X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=b565a3a498604de9b834ae91a247ae9f15d7ed4f;hb=5bf7c51796867388334836847a6874640bc83f89;hp=e94cb485419c56c470a8b5e397dbba115783d86a;hpb=020d769ac045f06318b7061bfdfa0e1adfd9edd5;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index e94cb485..b565a3a4 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,14 +1,14 @@ -/*========================================================================= + /*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/09/13 07:49:36 $ - Version: $Revision: 1.125 $ + Date: $Date: 2004/10/20 14:30:40 $ + Version: $Revision: 1.146 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -18,16 +18,16 @@ #include "gdcmFile.h" #include "gdcmDebug.h" -#include "jpeg/ljpg/jpegless.h" +namespace gdcm +{ typedef std::pair IterHT; //------------------------------------------------------------------------- // Constructor / Destructor /** - * \ingroup gdcmFile * \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 @@ -37,19 +37,18 @@ 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; - SetInitialValues(); + Initialise(); } /** - * \ingroup gdcmFile * \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 @@ -61,19 +60,59 @@ 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; - SetInitialValues(); + Initialise(); } /** - * \ingroup gdcmFile - * \brief Sets some initial for the Constructor + * \brief Factorization for various forms of constructors. */ -void gdcmFile::SetInitialValues() -{ +void File::Initialise() +{ + if ( HeaderInternal->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( HeaderInternal->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } + + PixelConverter = new PixelConvert; + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + } + SaveInitialValues(); +} + +/** + * \brief canonical destructor + * \note If the Header was created by the File constructor, + * it is destroyed by the File + */ +File::~File() +{ + if( SelfHeader ) + { + delete HeaderInternal; + } + HeaderInternal = 0; + + DeleteInitialValues(); +} + +/** + * \brief Sets some initial values for the Constructor + * \warning not end user intended + */ +void File::SaveInitialValues() +{ + PixelRead = -1; // no ImageData read yet. LastAllocatedPixelDataLength = 0; Pixel_Data = 0; @@ -82,6 +121,7 @@ void gdcmFile::SetInitialValues() InitialPhotInt = ""; InitialPlanConfig = ""; InitialBitsAllocated = ""; + InitialHighBit = ""; InitialRedLUTDescr = 0; InitialGreenLUTDescr = 0; @@ -90,47 +130,102 @@ void gdcmFile::SetInitialValues() InitialGreenLUTData = 0; InitialBlueLUTData = 0; - if ( Header->IsReadable() ) + if ( HeaderInternal->IsReadable() ) { - SetPixelDataSizeFromHeader(); - // 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); - InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); - + InitialSpp = HeaderInternal->GetEntryByNumber(0x0028,0x0002); + InitialPhotInt = HeaderInternal->GetEntryByNumber(0x0028,0x0004); + InitialPlanConfig = HeaderInternal->GetEntryByNumber(0x0028,0x0006); + + 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); - InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201); - InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202); - InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203); + InitialRedLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1101); + InitialGreenLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1102); + InitialBlueLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1103); + + InitialRedLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1201); + InitialGreenLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1202); + InitialBlueLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1203); } } /** - * \ingroup gdcmFile - * \brief canonical destructor - * \note If the gdcmHeader was created by the gdcmFile constructor, - * it is destroyed by the gdcmFile + * \brief restores some initial values + * \warning not end user intended */ -gdcmFile::~gdcmFile() -{ - if( SelfHeader ) - { - delete Header; +void File::RestoreInitialValues() +{ + if ( HeaderInternal->IsReadable() ) + { + // the following values *may* have been modified + // by File::GetImageDataIntoVectorRaw + // we restore their initial value. + if ( InitialSpp != "") + HeaderInternal->SetEntryByNumber(InitialSpp,0x0028,0x0002); + if ( InitialPhotInt != "") + HeaderInternal->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); + if ( InitialPlanConfig != "") + + HeaderInternal->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); + if ( InitialBitsAllocated != "") + HeaderInternal->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); + if ( InitialHighBit != "") + HeaderInternal->SetEntryByNumber(InitialHighBit,0x0028,0x0102); + + // the following entries *may* be have been removed from the H table + // (NOT deleted ...) by File::GetImageDataIntoVectorRaw + // we restore them. + + if (InitialRedLUTDescr) + HeaderInternal->AddEntry(InitialRedLUTDescr); + if (InitialGreenLUTDescr) + HeaderInternal->AddEntry(InitialGreenLUTDescr); + if (InitialBlueLUTDescr) + HeaderInternal->AddEntry(InitialBlueLUTDescr); + + if (InitialRedLUTData) + HeaderInternal->AddEntry(InitialBlueLUTDescr); + if (InitialGreenLUTData) + HeaderInternal->AddEntry(InitialGreenLUTData); + if (InitialBlueLUTData) + HeaderInternal->AddEntry(InitialBlueLUTData); } - Header = 0; +} + +/** + * \brief delete initial values (il they were saved) + * of InitialLutDescriptors and InitialLutData + */ +void File::DeleteInitialValues() +{ // InitialLutDescriptors and InitialLutData // will have to be deleted if the don't belong any longer -// to the Header H table ... +// 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; } //----------------------------------------------------------------------------- @@ -140,14 +235,12 @@ gdcmFile::~gdcmFile() // Public /** - * \ingroup gdcmFile * \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). - * \warning : not end user intended ? */ -void gdcmFile::SetPixelDataSizeFromHeader() +int File::ComputeDecompressedPixelDataSizeFromHeader() { // see PS 3.3-2003 : C.7.6.3.2.1 // @@ -175,39 +268,26 @@ void gdcmFile::SetPixelDataSizeFromHeader() // 0028|1202 [US] [Green Palette Color Lookup Table Data] // 0028|1203 [US] [Blue Palette Color Lookup Table Data] - // Number of "Bits Allocated" - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - - if ( str_nb == GDCM_UNFOUND ) + 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 ) ) { - nb = 16; + numberBitsAllocated = 16; } - else - { - nb = atoi( str_nb.c_str() ); - if (nb == 12) - { - nb =16; - } - } - ImageDataSize = - ImageDataSizeRaw = Header->GetXSize() * Header->GetYSize() - * Header->GetZSize() * (nb/8) * Header->GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); - - // if ( str_PhotometricInterpretation == "PALETTE COLOR " ), - // pb when undealt Segmented Palette Color + + int DecompressedSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); - if ( Header->HasLUT() ) - { - ImageDataSize *= 3; - } + return DecompressedSize; } /** - * \ingroup gdcmFile * \brief - Allocates necessary memory, * - Reads the pixels from disk (uncompress if necessary), * - Transforms YBR pixels, if any, into RGB pixels @@ -217,7 +297,7 @@ void gdcmFile::SetPixelDataSizeFromHeader() * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ -void *gdcmFile::GetImageData() +uint8_t* File::GetImageData() { // FIXME (Mathieu) // I need to deallocate Pixel_Data before doing any allocation: @@ -240,7 +320,7 @@ void *gdcmFile::GetImageData() GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); // Will be 7fe0, 0010 in standard case - GetHeader()->SetEntryVoidAreaByNumber( Pixel_Data, + GetHeader()->SetEntryBinAreaByNumber( Pixel_Data, GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } PixelRead = 0; // no PixelRaw @@ -249,7 +329,6 @@ void *gdcmFile::GetImageData() } /** - * \ingroup gdcmFile * \brief * Read the pixels from disk (uncompress if necessary), * Transforms YBR pixels, if any, into RGB pixels @@ -274,50 +353,39 @@ void *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; } - // 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 ) + FILE* fp = HeaderInternal->OpenFile(); + if ( PixelConverter->BuildRGBImage( fp ) ) { - int j; - // move Gray pixels to temp area - memmove(newDest, destination, ImageDataSizeRaw); - for (size_t i=0; iGetRGB(), + PixelConverter->GetRGBSize() ); - // now, it's an RGB image - // Lets's write it in the Header + // now, it's an RGB image + // Lets's write it in the Header - // FIXME : Better use CreateOrReplaceIfExist ? + // 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); + 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); } - else // GetLUTRGBA() failed + else { + // PixelConverter->BuildRGBImage() failed probably because + // PixelConverter->GetLUTRGBA() failed: // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color // that are *more* than 65535 long ?!? // No idea how to manage such an image ! @@ -325,15 +393,15 @@ 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); } + HeaderInternal->CloseFile(); /// \todo Drop Palette Color out of the Header? return ImageDataSize; } /** - * \ingroup gdcmFile * \brief Allocates necessary memory, * Transforms YBR pixels (if any) into RGB pixels * Transforms 3 planes R, G, B (if any) into a single RGB Plane @@ -342,11 +410,11 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -void * 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; @@ -372,7 +440,7 @@ void * gdcmFile::GetImageDataRaw () GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); // will be 7fe0, 0010 in standard cases - GetHeader()->SetEntryVoidAreaByNumber(Pixel_Data, + GetHeader()->SetEntryBinAreaByNumber(Pixel_Data, GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } PixelRead = 1; // PixelRaw @@ -381,7 +449,6 @@ void * gdcmFile::GetImageDataRaw () } /** - * \ingroup gdcmFile * \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 @@ -404,300 +471,77 @@ void * 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) +void File::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) { - int nb, nbu, highBit, sign; - // 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 never "read" before + if ( PixelRead != -1 ) // File was "read" before { - InitialSpp = Header->GetEntryByNumber(0x0028,0x0002); - InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004); - InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006); - InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); - } - else // File was already "read", the following *may* have been modified - // we restore them to be in a disk-consistent state - { - // FIXME : What happened with the LUTs ? - Header->SetEntryByNumber(InitialSpp,0x0028,0x0002); - Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); - Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); - Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); + RestoreInitialValues(); } PixelRead = 1 ; // PixelRaw 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; - } - - ReadPixelData( destination ); - - // Number of Bits Allocated for storing a Pixel - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) - { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - // FIXME - // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated - // separately, correct ? - } - - // Number of Bits actually used - std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101); - if ( str_nbu == GDCM_UNFOUND ) - { - nbu = nb; - } - else - { - nbu = atoi( str_nbu.c_str() ); - } - - // High Bit Position - std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102); - if ( str_highBit == GDCM_UNFOUND ) - { - highBit = nb - 1; + return; } - else - { - highBit = atoi( str_highBit.c_str() ); - } - // Pixel sign - // 0 = Unsigned - // 1 = Signed - std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103); - if ( str_sign == GDCM_UNFOUND ) - { - sign = 0; // default is unsigned - } - else - { - sign = atoi( str_sign.c_str() ); - } + FILE* fp = HeaderInternal->OpenFile(); + PixelConverter->ReadAndDecompressPixelData( fp ); + HeaderInternal->CloseFile(); + memmove( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); - // re arange bytes inside the integer (processor endianity) - if ( nb != 8 ) + if ( ! PixelConverter->IsDecompressedRGB() ) { - SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); - } - - // to avoid pb with some xmedcon breakers images - if ( nb == 16 && nbu < nb && sign == 0) - { - int l = (int)(ImageDataSize / (nb/8)); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> (nb-nbu); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } - } - else if ( nb == 32 ) - { - uint32_t mask = 0xffffffff; - mask = mask >> (nb - nbu); - uint32_t *deb = (uint32_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } - } - else - { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); - return 0; - } + return; } -// DO NOT remove this code commented out. -// Nobody knows what's expecting you ... -// Just to 'see' what was actually read on disk :-( -// FILE * f2; -// f2 = fopen("SpuriousFile.RAW","wb"); -// fwrite(destination,ImageDataSize,1,f2); -// fclose(f2); - - // Deal with the color - // ------------------- - - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); - - if ( str_PhotometricInterpretation == "MONOCHROME1 " - || str_PhotometricInterpretation == "MONOCHROME2 " ) - { - 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(); // 0028,0006 - - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if ( str_PhotometricInterpretation == "PALETTE COLOR ") - { - planConf = 2; - } - - switch ( planConf ) - { - case 0: - // Pixels are already RGB - break; - case 1: - if (str_PhotometricInterpretation == "YBR_FULL") - { - // Warning : YBR_FULL_422 acts as RGB - // : we need to make RGB Pixels from Planes Y,cB,cR - - // 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* newDest = new uint8_t[ImageDataSize]; - uint8_t* x = newDest; - uint8_t* a = (uint8_t*)destination; - uint8_t* b = a + l; - uint8_t* c = b + l; - double R,G,B; - - /// \todo : Replace by the 'well known' integer computation - /// counterpart - /// see 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++) - { - 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; - - *(x++) = (uint8_t)R; - *(x++) = (uint8_t)G; - *(x++) = (uint8_t)B; - a++; b++; c++; - } - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - else - { - // need to make RGB Pixels from R,G,B Planes - // (all the Frames at a time) - - int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); - - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *x = newDest; - uint8_t *a = (uint8_t *)destination; - uint8_t *b = a + l; - uint8_t *c = b + l; - - for (int j = 0; j < l; j++) - { - *(x++) = *(a++); - *(x++) = *(b++); - *(x++) = *(c++); - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - break; - case 2: - // Palettes were found - // Let the user deal with them ! - return ImageDataSize; - } +/////////////////////////////////////////////////// // 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. - // CreateOrReplaceIfExist ? + // 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); + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); - /// \todo Drop Palette Color out of the Header? - return ImageDataSize; + return; } /** - * \ingroup gdcmFile - * \brief performs a shalow