X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=837df465e8139d9a30e94288c38bbb71e6ec6dc0;hb=bac2910466f502dec4c1842527aa81a8f83f04b8;hp=da8105e3b8eaca4f2bb10fb1851c8397f510ae9e;hpb=e28b183ba68aa3cc84a44a779a31f9d906a1ad2f;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index da8105e3..837df465 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/10/18 12:49:22 $ - Version: $Revision: 1.145 $ + Date: $Date: 2004/11/16 16:20:23 $ + Version: $Revision: 1.157 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -18,6 +18,9 @@ #include "gdcmFile.h" #include "gdcmDebug.h" +#include "gdcmUtil.h" +#include "gdcmBinEntry.h" +#include namespace gdcm { @@ -72,6 +75,7 @@ File::File(std::string const & filename ) */ void File::Initialise() { + PixelConverter = NULL; //just in case if ( HeaderInternal->IsReadable() ) { ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); @@ -84,7 +88,8 @@ void File::Initialise() ImageDataSize = ImageDataSizeRaw; } - PixelConverter.GrabInformationsFromHeader( HeaderInternal ); + PixelConverter = new PixelConvert; + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); } SaveInitialValues(); } @@ -103,6 +108,10 @@ File::~File() HeaderInternal = 0; DeleteInitialValues(); + if( PixelConverter ) + { + delete PixelConverter; + } } /** @@ -128,7 +137,7 @@ void File::SaveInitialValues() InitialRedLUTData = 0; InitialGreenLUTData = 0; InitialBlueLUTData = 0; - + if ( HeaderInternal->IsReadable() ) { // the following values *may* be modified @@ -203,28 +212,29 @@ void File::RestoreInitialValues() */ void File::DeleteInitialValues() { - // InitialLutDescriptors and InitialLutData // will have to be deleted if the don't belong any longer // to the Header H table when the header is deleted... - if ( InitialRedLUTDescr ) +// FIXME +// We don't know if the InitialLutData are still in the header or not ! +/* if ( InitialRedLUTDescr ) delete InitialRedLUTDescr; if ( InitialGreenLUTDescr ) delete InitialGreenLUTDescr; - if ( InitialBlueLUTDescr ) - delete InitialBlueLUTDescr; + if ( InitialBlueLUTDescr ) + delete InitialBlueLUTDescr; - if ( InitialRedLUTData ) + if ( InitialRedLUTData ) delete InitialRedLUTData; - if ( InitialGreenLUTData != NULL) + if ( InitialGreenLUTData ) delete InitialGreenLUTData; - if ( InitialBlueLUTData != NULL) - delete InitialBlueLUTData; + if ( InitialBlueLUTData ) + delete InitialBlueLUTData;*/ } //----------------------------------------------------------------------------- @@ -272,7 +282,7 @@ 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; } @@ -298,33 +308,81 @@ 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() ) { - LastAllocatedPixelDataLength = ImageDataSize; - - // we load the pixels (and transform grey level + LUT into RGB) - GetImageDataIntoVector(Pixel_Data, ImageDataSize); + // If the decompression failed nothing can be done. + return 0; + } + + uint8_t* pixelData; + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + pixelData = PixelConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the decompressed + pixelData = PixelConverter->GetDecompressed(); + } - // We say the value *is* loaded. - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); +// 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 = Util::DicomString("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 + } + } - // Will be 7fe0, 0010 in standard case - GetHeader()->SetEntryBinAreaByNumber( Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } - PixelRead = 0; // no PixelRaw + // We say the value *is* loaded. + SetPixelData(pixelData); +// END PIXELCONVERT CLEANME - return Pixel_Data; + return pixelData; } /** @@ -354,50 +412,37 @@ 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; } - - FILE* fp = HeaderInternal->OpenFile(); - if ( PixelConverter.BuildRGBImage( fp ) ) - { - memmove( destination, - (void*)PixelConverter.GetRGB(), - PixelConverter.GetRGBSize() ); - - // 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); + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + if ( PixelConverter->GetRGBSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memcpy( destination, + (void*)PixelConverter->GetRGB(), + PixelConverter->GetRGBSize() ); + return PixelConverter->GetRGBSize(); } - else - { - // PixelConverter.BuildRGBImage( fp ) failed probably because - // PixelConverter.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); - } - HeaderInternal->CloseFile(); - /// \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; + } + memcpy( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + return PixelConverter->GetDecompressedSize(); } /** @@ -411,118 +456,72 @@ 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());*/ + SetPixelData(decompressed); - // 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; } /** @@ -560,14 +559,14 @@ 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; } @@ -635,22 +634,21 @@ 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); } // -------------------------------------------------------------- @@ -705,20 +703,37 @@ 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 PixelConvertver RGBA LUT + * \brief Access to the underlying \ref PixelConverter RGBA LUT */ uint8_t* File::GetLutRGBA() { - return PixelConverter.GetLutRGBA(); + return PixelConverter->GetLutRGBA(); } +//----------------------------------------------------------------------------- +// Private +void File::SetPixelData(uint8_t* data) +{ + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // Will be 7fe0, 0010 in standard case + DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + if ( currentEntry ) + { + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + // Flag is to false because datas are kept in the gdcmPixelConvert + binEntry->SetBinArea( data, false ); + } +} + +//----------------------------------------------------------------------------- } // end namespace gdcm