X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=d198c1c96c7c1f19cfef5ac4d8a1493ab23f2540;hb=d01d35846e6b6918f2e11b2f15e13555e78a39b6;hp=323cdba54346ab1add3ab41eb4006c14a11459e3;hpb=15424662ec90f5a5071bcf32e7f6dc09cead024d;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 323cdba5..d198c1c9 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/10/08 17:02:53 $ - Version: $Revision: 1.136 $ + Date: $Date: 2004/11/23 11:14:13 $ + Version: $Revision: 1.159 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -18,16 +18,19 @@ #include "gdcmFile.h" #include "gdcmDebug.h" -#include "gdcmPixelConvert.h" -#include "jpeg/ljpg/jpegless.h" +#include "gdcmUtil.h" +#include "gdcmBinEntry.h" +#include +namespace gdcm +{ typedef std::pair IterHT; //------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (gdcmHeader only deals with the ... header) + * file (Header only deals with the ... header) * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. * It will be up to the user to load the pixels into memory @@ -37,18 +40,18 @@ typedef std::pair IterHT; * This avoid a double parsing of public part of the header when * user sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). - * @param header already built gdcmHeader + * @param header already built Header */ -gdcmFile::gdcmFile(gdcmHeader *header) +File::File(Header *header) { - Header = header; + HeaderInternal = header; SelfHeader = false; Initialise(); } /** * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (gdcmHeader only deals with the ... header) + * file (Header only deals with the ... header) * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. * It will be up to the user to load the pixels into memory @@ -60,9 +63,9 @@ gdcmFile::gdcmFile(gdcmHeader *header) * seen as a side effect). * @param filename file to be opened for parsing */ -gdcmFile::gdcmFile(std::string const & filename ) +File::File(std::string const & filename ) { - Header = new gdcmHeader( filename ); + HeaderInternal = new Header( filename ); SelfHeader = true; Initialise(); } @@ -70,12 +73,17 @@ gdcmFile::gdcmFile(std::string const & filename ) /** * \brief Factorization for various forms of constructors. */ -void gdcmFile::Initialise() +void File::Initialise() { - if ( Header->IsReadable() ) + WriteMode = WMODE_DECOMPRESSED; + WriteType = WTYPE_IMPL_VR; + PixelConverter = NULL; //just in case + Archive = NULL; + + if ( HeaderInternal->IsReadable() ) { ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); - if ( Header->HasLUT() ) + if ( HeaderInternal->HasLUT() ) { ImageDataSize = 3 * ImageDataSizeRaw; } @@ -83,22 +91,37 @@ void gdcmFile::Initialise() { ImageDataSize = ImageDataSizeRaw; } + + PixelConverter = new PixelConvert; + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + + Archive = new DocEntryArchive( HeaderInternal ); } + SaveInitialValues(); } /** * \brief canonical destructor - * \note If the gdcmHeader was created by the gdcmFile constructor, - * it is destroyed by the gdcmFile + * \note If the Header was created by the File constructor, + * it is destroyed by the File */ -gdcmFile::~gdcmFile() +File::~File() { + if( PixelConverter ) + { + delete PixelConverter; + } + if( Archive ) + { + delete Archive; + } + if( SelfHeader ) { - delete Header; + delete HeaderInternal; } - Header = 0; + HeaderInternal = 0; DeleteInitialValues(); } @@ -107,9 +130,8 @@ gdcmFile::~gdcmFile() * \brief Sets some initial values for the Constructor * \warning not end user intended */ -void gdcmFile::SaveInitialValues() +void File::SaveInitialValues() { - PixelRead = -1; // no ImageData read yet. LastAllocatedPixelDataLength = 0; Pixel_Data = 0; @@ -126,29 +148,29 @@ void gdcmFile::SaveInitialValues() InitialRedLUTData = 0; InitialGreenLUTData = 0; InitialBlueLUTData = 0; - - if ( Header->IsReadable() ) + + if ( HeaderInternal->IsReadable() ) { // the following values *may* be modified - // by gdcmFile::GetImageDataIntoVectorRaw + // by File::GetImageDataIntoVectorRaw // we save their initial value. - InitialSpp = Header->GetEntryByNumber(0x0028,0x0002); - InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004); - InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006); + InitialSpp = HeaderInternal->GetEntryByNumber(0x0028,0x0002); + InitialPhotInt = HeaderInternal->GetEntryByNumber(0x0028,0x0004); + InitialPlanConfig = HeaderInternal->GetEntryByNumber(0x0028,0x0006); - InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); - InitialHighBit = Header->GetEntryByNumber(0x0028,0x0102); + InitialBitsAllocated = HeaderInternal->GetEntryByNumber(0x0028,0x0100); + InitialHighBit = HeaderInternal->GetEntryByNumber(0x0028,0x0102); // the following entries *may* be removed from the H table - // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw + // (NOT deleted ...) by File::GetImageDataIntoVectorRaw // we keep a pointer on them. - InitialRedLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1101); - InitialGreenLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1102); - InitialBlueLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1103); + InitialRedLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1101); + InitialGreenLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1102); + InitialBlueLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1103); - InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201); - InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202); - InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203); + InitialRedLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1201); + InitialGreenLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1202); + InitialBlueLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1203); } } @@ -156,42 +178,42 @@ void gdcmFile::SaveInitialValues() * \brief restores some initial values * \warning not end user intended */ -void gdcmFile::RestoreInitialValues() +void File::RestoreInitialValues() { - if ( Header->IsReadable() ) + if ( HeaderInternal->IsReadable() ) { // the following values *may* have been modified - // by gdcmFile::GetImageDataIntoVectorRaw + // by File::GetImageDataIntoVectorRaw // we restore their initial value. if ( InitialSpp != "") - Header->SetEntryByNumber(InitialSpp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(InitialSpp,0x0028,0x0002); if ( InitialPhotInt != "") - Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); if ( InitialPlanConfig != "") - Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); + HeaderInternal->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); if ( InitialBitsAllocated != "") - Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); + HeaderInternal->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); if ( InitialHighBit != "") - Header->SetEntryByNumber(InitialHighBit,0x0028,0x0102); + HeaderInternal->SetEntryByNumber(InitialHighBit,0x0028,0x0102); // the following entries *may* be have been removed from the H table - // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw + // (NOT deleted ...) by File::GetImageDataIntoVectorRaw // we restore them. if (InitialRedLUTDescr) - Header->AddEntry(InitialRedLUTDescr); + HeaderInternal->AddEntry(InitialRedLUTDescr); if (InitialGreenLUTDescr) - Header->AddEntry(InitialGreenLUTDescr); + HeaderInternal->AddEntry(InitialGreenLUTDescr); if (InitialBlueLUTDescr) - Header->AddEntry(InitialBlueLUTDescr); + HeaderInternal->AddEntry(InitialBlueLUTDescr); if (InitialRedLUTData) - Header->AddEntry(InitialBlueLUTDescr); + HeaderInternal->AddEntry(InitialBlueLUTDescr); if (InitialGreenLUTData) - Header->AddEntry(InitialGreenLUTData); + HeaderInternal->AddEntry(InitialGreenLUTData); if (InitialBlueLUTData) - Header->AddEntry(InitialBlueLUTData); + HeaderInternal->AddEntry(InitialBlueLUTData); } } @@ -199,30 +221,31 @@ void gdcmFile::RestoreInitialValues() * \brief delete initial values (il they were saved) * of InitialLutDescriptors and InitialLutData */ -void gdcmFile::DeleteInitialValues() +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;*/ } //----------------------------------------------------------------------------- @@ -237,7 +260,7 @@ void gdcmFile::DeleteInitialValues() * \warning : it is NOT the group 7FE0 length * (no interest for compressed images). */ -int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader() +int File::ComputeDecompressedPixelDataSizeFromHeader() { // see PS 3.3-2003 : C.7.6.3.2.1 // @@ -265,18 +288,21 @@ int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader() // 0028|1202 [US] [Green Palette Color Lookup Table Data] // 0028|1203 [US] [Blue Palette Color Lookup Table Data] - // Number of "Bits Allocated" - int numberBitsAllocated = Header->GetBitsAllocated(); - if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + // Number of "Bits Allocated" is fixed to 16 when: + // - 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 ) { numberBitsAllocated = 16; } - int DecompressedSize = Header->GetXSize() - * Header->GetYSize() - * Header->GetZSize() + int DecompressedSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() * ( numberBitsAllocated / 8 ) - * Header->GetSamplesPerPixel(); + * HeaderInternal->GetSamplesPerPixel(); return DecompressedSize; } @@ -291,35 +317,83 @@ int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader() * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ -uint8_t* gdcmFile::GetImageData() +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; } /** @@ -347,62 +421,39 @@ uint8_t* gdcmFile::GetImageData() * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ -size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) +size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) { - GetImageDataIntoVectorRaw (destination, maxSize); - PixelRead = 0 ; // =0 : no ImageDataRaw - if ( !Header->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 = Header->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 - Header->SetEntryByNumber(spp,0x0028,0x0002); - std::string rgb = "RGB "; // Photometric Interpretation - Header->SetEntryByNumber(rgb,0x0028,0x0004); - std::string planConfig = "0"; // Planar Configuration - Header->SetEntryByNumber(planConfig,0x0028,0x0006); - + memcpy( 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 - Header->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; + } + memcpy( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + return PixelConverter->GetDecompressedSize(); } /** @@ -414,319 +465,68 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -uint8_t* gdcmFile::GetImageDataRaw () -{ - size_t imgDataSize; - if ( Header->HasLUT() ) - /// \todo Let gdcmHeader 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]; - - if ( Pixel_Data ) - { - LastAllocatedPixelDataLength = imgDataSize; - - // we load the pixels ( grey level or RGB, but NO transformation) - GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize); - - // We say the value *is* loaded. - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - - // will be 7fe0, 0010 in standard cases - GetHeader()->SetEntryBinAreaByNumber(Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } - PixelRead = 1; // PixelRaw - - return Pixel_Data; -} - -/** - * \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. - */ -size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) +uint8_t* File::GetImageDataRaw () { - // 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, "gdcmFile::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return (size_t)0; - } - - ReadPixelData( destination ); - - // Number of Bits Allocated for storing a Pixel - int numberBitsAllocated = Header->GetBitsAllocated(); - if ( numberBitsAllocated == 0 ) - { - numberBitsAllocated = 16; - } - - // Number of Bits actually used - int numberBitsStored = Header->GetBitsStored(); - if ( numberBitsStored == 0 ) - { - numberBitsStored = numberBitsAllocated; - } - - // High Bit Position - int highBitPosition = Header->GetHighBitPosition(); - if ( highBitPosition == 0 ) - { - highBitPosition = numberBitsAllocated - 1; - } - - bool signedPixel = Header->IsSignedPixelData(); - - gdcmPixelConvert::ConvertReorderEndianity( - (uint8_t*) destination, - ImageDataSize, - numberBitsStored, - numberBitsAllocated, - Header->GetSwapCode(), - signedPixel ); - - ConvertReArrangeBits( (uint8_t*) destination, - ImageDataSize, - numberBitsStored, - numberBitsAllocated, - highBitPosition ); - -#ifdef GDCM_DEBUG - FILE* DebugFile; - DebugFile = fopen( "SpuriousFile.RAW", "wb" ); - fwrite( PixelConvertor.GetUncompressed(), - PixelConvertor.GetUncompressedsSize(), - 1, DebugFile ); - fclose( DebugFile ); -#endif //GDCM_DEBUG - -// SPLIT ME -////////////////////////////////// -// Deal with the color - - // Monochrome pictures don't require color intervention - if ( Header->IsMonochrome() ) - { - return ImageDataSize; - } - - // Planar configuration = 0 : Pixels are already RGB - // Planar configuration = 1 : 3 planes : R, G, B - // Planar configuration = 2 : 1 gray Plane + 3 LUT - - // Well ... supposed to be ! - // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0, - // PhotometricInterpretation=PALETTE COLOR - // and heuristic has to be found :-( - - int planConf = Header->GetPlanarConfiguration(); - - // Planar configuration = 2 ==> 1 gray Plane + 3 LUT - // ...and... - // whatever the Planar Configuration might be, "PALETTE COLOR " - // implies that we deal with the palette. - if ( ( planConf == 2 ) || Header->IsPaletteColor() ) + uint8_t* decompressed = GetDecompressed(); + if ( ! decompressed ) { - return ImageDataSize; + return 0; } - // When planConf is 0, pixels are allready in RGB - - if ( planConf == 1 ) +/*// 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 { - uint8_t* newDest = new uint8_t[ImageDataSize]; - // Warning : YBR_FULL_422 acts as RGB - if ( Header->IsYBRFull() ) - { - ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest); - } - else - { - ConvertRGBPlanesToRGBPixels((uint8_t*)destination, newDest); - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - -/////////////////////////////////////////////////// - // 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 - - Header->SetEntryByNumber(spp,0x0028,0x0002); - Header->SetEntryByNumber(photInt,0x0028,0x0004); - Header->SetEntryByNumber(planConfig,0x0028,0x0006); + 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. + SetPixelData(decompressed); - return ImageDataSize; -} + PixelRead = 1; // PixelRaw +// END PIXELCONVERT CLEANME*/ -/** - * \brief Re-arrange the bits within the bytes. - */ -void gdcmFile::ConvertReArrangeBits( uint8_t* pixelZone, - size_t imageDataSize, - int numberBitsStored, - int numberBitsAllocated, - int highBitPosition) - throw ( gdcmFormatError ) -{ - if ( numberBitsStored != numberBitsAllocated ) - { - int l = (int)(imageDataSize / (numberBitsAllocated/8)); - if ( numberBitsAllocated == 16 ) - { - uint16_t mask = 0xffff; - mask = mask >> ( numberBitsAllocated - numberBitsStored ); - uint16_t* deb = (uint16_t*)pixelZone; - for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; - deb++; - } - } - else if ( numberBitsAllocated == 32 ) - { - uint32_t mask = 0xffffffff; - mask = mask >> ( numberBitsAllocated - numberBitsStored ); - uint32_t* deb = (uint32_t*)pixelZone; - for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; - deb++; - } - } - else - { - dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image"); - throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()", - "weird image !?" ); - } - } + return decompressed; } -/** - * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels - * \warning Works on all the frames at a time - */ -void gdcmFile::ConvertYcBcRPlanesToRGBPixels(uint8_t* source, - uint8_t* destination) +uint8_t* File::GetDecompressed() { - // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : - // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf - // and be *very* affraid - // - int l = Header->GetXSize() * Header->GetYSize(); - int nbFrames = Header->GetZSize(); - - uint8_t* a = source; - uint8_t* b = source + l; - uint8_t* c = source + l + l; - double R, G, B; - - /// \todo : Replace by the 'well known' integer computation - /// counterpart. Refer to - /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - /// for code optimisation. - - for (int i = 0; i < nbFrames; i++) - { - for (int j = 0; j < l; j++) + uint8_t* decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + // 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 ) { - R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; - G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; - B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; - - if (R < 0.0) R = 0.0; - if (G < 0.0) G = 0.0; - if (B < 0.0) B = 0.0; - if (R > 255.0) R = 255.0; - if (G > 255.0) G = 255.0; - if (B > 255.0) B = 