X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=3484aecf075b7f470081797e839877fc5ff296f3;hb=1d69b92978803204089d270599133917d944c651;hp=6b9138b2ad26ea1e6d59b624994fc358ef04e202;hpb=88f0914a8dd9327056361ae14d62ead303f2a9ed;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 6b9138b2..3484aecf 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/10/01 12:40:57 $ - Version: $Revision: 1.134 $ + Date: $Date: 2004/10/12 04:35:46 $ + Version: $Revision: 1.139 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -18,15 +18,17 @@ #include "gdcmFile.h" #include "gdcmDebug.h" -#include "jpeg/ljpg/jpegless.h" +#include "gdcmPixelConvert.h" +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 @@ -36,18 +38,18 @@ 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 @@ -59,9 +61,9 @@ 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(); } @@ -69,12 +71,12 @@ gdcmFile::gdcmFile(std::string const & filename ) /** * \brief Factorization for various forms of constructors. */ -void gdcmFile::Initialise() +void File::Initialise() { - if ( Header->IsReadable() ) + if ( HeaderInternal->IsReadable() ) { ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); - if ( Header->HasLUT() ) + if ( HeaderInternal->HasLUT() ) { ImageDataSize = 3 * ImageDataSizeRaw; } @@ -88,16 +90,16 @@ void gdcmFile::Initialise() /** * \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( SelfHeader ) { - delete Header; + delete HeaderInternal; } - Header = 0; + HeaderInternal = 0; DeleteInitialValues(); } @@ -106,7 +108,7 @@ 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. @@ -126,28 +128,28 @@ void gdcmFile::SaveInitialValues() 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); } } @@ -155,42 +157,42 @@ 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); } } @@ -198,7 +200,7 @@ void gdcmFile::RestoreInitialValues() * \brief delete initial values (il they were saved) * of InitialLutDescriptors and InitialLutData */ -void gdcmFile::DeleteInitialValues() +void File::DeleteInitialValues() { // InitialLutDescriptors and InitialLutData @@ -236,7 +238,7 @@ 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 // @@ -265,17 +267,17 @@ int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader() // 0028|1203 [US] [Blue Palette Color Lookup Table Data] // Number of "Bits Allocated" - int numberBitsAllocated = Header->GetBitsAllocated(); + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); 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; } @@ -290,7 +292,7 @@ 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: @@ -346,11 +348,11 @@ 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 ( !HeaderInternal->HasLUT() ) { return ImageDataSize; } @@ -358,7 +360,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) // 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(); + uint8_t *lutRGBA = HeaderInternal->GetLUTRGBA(); if ( lutRGBA ) { @@ -381,11 +383,11 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) // FIXME : Better use CreateOrReplaceIfExist ? std::string spp = "3"; // Samples Per Pixel - Header->SetEntryByNumber(spp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); std::string rgb = "RGB "; // Photometric Interpretation - Header->SetEntryByNumber(rgb,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - Header->SetEntryByNumber(planConfig,0x0028,0x0006); + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); } else // GetLUTRGBA() failed @@ -397,7 +399,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) // It seems that *no Dicom Viewer* has any idea :-( std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation - Header->SetEntryByNumber(photomInterp,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(photomInterp,0x0028,0x0004); } /// \todo Drop Palette Color out of the Header? @@ -413,11 +415,11 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -uint8_t* gdcmFile::GetImageDataRaw () +uint8_t* File::GetImageDataRaw () { size_t imgDataSize; - if ( Header->HasLUT() ) - /// \todo Let gdcmHeader user a chance to get the right value + if ( HeaderInternal->HasLUT() ) + /// \todo Let Header user a chance to get the right value imgDataSize = ImageDataSizeRaw; else imgDataSize = ImageDataSize; @@ -474,7 +476,7 @@ uint8_t* gdcmFile::GetImageDataRaw () * @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) +size_t File::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) { // we