X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=4921affdf3820fe2858911157c0295bcd9f98eaa;hb=8da9df62c47908e7b9a67238a6c12b92ba6cae7a;hp=2cd116775855d125c2ab91b0342d6617c8ab7b91;hpb=da6bc02a3bb5627685bd70f5503305a7f9b3d7cd;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 2cd11677..4921affd 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/10/10 16:44:00 $ - Version: $Revision: 1.138 $ + Date: $Date: 2004/11/25 13:12:02 $ + Version: $Revision: 1.164 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -17,16 +17,21 @@ =========================================================================*/ #include "gdcmFile.h" +#include "gdcmDocument.h" #include "gdcmDebug.h" -#include "gdcmPixelConvert.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 @@ -36,18 +41,18 @@ 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 +64,9 @@ 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(); } @@ -69,159 +74,44 @@ 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 = new PixelConvert; + Archive = new DocEntryArchive( HeaderInternal ); + + if ( HeaderInternal->IsReadable() ) { - ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); - if ( Header->HasLUT() ) - { - ImageDataSize = 3 * ImageDataSizeRaw; - } - else - { - ImageDataSize = ImageDataSizeRaw; - } + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); } - SaveInitialValues(); + + Pixel_Data = 0; + ImageDataSize = 0; } /** * \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 ) + if( PixelConverter ) { - delete Header; + delete PixelConverter; } - Header = 0; - - DeleteInitialValues(); -} - -/** - * \brief Sets some initial values for the Constructor - * \warning not end user intended - */ -void gdcmFile::SaveInitialValues() -{ - - PixelRead = -1; // no ImageData read yet. - LastAllocatedPixelDataLength = 0; - Pixel_Data = 0; - - InitialSpp = ""; - InitialPhotInt = ""; - InitialPlanConfig = ""; - InitialBitsAllocated = ""; - InitialHighBit = ""; - - InitialRedLUTDescr = 0; - InitialGreenLUTDescr = 0; - InitialBlueLUTDescr = 0; - InitialRedLUTData = 0; - InitialGreenLUTData = 0; - InitialBlueLUTData = 0; - - if ( Header->IsReadable() ) + if( Archive ) { - // the following values *may* be modified - // by gdcmFile::GetImageDataIntoVectorRaw - // we save their initial value. - InitialSpp = Header->GetEntryByNumber(0x0028,0x0002); - InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004); - InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006); - - InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); - InitialHighBit = Header->GetEntryByNumber(0x0028,0x0102); - - // the following entries *may* be removed from the H table - // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw - // we keep a pointer on them. - InitialRedLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1101); - InitialGreenLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1102); - InitialBlueLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1103); - - InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201); - InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202); - InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203); + delete Archive; } -} -/** - * \brief restores some initial values - * \warning not end user intended - */ -void gdcmFile::RestoreInitialValues() -{ - if ( Header->IsReadable() ) - { - // the following values *may* have been modified - // by gdcmFile::GetImageDataIntoVectorRaw - // we restore their initial value. - if ( InitialSpp != "") - Header->SetEntryByNumber(InitialSpp,0x0028,0x0002); - if ( InitialPhotInt != "") - Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); - if ( InitialPlanConfig != "") - - Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); - if ( InitialBitsAllocated != "") - Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); - if ( InitialHighBit != "") - Header->SetEntryByNumber(InitialHighBit,0x0028,0x0102); - - // the following entries *may* be have been removed from the H table - // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw - // we restore them. - - if (InitialRedLUTDescr) - Header->AddEntry(InitialRedLUTDescr); - if (InitialGreenLUTDescr) - Header->AddEntry(InitialGreenLUTDescr); - if (InitialBlueLUTDescr) - Header->AddEntry(InitialBlueLUTDescr); - - if (InitialRedLUTData) - Header->AddEntry(InitialBlueLUTDescr); - if (InitialGreenLUTData) - Header->AddEntry(InitialGreenLUTData); - if (InitialBlueLUTData) - Header->AddEntry(InitialBlueLUTData); + if( SelfHeader ) + { + delete