255.0; - - *(destination++) = (uint8_t)R; - *(destination++) = (uint8_t)G; - *(destination++) = (uint8_t)B; - a++; - b++; - c++; + dbg.Verbose(0, "File::GetDecompressed: read/decompress of " + "pixel data apparently went wrong."); + return 0; } } -} - -/** - * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels - * \warning Works on all the frames at a time - */ -void gdcmFile::ConvertRGBPlanesToRGBPixels(uint8_t* source, - uint8_t* destination) -{ - int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); - - uint8_t* a = source; - uint8_t* b = source + l; - uint8_t* c = source + l + l; - for (int j = 0; j < l; j++) - { - *(destination++) = *(a++); - *(destination++) = *(b++); - *(destination++) = *(c++); - } + return decompressed; } /** @@ -742,9 +542,9 @@ void gdcmFile::ConvertRGBPlanesToRGBPixels(uint8_t* source, * * @return boolean */ -bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize) +bool File::SetImageData(uint8_t* inData, size_t expectedSize) { - Header->SetImageDataSize( expectedSize ); + HeaderInternal->SetImageDataSize( expectedSize ); // FIXME : if already allocated, memory leak ! Pixel_Data = inData; ImageDataSize = ImageDataSizeRaw = expectedSize; @@ -762,16 +562,16 @@ bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize) * @return false if write fails */ -bool gdcmFile::WriteRawData(std::string const & fileName) +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; } @@ -785,9 +585,10 @@ bool gdcmFile::WriteRawData(std::string const & fileName) * @return false if write fails */ -bool gdcmFile::WriteDcmImplVR (std::string const & fileName) +bool File::WriteDcmImplVR (std::string const & fileName) { - return WriteBase(fileName, gdcmImplicitVR); + SetWriteTypeToDcmImplVR(); + return Write(fileName); } /** @@ -798,9 +599,10 @@ bool gdcmFile::WriteDcmImplVR (std::string const & fileName) * @return false if write fails */ -bool gdcmFile::WriteDcmExplVR (std::string const & fileName) +bool File::WriteDcmExplVR (std::string const & fileName) { - return WriteBase(fileName, gdcmExplicitVR); + SetWriteTypeToDcmExplVR(); + return Write(fileName); } /** @@ -817,9 +619,24 @@ bool gdcmFile::WriteDcmExplVR (std::string const & fileName) * @return false if write fails */ -bool gdcmFile::WriteAcr (std::string const & fileName) +bool File::WriteAcr (std::string const & fileName) { - return WriteBase(fileName, gdcmACR); + SetWriteTypeToAcr(); + return Write(fileName); +} + +bool File::Write(std::string const& fileName) +{ + switch(WriteType) + { + case WTYPE_IMPL_VR: + return WriteBase(fileName,ImplicitVR); + case WTYPE_EXPL_VR: + return WriteBase(fileName,ExplicitVR); + case WTYPE_ACR: + return WriteBase(fileName,ACR); + } + return(false); } //----------------------------------------------------------------------------- @@ -832,29 +649,41 @@ bool gdcmFile::WriteAcr (std::string const & fileName) * @param type file type (ExplicitVR, ImplicitVR, ...) * @return false if write fails */ -bool gdcmFile::WriteBase (std::string const & fileName, FileType type) +bool File::WriteBase (std::string const & fileName, FileType type) { - if ( PixelRead == -1 && type != gdcmExplicitVR) + if ( PixelRead == -1 && type != ExplicitVR) { 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 == gdcmImplicitVR || type == gdcmExplicitVR ) + 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); + fp1->write(filePreamble, 128); + fp1->write("DICM", 4); + } - delete[] filePreamble; + switch(WriteMode) + { + case WMODE_NATIVE : + SetWriteToNative(); + break; + case WMODE_DECOMPRESSED : + SetWriteToDecompressed(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; } // -------------------------------------------------------------- @@ -868,20 +697,16 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) /// but pb expected if user deals with, e.g. COMPLEX images std::string rows, columns; - if ( Header->GetFileType() == gdcmACR_LIBIDO) + if ( HeaderInternal->GetFileType() == ACR_LIBIDO) { - rows = Header->GetEntryByNumber(0x0028, 0x0010); - columns = Header->GetEntryByNumber(0x0028, 0x0011); - - Header->SetEntryByNumber(columns, 0x0028, 0x0010); - Header->SetEntryByNumber(rows , 0x0028, 0x0011); + SetWriteToLibido(); } // ----------------- End of Special Patch ---------------- - uint16_t