save the initial values of the following // in order to be able to restore the header in a disk-consistent state @@ -489,7 +491,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) if ( ImageDataSize > maxSize ) { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" "than caller's expected MaxSize"); return (size_t)0; } @@ -497,35 +499,38 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) ReadPixelData( destination ); // Number of Bits Allocated for storing a Pixel - int numberBitsAllocated = Header->GetBitsAllocated(); + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); if ( numberBitsAllocated == 0 ) { numberBitsAllocated = 16; } // Number of Bits actually used - int numberBitsStored = Header->GetBitsStored(); + int numberBitsStored = HeaderInternal->GetBitsStored(); if ( numberBitsStored == 0 ) { numberBitsStored = numberBitsAllocated; } // High Bit Position - int highBitPosition = Header->GetHighBitPosition(); + int highBitPosition = HeaderInternal->GetHighBitPosition(); if ( highBitPosition == 0 ) { highBitPosition = numberBitsAllocated - 1; } - bool signedPixel = Header->IsSignedPixelData(); + bool signedPixel = HeaderInternal->IsSignedPixelData(); - ConvertReorderEndianity( (uint8_t*) destination, - ImageDataSize, - numberBitsStored, - numberBitsAllocated, - signedPixel ); + PixelConvert::ConvertReorderEndianity( + (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + HeaderInternal->GetSwapCode(), + signedPixel ); - ConvertReArrangeBits( (uint8_t*) destination, + PixelConvert::ConvertReArrangeBits( + (uint8_t*) destination, ImageDataSize, numberBitsStored, numberBitsAllocated, @@ -545,7 +550,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) // Deal with the color // Monochrome pictures don't require color intervention - if ( Header->IsMonochrome() ) + if ( HeaderInternal->IsMonochrome() ) { return ImageDataSize; } @@ -559,13 +564,13 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( - int planConf = Header->GetPlanarConfiguration(); + int planConf = HeaderInternal->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() ) + if ( ( planConf == 2 ) || HeaderInternal->IsPaletteColor() ) { return ImageDataSize; } @@ -576,7 +581,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) { uint8_t* newDest = new uint8_t[ImageDataSize]; // Warning : YBR_FULL_422 acts as RGB - if ( Header->IsYBRFull() ) + if ( HeaderInternal->IsYBRFull() ) { ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest); } @@ -604,95 +609,18 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) 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); + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); return ImageDataSize; } -/** - * \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 !?" ); - } - } -} - -/** - * \brief Deal with endianity i.e. re-arange bytes inside the integer - */ -void gdcmFile::ConvertReorderEndianity( uint8_t* pixelZone, - size_t imageDataSize, - int numberBitsStored, - int numberBitsAllocated, - bool signedPixel) -{ - if ( numberBitsAllocated != 8 ) - { - SwapZone( pixelZone, Header->GetSwapCode(), ImageDataSize, - numberBitsAllocated ); - } - - // Special kludge in order to deal with xmedcon broken images: - if ( ( numberBitsAllocated == 16 ) - && ( numberBitsStored < numberBitsAllocated ) - && ( ! signedPixel ) ) - { - int l = (int)(ImageDataSize / (numberBitsAllocated/8)); - uint16_t *deb = (uint16_t *)pixelZone; - for(int i = 0; iGetXSize() * Header->GetYSize(); - int nbFrames = Header->GetZSize(); + int l = HeaderInternal->GetXSize() * HeaderInternal->GetYSize(); + int nbFrames = HeaderInternal->GetZSize(); uint8_t* a = source; uint8_t* b = source + l; @@ -742,10 +670,10 @@ void gdcmFile::ConvertYcBcRPlanesToRGBPixels(uint8_t* source, * \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, +void File::ConvertRGBPlanesToRGBPixels(uint8_t* source, uint8_t* destination) { - int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); + int l = HeaderInternal->GetXSize() * HeaderInternal->GetYSize() * HeaderInternal->GetZSize(); uint8_t* a = source; uint8_t* b = source + l; @@ -772,9 +700,9 @@ 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; @@ -792,7 +720,7 @@ 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) @@ -815,9 +743,9 @@ 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); + return