HeaderInternal; } -} - -/** - * \brief delete initial values (il they were saved) - * of InitialLutDescriptors and InitialLutData - */ -void gdcmFile::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 ) - delete InitialRedLUTDescr; - - if ( InitialGreenLUTDescr ) - delete InitialGreenLUTDescr; - - if ( InitialBlueLUTDescr ) - delete InitialBlueLUTDescr; - - if ( InitialRedLUTData ) - delete InitialRedLUTData; - - if ( InitialGreenLUTData != NULL) - delete InitialGreenLUTData; - - if ( InitialBlueLUTData != NULL) - delete InitialBlueLUTData; + HeaderInternal = 0; } //----------------------------------------------------------------------------- @@ -229,55 +119,28 @@ void gdcmFile::DeleteInitialValues() //----------------------------------------------------------------------------- // Public - /** - * \brief computes the length (in bytes) we must ALLOCATE to receive the - * image(s) pixels (multiframes taken into account) - * \warning : it is NOT the group 7FE0 length - * (no interest for compressed images). + * \brief Get the size of the image data + * + * If the image can be RGB (with a lut or by default), the size + * corresponds to the RGB image + * @return The image size */ -int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader() +size_t File::GetImageDataSize() { - // see PS 3.3-2003 : C.7.6.3.2.1 - // - // MONOCHROME1 - // MONOCHROME2 - // PALETTE COLOR - // RGB - // HSV (Retired) - // ARGB (Retired) - // CMYK (Retired) - // YBR_FULL - // YBR_FULL_422 (no LUT, no Palette) - // YBR_PARTIAL_422 - // YBR_ICT - // YBR_RCT - - // LUT's - // ex : gdcm-US-ALOKA-16.dcm - // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data] - // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data] - // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data] - - // ex : OT-PAL-8-face.dcm - // 0028|1201 [US] [Red Palette Color Lookup Table Data] - // 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 ) ) - { - numberBitsAllocated = 16; - } + return PixelConverter->GetRGBSize(); +} - int DecompressedSize = Header->GetXSize() - * Header->GetYSize() - * Header->GetZSize() - * ( numberBitsAllocated / 8 ) - * Header->GetSamplesPerPixel(); - - return DecompressedSize; +/** + * \brief Get the size of the image data + * + * If the image can be RGB by transformation in a LUT, this + * transformation isn't considered + * @return The raw image size + */ +size_t File::GetImageDataRawSize() +{ + return PixelConverter->GetDecompressedSize(); } /** @@ -290,35 +153,23 @@ 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); - - // 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 + // If the decompression failed nothing can be done. + return 0; + } - return Pixel_Data; + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + return PixelConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the decompressed + return PixelConverter->GetDecompressed(); + } } /** @@ -346,62 +197,39 @@ 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(); } /** @@ -413,276 +241,32 @@ 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 ); - - gdcmPixelConvert::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() ) - { - return ImageDataSize; - } - - // When planConf is 0, pixels are allready in RGB - - if ( planConf == 1 ) - { - 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); - - return ImageDataSize; + return GetDecompressed(); } -/** - * \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++) + uint8_t* decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) { - for (int j = 0; j < l; j++) + // 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; } /** @@ -698,13 +282,11 @@ 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 ); // FIXME : if already allocated, memory leak ! Pixel_Data = inData; - ImageDataSize = ImageDataSizeRaw = expectedSize; - PixelRead = 1; + ImageDataSize = expectedSize; // FIXME : 7fe0, 0010 IS NOT set ... return true; } @@ -718,16 +300,16 @@ 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; } @@ -741,9 +323,10 @@ 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); } /** @@ -754,9 +337,10 @@ 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); } /** @@ -773,9 +357,32 @@ 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) +{ + 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); +} + +/** + * \brief Access to the underlying \ref PixelConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() { - return WriteBase(fileName, gdcmACR); + return