grPixel = Header->GetGrPixel(); - uint16_t numPixel = Header->GetNumPixel();; + uint16_t grPixel = HeaderInternal->GetGrPixel(); + uint16_t numPixel = HeaderInternal->GetNumPixel();; - gdcmDocEntry* PixelElement = + DocEntry* PixelElement = GetHeader()->GetDocEntryByNumber(grPixel, numPixel); if ( PixelRead == 1 ) @@ -895,7 +720,7 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) PixelElement->SetLength( ImageDataSize ); } - Header->Write(fp1, type); + HeaderInternal->Write(fp1, type); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -903,203 +728,187 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) // ...and we restore the Header to be Dicom Compliant again // just after writting - if ( Header->GetFileType() == gdcmACR_LIBIDO ) + if ( HeaderInternal->GetFileType() == ACR_LIBIDO ) { - Header->SetEntryByNumber(rows , 0x0028, 0x0010); - Header->SetEntryByNumber(columns, 0x0028, 0x0011); + RestoreWriteFromLibido(); } // ----------------- End of Special Patch ---------------- - - // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now - fclose (fp1); + + RestoreWrite(); + + + fp1->close (); + delete fp1; return true; } +/** + * \brief Access to the underlying \ref PixelConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); +} + //----------------------------------------------------------------------------- // Private /** - * \brief Read pixel data from disk (optionaly decompressing) into the - * caller specified memory location. - * @param destination where the pixel data should be stored. - * + * \brief Set the pixel datas in the good entry of the Header */ -bool gdcmFile::ReadPixelData(void* destination) +void File::SetPixelData(uint8_t* data) { - FILE* fp = Header->OpenFile(); + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - if ( !fp ) + // Will be 7fe0, 0010 in standard case + DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + if ( currentEntry ) { - return false; - } - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) - { - Header->CloseFile(); - return false; + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + // Flag is to false because datas are kept in the gdcmPixelConvert + binEntry->SetBinArea( data, false ); } +} - if ( Header->GetBitsAllocated() == 12 ) - { - gdcmPixelConvert::ConvertDecompress12BitsTo16Bits( - (uint8_t*)destination, - Header->GetXSize(), - Header->GetYSize(), - fp); - Header->CloseFile(); - return true; - } +void File::SetWriteToNative() +{ +// Nothing to do +} - // ---------------------- Uncompressed File - if ( !Header->IsDicomV3() || - Header->IsImplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) +void File::SetWriteToDecompressed() +{ +// if (( !HeaderInternal->HasLUT() ) || (!PixelConverter->BuildRGBImage())) + if(HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage()) { - size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - Header->CloseFile(); - if ( ItemRead != 1 ) - { - return false; - } - else - { - return true; - } - } + SetWriteToRGB(); + } + else + { + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("MONOCHROME1 "); + photInt->SetLength(12); + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); - // ---------------------- Run Length Encoding - if ( Header->IsRLELossLessTransferSyntax() ) + Archive->Push(photInt); + Archive->Push(pixel); + } +/* else { - bool res = gdcmPixelConvert::gdcm_read_RLE_file ( destination, - Header->GetXSize(), - Header->GetYSize(), - Header->GetZSize(), - Header->GetBitsAllocated(), - &(Header->RLEInfo), - fp ); - Header->CloseFile(); - return res; - } - - // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int numberBitsAllocated = Header->GetBitsAllocated(); - if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) + SetWriteToRGB(); + } */ +} + +void File::SetWriteToRGB() +{ + if(PixelConverter->BuildRGBImage()) { - numberBitsAllocated = 16; - } + ValEntry* spp = CopyValEntry(0x0028,0x0002); + spp->SetValue("3 "); + spp->SetLength(2); - int nBytes= numberBitsAllocated/8; - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("RGB "); + photInt->SetLength(4); - bool jpg2000 = Header->IsJPEG2000(); - bool jpgLossless = Header->IsJPEGLossless(); + ValEntry* planConfig = CopyValEntry(0x0028,0x0006); + planConfig->SetValue("0 "); + planConfig->SetLength(2); - bool res = true; - uint16_t ItemTagGr, ItemTagEl; - int ln; - - // Position on begining of Jpeg Pixels - - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) - { - ItemTagGr = Header->SwapShort(ItemTagGr); - ItemTagEl = Header->SwapShort(ItemTagEl); - } + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelConverter->GetRGB(),false); + pixel->SetLength(PixelConverter->GetRGBSize()); - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) + Archive->Push(spp); + Archive->Push(photInt); + Archive->Push(planConfig); + Archive->Push(pixel); + } + else { - ln = Header->SwapLong( ln ); // Basic Offset Table Item length + SetWriteToDecompressed(); } +} + +void File::RestoreWrite() +{ + Archive->Restore(0x0028,0x0002); + Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); + Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); +} - if ( ln != 0 ) +void File::SetWriteToLibido() +{ + ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); + ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); + + if( oldRow && oldCol ) { - // What is it used for ?!? - uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); - //delete[] BasicOffsetTableItemValue; + std::string rows, columns; + + ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); + ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + + newRow->Copy(oldCol); + newCol->Copy(oldRow); + + newRow->SetValue(oldCol->GetValue()); + newCol->SetValue(oldRow->GetValue()); + + Archive->Push(newRow); + Archive->Push(newCol); } +} - // first Fragment initialisation - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if( Header->GetSwapCode() ) +void File::RestoreWriteFromLibido() +{ + Archive->Restore(0x0028,0x0010); + Archive->Restore(0x0028,0x0011); +} + +ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + ValEntry* newE; + + if(oldE) { - ItemTagGr = Header->SwapShort( ItemTagGr ); - ItemTagEl = Header->SwapShort( ItemTagEl ); + newE = new ValEntry(oldE->GetDictEntry()); + newE->Copy(oldE); } - - // parsing fragments until Sequence Delim. Tag found - while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd ) + else { - // --- for each Fragment - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) - { - ln = Header->SwapLong(ln); // Fragment Item length - } - fragmentBegining = ftell( fp ); + newE = GetHeader()->NewValEntryByNumber(group,element); + } - if ( jpg2000 ) - { - // JPEG 2000 : call to ??? - res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written - // ------------------------------------- endif (JPEG2000) - } - else if (jpgLossless) - { - // JPEG LossLess : call to xmedcom Lossless JPEG - // Reading Fragment pixels - JPEGLosslessDecodeImage (fp, (uint16_t*)destination, - Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln); - res = 1; // in order not to break the loop - - } // ------------------------------------- endif (JPEGLossless) - else - { - // JPEG Lossy : call to IJG 6b - if ( Header->GetBitsStored() == 8) - { - // Reading Fragment pixels - res = gdcm_read_JPEG_file (fp,destination); - } - else - { - // Reading Fragment pixels - res = gdcm_read_JPEG_file12 (fp,destination); - } - // ------------------------------------- endif (JPEGLossy) - } + return(newE); +} - if ( !res ) - { - break; - } - - // location in user's memory - // for next fragment (if any) - destination = (uint8_t*)destination + taille * nBytes; +BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + BinEntry* newE; - fseek(fp,fragmentBegining, SEEK_SET); // To be sure we start - fseek(fp,ln,SEEK_CUR); // at the begining of next fragment - - ItemTagGr = ItemTagEl = 0; - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if( Header->GetSwapCode() ) - { - ItemTagGr = Header->SwapShort( ItemTagGr ); - ItemTagEl = Header->SwapShort( ItemTagEl ); - } + if(oldE) + { + newE = new BinEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewBinEntryByNumber(group,element); } - // endWhile parsing fragments until Sequence Delim. Tag found - Header->CloseFile(); - return res; + + return(newE); } +//----------------------------------------------------------------------------- +} // end namespace gdcm +