixelConverter.SetXSize( HeaderInternal->GetXSize() ); - PixelConverter.SetYSize( HeaderInternal->GetYSize() ); - PixelConverter.SetZSize( HeaderInternal->GetZSize() ); - PixelConverter.SetSamplesPerPixel( HeaderInternal->GetSamplesPerPixel() ); - PixelConverter.SetPixelSize( HeaderInternal->GetPixelSize() ); - PixelConverter.SetPixelSign( HeaderInternal->IsSignedPixelData() ); - PixelConverter.SetSwapCode( HeaderInternal->GetSwapCode() ); - PixelConverter.SetIsUncompressed( - ! HeaderInternal->IsDicomV3() - || HeaderInternal->IsImplicitVRLittleEndianTransferSyntax() - || HeaderInternal->IsExplicitVRLittleEndianTransferSyntax() - || HeaderInternal->IsExplicitVRBigEndianTransferSyntax() - || HeaderInternal->IsDeflatedExplicitVRLittleEndianTransferSyntax() ); - PixelConverter.SetIsJPEG2000( HeaderInternal->IsJPEG2000() ); - PixelConverter.SetIsJPEGLossless( HeaderInternal->IsJPEGLossless() ); - PixelConverter.SetIsRLELossless( - HeaderInternal->IsRLELossLessTransferSyntax() ); - PixelConverter.SetPixelOffset( HeaderInternal->GetPixelOffset() ); - PixelConverter.SetPixelDataLength( HeaderInternal->GetPixelAreaLength() ); - PixelConverter.SetRLEInfo( &(HeaderInternal->RLEInfo) ); - PixelConverter.SetJPEGInfo( &(HeaderInternal->JPEGInfo) ); - PixelConverter.SetHasLUT( HeaderInternal->HasLUT() ); - - PixelConverter.SetPlanarConfiguration( - HeaderInternal->GetPlanarConfiguration() ); - PixelConverter.SetIsMonochrome( HeaderInternal->IsMonochrome() ); - PixelConverter.SetIsPaletteColor( HeaderInternal->IsPaletteColor() ); - PixelConverter.SetIsYBRFull( HeaderInternal->IsYBRFull() ); - - HeaderInternal->CloseFile(); - + PixelConverter = new PixelConvert; //LEAK ! + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); } SaveInitialValues(); } @@ -166,6 +106,11 @@ File::~File() HeaderInternal = 0; DeleteInitialValues(); + if( PixelConverter ) + { + delete PixelConverter; + } + } /** @@ -335,7 +280,7 @@ int File::ComputeDecompressedPixelDataSizeFromHeader() // - it is not defined (i.e. it's value is 0) // - it's 12, since we will expand the image to 16 bits (see // PixelConvert::ConvertDecompress12BitsTo16Bits() ) - if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) + if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) { numberBitsAllocated = 16; } @@ -361,33 +306,86 @@ int File::ComputeDecompressedPixelDataSizeFromHeader() */ uint8_t* File::GetImageData() { - // FIXME (Mathieu) - // I need to deallocate Pixel_Data before doing any allocation: - - if ( Pixel_Data ) - if ( LastAllocatedPixelDataLength != ImageDataSize ) - free(Pixel_Data); - if ( !Pixel_Data ) - Pixel_Data = new uint8_t[ImageDataSize]; - - if ( Pixel_Data ) + if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + uint8_t* pixelData; + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + pixelData = PixelConverter->GetRGB(); + } + else { - LastAllocatedPixelDataLength = ImageDataSize; + // When no LUT or LUT conversion fails, return the decompressed + pixelData = PixelConverter->GetDecompressed(); + } - // we load the pixels (and transform grey level + LUT into RGB) - GetImageDataIntoVector(Pixel_Data, ImageDataSize); +// PIXELCONVERT CLEANME + // Restore the header in a disk-consistent state + // (if user asks twice to get the pixels from disk) + if ( PixelRead != -1 ) // File was "read" before + { + RestoreInitialValues(); + } + if ( PixelConverter->GetRGB() ) + { + // now, it's an RGB image + // Lets's write it in the Header + std::string spp = "3"; // Samples Per Pixel + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + std::string rgb = "RGB "; // Photometric Interpretation + HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004); + std::string planConfig = "0"; // Planar Configuration + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); + PixelRead = 0; // no PixelRaw + } + else + { + if ( HeaderInternal->HasLUT() ) + { + // The LUT interpretation failed + std::string photometricInterpretation = "MONOCHROME1 "; + HeaderInternal->SetEntryByNumber( photometricInterpretation, + 0x0028, 0x0004 ); + PixelRead = 0; // no PixelRaw + } + else + { + if ( PixelConverter->IsDecompressedRGB() ) + { + /////////////////////////////////////////////////// + // now, it's an RGB image + // Lets's write it in the Header + // Droping Palette Color out of the Header + // has been moved to the Write process. + // TODO : move 'values' modification to the write process + // : save also (in order to be able to restore) + // : 'high bit' -when not equal to 'bits stored' + 1 + // : 'bits allocated', when it's equal to 12 ?! + std::string spp = "3"; // Samples Per Pixel + std::string photInt = "RGB "; // Photometric Interpretation + std::string planConfig = "0"; // Planar Configuration + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); + } + PixelRead = 1; // PixelRaw + } + } - // We say the value *is* loaded. - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - // Will