WriteBase(fileName, ImplicitVR); } /** @@ -828,9 +756,9 @@ 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); + return WriteBase(fileName, ExplicitVR); } /** @@ -847,9 +775,9 @@ 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); + return WriteBase(fileName, ACR); } //----------------------------------------------------------------------------- @@ -862,9 +790,9 @@ 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; } @@ -876,7 +804,7 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) return false; } - if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + if ( type == ImplicitVR || type == ExplicitVR ) { // writing Dicom File Preamble uint8_t* filePreamble = new uint8_t[128]; @@ -898,20 +826,20 @@ 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); + rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010); + columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011); - Header->SetEntryByNumber(columns, 0x0028, 0x0010); - Header->SetEntryByNumber(rows , 0x0028, 0x0011); + HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0010); + HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- 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 ) @@ -925,7 +853,7 @@ 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 @@ -933,10 +861,10 @@ 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); + HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010); + HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- @@ -948,128 +876,46 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) //----------------------------------------------------------------------------- // Private -/** - * \brief Swap the bytes, according to swap code. - * \warning not end user intended - * @param im area to deal with - * @param swap swap code - * @param lgr Area Length - * @param nb Pixels Bit number - */ -void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) -{ - int i; - - if( nb == 16 ) - { - uint16_t* im16 = (uint16_t*)im; - switch( swap ) - { - case 0: - case 12: - case 1234: - break; - case 21: - case 3412: - case 2143: - case 4321: - for(i=0; i < lgr/2; i++) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - break; - default: - std::cout << "SWAP value (16 bits) not allowed :i" << swap << - std::endl; - } - } - else if( nb == 32 ) - { - uint32_t s32; - uint16_t fort, faible; - uint32_t* im32 = (uint32_t*)im; - switch ( swap ) - { - case 0: - case 1234: - break; - case 4321: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 4321 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8 ) | ( faible << 8); - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; - } - break; - case 2143: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 2143 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8) | ( faible << 8); - s32 = fort; - im32[i] = ( s32 << 16 ) | faible; - } - break; - case 3412: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 3412 - fort = im32[i] >> 16; - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; - } - break; - default: - std::cout << "SWAP value (32 bits) not allowed : " << swap << - std::endl; - } - } -} - /** * \brief Read pixel data from disk (optionaly decompressing) into the * caller specified memory location. * @param destination where the pixel data should be stored. * */ -bool gdcmFile::ReadPixelData(void* destination) +bool File::ReadPixelData(void* destination) { - FILE* fp = Header->OpenFile(); + FILE* fp = HeaderInternal->OpenFile(); if ( !fp ) { return false; } - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) + if ( fseek(fp, HeaderInternal->GetPixelOffset(), SEEK_SET) == -1 ) { - Header->CloseFile(); + HeaderInternal->CloseFile(); return false; } - if ( Header->GetBitsAllocated() == 12 ) + if ( HeaderInternal->GetBitsAllocated() == 12 ) { - ConvertDecompress12BitsTo16Bits( (uint8_t*)destination, - Header->GetXSize(), - Header->GetYSize(), + PixelConvert::ConvertDecompress12BitsTo16Bits( + (uint8_t*)destination, + HeaderInternal->GetXSize(), + HeaderInternal->GetYSize(), fp); - Header->CloseFile(); + HeaderInternal->CloseFile(); return true; } // ---------------------- Uncompressed File - if ( !Header->IsDicomV3() || - Header->IsImplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) - { - size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - Header->CloseFile(); + if ( !HeaderInternal->IsDicomV3() || + HeaderInternal->IsImplicitVRLittleEndianTransferSyntax() || + HeaderInternal->IsExplicitVRLittleEndianTransferSyntax() || + HeaderInternal->IsExplicitVRBigEndianTransferSyntax() || + HeaderInternal->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) + { + size_t ItemRead = fread(destination, HeaderInternal->GetPixelAreaLength(), 1, fp); + HeaderInternal->CloseFile(); if ( ItemRead != 1 ) { return false; @@ -1081,184 +927,42 @@ bool gdcmFile::ReadPixelData(void* destination) } // ---------------------- Run Length Encoding - if ( Header->IsRLELossLessTransferSyntax() ) - { - bool res = gdcm_read_RLE_file (fp,destination); - Header->CloseFile(); + if ( HeaderInternal->IsRLELossLessTransferSyntax() ) + { + bool res = PixelConvert::ReadAndDecompressRLEFile( + destination, + HeaderInternal->GetXSize(), + HeaderInternal->GetYSize(), + HeaderInternal->GetZSize(), + HeaderInternal->GetBitsAllocated(), + &(HeaderInternal->RLEInfo), + fp ); + HeaderInternal->CloseFile(); return res; } // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int numberBitsAllocated = Header->GetBitsAllocated(); + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) { numberBitsAllocated = 16; } - int nBytes= numberBitsAllocated/8; - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek - - bool jpg2000 = Header->IsJPEG2000(); - bool jpgLossless = Header->IsJPEGLossless(); - - 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); - } - - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) - { - ln = Header->SwapLong( ln ); // Basic Offset Table Item length - } - - if ( ln != 0 ) - { - // What is it used for ?!? - uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); - //delete[] BasicOffsetTableItemValue; - } - - // 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() ) - { - ItemTagGr = Header->SwapShort( ItemTagGr ); - ItemTagEl = Header->SwapShort( ItemTagEl ); - } - - // parsing fragments until Sequence Delim. Tag found - while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd ) - { - // --- for each Fragment - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) - { - ln = Header->SwapLong(ln); // Fragment Item length - } - fragmentBegining = ftell( fp ); - - 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) - } - - if ( !res ) - { - break; - } - - // location in user's memory - // for next fragment (if any) - destination = (uint8_t*)destination + taille * nBytes; - - 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 ); - } - } - // endWhile parsing fragments until Sequence Delim. Tag found - - Header->CloseFile(); + bool res = PixelConvert::ReadAndDecompressJPEGFile( + (uint8_t*)destination, + HeaderInternal->GetXSize(), + HeaderInternal->GetYSize(), + HeaderInternal->GetBitsAllocated(), + HeaderInternal->GetBitsStored(), + HeaderInternal->GetSamplesPerPixel(), + HeaderInternal->GetPixelSize(), + HeaderInternal->IsJPEG2000(), + HeaderInternal->IsJPEGLossless(), + &(HeaderInternal->JPEGInfo), + fp ); + HeaderInternal->CloseFile(); return res; } -/** - * \brief Read from file a 12 bits per pixel image and uncompress it - * into a 16 bits per pixel image. - */ -void gdcmFile::ConvertDecompress12BitsTo16Bits( - uint8_t* pixelZone, - int sizeX, - int sizeY, - FILE* filePtr) - throw ( gdcmFormatError ) -{ - int nbPixels = sizeX * sizeY; - uint16_t* destination = (uint16_t*)pixelZone; - - for( int p = 0; p < nbPixels; p += 2 ) - { - uint8_t b0, b1, b2; - size_t ItemRead; - - ItemRead = fread( &b0, 1, 1, filePtr); - if ( ItemRead != 1 ) - { - throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", - "Unfound first block" ); - } - - ItemRead = fread( &b1, 1, 1, filePtr); - if ( ItemRead != 1 ) - { - throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", - "Unfound second block" ); - } +} // end namespace gdcm - ItemRead = fread( &b2, 1, 1, filePtr); - if ( ItemRead != 1 ) - { - throw gdcmFormatError( "gdcmFile::ConvertDecompress12BitsTo16Bits()", - "Unfound second block" ); - } - - // Two steps are necessary to please VC++ - // - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - // A B D - *destination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // F C E - *destination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - - /// \todo JPR Troubles expected on Big-Endian processors ? - } -} -//-----------------------------------------------------------------------------