copy (not a deep copy) of the user given - * pixel area. - * 'image' Pixels are presented as C-like 2D arrays : line per line. - * 'volume'Pixels are presented as C-like 3D arrays : plane per plane - * \warning user is kindly requested NOT TO 'free' the Pixel area + * \brief Points the internal Pixel_Data pointer to the callers inData + * image representation, BUT WITHOUT COPYING THE DATA. + * 'image' Pixels are presented as C-like 2D arrays : line per line. + * 'volume'Pixels are presented as C-like 3D arrays : plane per plane + * \warning Since the pixels are not copied, it is the caller's responsability + * not to deallocate it's data before gdcm uses them (e.g. with + * the Write() method. * @param inData user supplied pixel area * @param expectedSize total image size, in Bytes * * @return boolean */ -bool gdcmFile::SetImageData(void *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; @@ -707,7 +551,6 @@ bool gdcmFile::SetImageData(void *inData, size_t expectedSize) } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file * NO test is performed on processor "Endiannity". * It's up to the user to call his Reader properly @@ -716,9 +559,9 @@ bool gdcmFile::SetImageData(void *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"); + FILE* fp1 = fopen(fileName.c_str(), "wb"); if (fp1 == NULL) { printf("Fail to open (write) file [%s] \n", fileName.c_str()); @@ -731,7 +574,6 @@ bool gdcmFile::WriteRawData(std::string const & fileName) } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the Implicit Value Representation convention * NO test is performed on processor "Endiannity". @@ -740,13 +582,12 @@ 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); } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the Explicit Value Representation convention * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created @@ -754,13 +595,12 @@ 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); } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the ACR-NEMA convention * NO test is performed on processor "Endiannity". @@ -774,15 +614,14 @@ 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); } //----------------------------------------------------------------------------- // Protected /** - * \ingroup gdcmFile * \brief NOT a end user inteded function * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) * @param fileName name of the file to be created @@ -790,21 +629,21 @@ 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"); + 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 ) + if ( type == ImplicitVR || type == ExplicitVR ) { // writing Dicom File Preamble uint8_t* filePreamble = new uint8_t[128]; @@ -826,20 +665,20 @@ 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 ) @@ -853,7 +692,7 @@ 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 @@ -861,10 +700,10 @@ 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 ---------------- @@ -874,297 +713,13 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) return true; } -//----------------------------------------------------------------------------- -// Private /** - * \ingroup gdcmFile - * \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 + * \brief Access to the underlying \ref PixelConverter RGBA LUT */ -void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) +uint8_t* File::GetLutRGBA() { - 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; - } - } + return PixelConverter->GetLutRGBA(); } -/** - * \ingroup gdcmFile - * \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) -{ - FILE *fp = Header->OpenFile(); - - if ( !fp ) - { - return false; - } - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) - { - Header->CloseFile(); - return false; - } +} // end namespace gdcm - // ---------------------- Compacted File (12 Bits Per Pixel) - // unpack 12 Bits pixels into 16 Bits pixels - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - - if ( Header->GetBitsAllocated() == 12 ) - { - int nbPixels = Header->GetXSize() * Header->GetYSize(); - uint8_t b0, b1, b2; - - uint16_t* pdestination = (uint16_t*)destination; - for(int p = 0; p < nbPixels; p += 2 ) - { - fread(&b0,1,1,fp); - fread(&b1,1,1,fp); - fread(&b2,1,1,fp); - - //Two steps is necessary to please VC++ - *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // A B D - *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - // F C E - - // Troubles expected on Big-Endian processors ? - } - - Header->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 ( ItemRead != 1 ) - { - return false; - } - else - { - return true; - } - } - - // ---------------------- Run Length Encoding - if ( Header->IsRLELossLessTransferSyntax() ) - { - bool res = gdcm_read_RLE_file (fp,destination); - Header->CloseFile(); - return res; - } - - // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) - { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - if ( nb == 12 ) - { - nb = 16; // ?? 12 should be ACR-NEMA only - } - } - - int nBytes= nb/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(); - return res; -} -//-----------------------------------------------------------------------------