be 7fe0, 0010 in standard case - GetHeader()->SetEntryBinAreaByNumber( Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } - PixelRead = 0; // no PixelRaw + // Will be 7fe0, 0010 in standard case + GetHeader()->SetEntryBinAreaByNumber( pixelData, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); +// END PIXELCONVERT CLEANME - return Pixel_Data; + return pixelData; } /** @@ -417,60 +415,37 @@ uint8_t* File::GetImageData() */ size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) { - GetImageDataIntoVectorRaw (destination, maxSize); - PixelRead = 0 ; // =0 : no ImageDataRaw - if ( !HeaderInternal->HasLUT() ) + if ( ! GetDecompressed() ) { - return ImageDataSize; + // If the decompression failed nothing can be done. + return 0; } - - // from Lut R + Lut G + Lut B - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *a = (uint8_t *)destination; - uint8_t *lutRGBA = HeaderInternal->GetLUTRGBA(); - if ( lutRGBA ) + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) { - int j; - // move Gray pixels to temp area - memmove(newDest, destination, ImageDataSizeRaw); - for (size_t i=0; iGetRGBSize() > maxSize ) { - // Build RGB Pixels - j = newDest[i]*4; - *a++ = lutRGBA[j]; - *a++ = lutRGBA[j+1]; - *a++ = lutRGBA[j+2]; + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; } - delete[] newDest; - - // now, it's an RGB image - // Lets's write it in the Header - - // FIXME : Better use CreateOrReplaceIfExist ? - - std::string spp = "3"; // Samples Per Pixel - HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); - std::string rgb = "RGB "; // Photometric Interpretation - HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004); - std::string planConfig = "0"; // Planar Configuration - HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); - + memmove( destination, + (void*)PixelConverter->GetRGB(), + PixelConverter->GetRGBSize() ); + return PixelConverter->GetRGBSize(); } - else // GetLUTRGBA() failed - { - // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color - // that are *more* than 65535 long ?!? - // No idea how to manage such an image ! - // Need to make RGB Pixels (?) from grey Pixels (?!) and Gray Lut (!?!) - // It seems that *no Dicom Viewer* has any idea :-( - - std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation - HeaderInternal->SetEntryByNumber(photomInterp,0x0028,0x0004); - } - /// \todo Drop Palette Color out of the Header? - return ImageDataSize; + // Either no LUT conversion necessary or LUT conversion failed + if ( PixelConverter->GetDecompressedSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memmove( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + return PixelConverter->GetDecompressedSize(); } /** @@ -484,118 +459,71 @@ size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) */ uint8_t* File::GetImageDataRaw () { - size_t imgDataSize; - if ( HeaderInternal->HasLUT() ) - /// \todo Let Header user a chance to get the right value - imgDataSize = ImageDataSizeRaw; - else - imgDataSize = ImageDataSize; - - // FIXME (Mathieu) - // I need to deallocate Pixel_Data before doing any allocation: - - if ( Pixel_Data ) - if ( LastAllocatedPixelDataLength != imgDataSize ) - free(Pixel_Data); - if ( !Pixel_Data ) - Pixel_Data = new uint8_t[imgDataSize]; + uint8_t* decompressed = GetDecompressed(); + if ( ! decompressed ) + { + return 0; + } - if ( Pixel_Data ) +// PIXELCONVERT CLEANME + // Restore the header in a disk-consistent state + // (if user asks twice to get the pixels from disk) + if ( PixelRead != -1 ) // File was "read" before { - LastAllocatedPixelDataLength = imgDataSize; - - // we load the pixels ( grey level or RGB, but NO transformation) - GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize); + RestoreInitialValues(); + } + if ( PixelConverter->IsDecompressedRGB() ) + { + /////////////////////////////////////////////////// + // now, it's an RGB image + // Lets's write it in the Header + // Droping Palette Color out of the Header + // has been moved to the Write process. + // TODO : move 'values' modification to the write process + // : save also (in order to be able to restore) + // : 'high bit' -when not equal to 'bits stored' + 1 + // : 'bits allocated', when it's equal to 12 ?! + std::string spp = "3"; // Samples Per Pixel + std::string photInt = "RGB "; // Photometric Interpretation + std::string planConfig = "0"; // Planar Configuration + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); + } - // We say the value *is* loaded. - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // will be 7fe0, 0010 in standard cases + GetHeader()->SetEntryBinAreaByNumber( decompressed, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - // will be 7fe0, 0010 in standard cases - GetHeader()->SetEntryBinAreaByNumber(Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } PixelRead = 1; // PixelRaw +// END PIXELCONVERT CLEANME - return Pixel_Data; + return