PixelConverter->GetLutRGBA(); } //----------------------------------------------------------------------------- @@ -788,29 +395,35 @@ 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) + switch(type) { - return false; + case ImplicitVR: + SetWriteFileTypeToImplicitVR(); + break; + case ExplicitVR: + SetWriteFileTypeToExplicitVR(); + break; + case ACR: + SetWriteFileTypeToACR(); + break; + case ACR_LIBIDO: + SetWriteFileTypeToACRLibido(); + break; } - - FILE* fp1 = fopen(fileName.c_str(), "wb"); - if (fp1 == NULL) - { - printf("Failed to open (write) File [%s] \n", fileName.c_str()); - return false; - } - - if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + + switch(WriteMode) { - // writing Dicom File Preamble - uint8_t* filePreamble = new uint8_t[128]; - memset(filePreamble, 0, 128); - fwrite(filePreamble, 128, 1, fp1); - fwrite("DICM", 4, 1, fp1); - - delete[] filePreamble; + case WMODE_NATIVE : + SetWriteToNative(); + break; + case WMODE_DECOMPRESSED : + SetWriteToDecompressed(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; } // -------------------------------------------------------------- @@ -819,146 +432,362 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) // if recognition code tells us we dealt with a LibIDO image // we reproduce on disk the switch between lineNumber and columnNumber // just before writting ... - /// \todo the best trick would be *change* the recognition code /// 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();; - - gdcmDocEntry* PixelElement = - GetHeader()->GetDocEntryByNumber(grPixel, numPixel); - - if ( PixelRead == 1 ) - { - // we read pixel 'as is' (no tranformation LUT -> RGB) - PixelElement->SetLength( ImageDataSizeRaw ); - } - else if ( PixelRead == 0 ) + + bool check = CheckWriteIntegrity(); + if(check) { - // we tranformed GrayLevel pixels + LUT into RGB Pixel - PixelElement->SetLength( ImageDataSize ); + check = HeaderInternal->Write(fileName,type); } - - Header->Write(fp1, type); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images // // ...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); - return true; + RestoreWrite(); + RestoreWriteFileType(); + + return check; } -//----------------------------------------------------------------------------- -// 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 Check the write integrity * + * The tests made are : + * - verify the size of the image to write with the possible write + * when the user set an image data + * @return true if the check successfulls */ -bool gdcmFile::ReadPixelData(void* destination) +bool File::CheckWriteIntegrity() { - FILE* fp = Header->OpenFile(); - - if ( !fp ) + if(Pixel_Data) { - return false; + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) + { + numberBitsAllocated = 16; + } + + int decSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + int rgbSize = decSize; + if( HeaderInternal->HasLUT() ) + rgbSize = decSize * 3; + + switch(WriteMode) + { + case WMODE_NATIVE : + break; + case WMODE_DECOMPRESSED : + if( decSize!=ImageDataSize ) + { + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); + //std::cerr<<"Dec : "<GetPixelOffset(), SEEK_SET) == -1 ) + + return true; +} + +void File::SetWriteToNative() +{ + if(Pixel_Data) { - Header->CloseFile(); - return false; + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + + Archive->Push(pixel); } +} - if ( Header->GetBitsAllocated() == 12 ) +void File::SetWriteToDecompressed() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + { + SetWriteToRGB(); + } + else { - gdcmPixelConvert::ConvertDecompress12BitsTo16Bits( - (uint8_t*)destination, - Header->GetXSize(), - Header->GetYSize(), - fp); - Header->CloseFile(); - return true; + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + if(HeaderInternal->HasLUT()) + { + photInt->SetValue("PALETTE COLOR "); + photInt->SetLength(14); + } + else + { + photInt->SetValue("MONOCHROME1 "); + photInt->SetLength(12); + } + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + if(Pixel_Data) + { + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + } + else + { + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); + } + + Archive->Push(photInt); + Archive->Push(pixel); } +} - // ---------------------- Uncompressed File - if ( !Header->IsDicomV3() || - Header->IsImplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) +void File::SetWriteToRGB() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3) { - size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - Header->CloseFile(); - if ( ItemRead != 1 ) + PixelConverter->BuildRGBImage(); + + ValEntry* spp = CopyValEntry(0x0028,0x0002); + spp->SetValue("3 "); + spp->SetLength(2); + + ValEntry* planConfig = CopyValEntry(0x0028,0x0006); + planConfig->SetValue("0 "); + planConfig->SetLength(2); + + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("RGB "); + photInt->SetLength(4); + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + if(Pixel_Data) { - return false; + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); } - else + else if(PixelConverter->GetRGB()) + { + pixel->SetBinArea(PixelConverter->GetRGB(),false); + pixel->SetLength(PixelConverter->GetRGBSize()); + } + else // Decompressed data { - return true; + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); } + + Archive->Push(spp); + Archive->Push(planConfig); + Archive->Push(photInt); + Archive->Push(pixel); + + // Remove any LUT + Archive->Push(0x0028,0x1101); + Archive->Push(0x0028,0x1102); + Archive->Push(0x0028,0x1103); + Archive->Push(0x0028,0x1201); + Archive->Push(0x0028,0x1202); + Archive->Push(0x0028,0x1203); + + // For old ACR-NEMA + // Thus, we have a RGB image and the bits allocated = 24 and + // samples per pixels = 1 (in the read file) + if(HeaderInternal->GetBitsAllocated()==24) + { + ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100); + bitsAlloc->SetValue("8 "); + bitsAlloc->SetLength(2); + + ValEntry* bitsStored = CopyValEntry(0x0028,0x0101); + bitsStored->SetValue("8 "); + bitsStored->SetLength(2); + + ValEntry* highBit = CopyValEntry(0x0028,0x0102); + highBit->SetValue("7 "); + highBit->SetLength(2); + + Archive->Push(bitsAlloc); + Archive->Push(bitsStored); + Archive->Push(highBit); + } + } + else + { + SetWriteToDecompressed(); + } +} + +void File::RestoreWrite() +{ + Archive->Restore(0x0028,0x0002); + Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); + Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + + // For old ACR-NEMA (24 bits problem) + Archive->Restore(0x0028,0x0100); + Archive->Restore(0x0028,0x0101); + Archive->Restore(0x0028,0x0102); + + // For the LUT + Archive->Restore(0x0028,0x1101); + Archive->Restore(0x0028,0x1102); + Archive->Restore(0x0028,0x1103); + Archive->Restore(0x0028,0x1201); + Archive->Restore(0x0028,0x1202); + Archive->Restore(0x0028,0x1203); +} + +void File::SetWriteFileTypeToACR() +{ + Archive->Push(0x0002,0x0010); +} + +void File::SetWriteFileTypeToACRLibido() +{ + SetWriteFileTypeToACR(); +} + +void File::SetWriteFileTypeToExplicitVR() +{ + std::string ts = + Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] ); + + ValEntry* tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + tss->SetLength(ts.length()); + + Archive->Push(tss); +} + +void File::SetWriteFileTypeToImplicitVR() +{ + std::string ts = + Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] ); + + ValEntry* tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + tss->SetLength(ts.length()); +} + +void File::RestoreWriteFileType() +{ + Archive->Restore(0x0002,0x0010); +} + +void File::SetWriteToLibido() +{ + ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); + ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); + + if( oldRow && oldCol ) + { + 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); } +} + +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) + { + newE = new ValEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewValEntryByNumber(group,element); + } + + return(newE); +} + +BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + BinEntry* newE; - // ---------------------- Run Length Encoding - if ( Header->IsRLELossLessTransferSyntax() ) + if(oldE) { - bool res = gdcmPixelConvert::ReadAndDecompressRLEFile( - 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 ) ) + newE = new BinEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else { - numberBitsAllocated = 16; + newE = GetHeader()->NewBinEntryByNumber(group,element); } - bool res = gdcmPixelConvert::ReadAndDecompressJPEGFile( - (uint8_t*)destination, - Header->GetXSize(), - Header->GetYSize(), - Header->GetBitsAllocated(), - Header->GetBitsStored(), - Header->GetSamplesPerPixel(), - Header->GetPixelSize(), - Header->IsJPEG2000(), - Header->IsJPEGLossless(), - &(Header->JPEGInfo), - fp ); - Header->CloseFile(); - return res; + + return(newE); } +//----------------------------------------------------------------------------- +// Private +/** + * \brief Set the pixel datas in the good entry of the Header + */ +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 +