decompressed; } -/** - * \brief Copies at most MaxSize bytes of pixel data to caller's - * memory space. - * \warning This function was designed to avoid people that want to build - * a volume from an image stack to need first to get the image pixels - * and then move them to the volume area. - * It's absolutely useless for any VTK user since vtk chooses - * to invert the lines of an image, that is the last line comes first - * (for some axis related reasons?). Hence he will have - * to load the image line by line, starting from the end. - * VTK users hace to call GetImageData - * \warning DOES NOT transform the Grey Plane + Palette Color (if any) - * into a single RGB Pixels Plane - * the (VTK) user will manage the palettes - * - * @param destination Address (in caller's memory space) at which the - * pixel data should be copied - * @param maxSize Maximum number of bytes to be copied. When MaxSize - * is not sufficient to hold the pixel data the copy is not - * executed (i.e. no partial copy). - * @return On success, the number of bytes actually copied. Zero on - * failure e.g. MaxSize is lower than necessary. - */ -void File::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) +uint8_t* File::GetDecompressed() { - // we save the initial values of the following - // in order to be able to restore the header in a disk-consistent state - // (if user asks twice to get the pixels from disk) - - if ( PixelRead != -1 ) // File was "read" before - { - RestoreInitialValues(); - } - - PixelRead = 1 ; // PixelRaw - - if ( ImageDataSize > maxSize ) - { - dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return; - } - - FILE* fp = HeaderInternal->OpenFile(); - PixelConverter.ReadAndDecompressPixelData( fp ); - HeaderInternal->CloseFile(); - memmove( destination, - (void*)PixelConverter.GetDecompressed(), - PixelConverter.GetDecompressedSize() ); - - if ( ! PixelConverter.IsDecompressedRGB() ) + uint8_t* decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) { - return; + // The decompressed image migth not be loaded yet: + std::ifstream* fp = HeaderInternal->OpenFile(); + PixelConverter->ReadAndDecompressPixelData( fp ); + if(fp) HeaderInternal->CloseFile(); + decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + dbg.Verbose(0, "File::GetDecompressed: read/decompress of " + "pixel data apparently went wrong."); + return 0; + } } -/////////////////////////////////////////////////// - // now, it's an RGB image - // Lets's write it in the Header - - // Droping Palette Color out of the Header - // has been moved to the Write process. - - // TODO : move 'values' modification to the write process - // : save also (in order to be able to restore) - // : 'high bit' -when not equal to 'bits stored' + 1 - // : 'bits allocated', when it's equal to 12 ?! - - std::string spp = "3"; // Samples Per Pixel - std::string photInt = "RGB "; // Photometric Interpretation - std::string planConfig = "0"; // Planar Configuration - - HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); - HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); - HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); - - return; + return decompressed; } /** @@ -633,14 +561,14 @@ bool File::SetImageData(uint8_t* inData, size_t expectedSize) bool File::WriteRawData(std::string const & fileName) { - FILE* fp1 = fopen(fileName.c_str(), "wb"); - if (fp1 == NULL) + std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); + if (!fp1) { - printf("Fail to open (write) file [%s] \n", fileName.c_str()); + dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); return false; } - fwrite (Pixel_Data, ImageDataSize, 1, fp1); - fclose (fp1); + fp1.write((char*)Pixel_Data, ImageDataSize); + fp1.close(); return true; } @@ -708,22 +636,21 @@ bool File::WriteBase (std::string const & fileName, FileType type) return false; } - FILE* fp1 = fopen(fileName.c_str(), "wb"); + std::ofstream* fp1 = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); if (fp1 == NULL) { - printf("Failed to open (write) File [%s] \n", fileName.c_str()); + dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); return false; } if ( type == ImplicitVR || type == ExplicitVR ) { // writing Dicom File Preamble - uint8_t* filePreamble = new uint8_t[128]; + char filePreamble[128]; memset(filePreamble, 0, 128); - fwrite(filePreamble, 128, 1, fp1); - fwrite("DICM", 4, 1, fp1); - - delete[] filePreamble; + fp1->write(filePreamble, 128); + fp1->write("DICM", 4); } // -------------------------------------------------------------- @@ -778,12 +705,19 @@ bool File::WriteBase (std::string const & fileName, FileType type) HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- - - // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now - fclose (fp1); + fp1->close (); + delete fp1; return true; } +/** + * \brief Access to the underlying \ref PixelConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); +} + } // end namespace gdcm