X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=2defabdaebfcadf3c4ec6046467059cda33038c6;hb=00e89cde772e18e4f2baab2b01680330af909d59;hp=c4672b6e9d3f9a021fa9817936a9e575aec2de40;hpb=4c8c80589b3770976ea27fc03b290b97db5da3e6;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index c4672b6e..2defabda 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,14 +1,14 @@ -/*========================================================================= + /*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/07/30 11:40:13 $ - Version: $Revision: 1.117 $ + Date: $Date: 2004/10/08 17:24:54 $ + Version: $Revision: 1.137 $ 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 @@ -18,83 +18,211 @@ #include "gdcmFile.h" #include "gdcmDebug.h" +#include "gdcmPixelConvert.h" #include "jpeg/ljpg/jpegless.h" typedef std::pair IterHT; -//----------------------------------------------------------------------------- +//------------------------------------------------------------------------- // Constructor / Destructor /** - * \ingroup gdcmFile - * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant - * file (see SetFileName, SetDcmTag and Write) + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (gdcmHeader 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 + * (see GetImageData, GetImageDataRaw) * \note the in-memory representation of all available tags found in * the DICOM header is post-poned to first header information access. * This avoid a double parsing of public part of the header when - * one sets an a posteriori shadow dictionary (efficiency can be + * user sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). - * @param header file to be opened for reading datas - * @return + * @param header already built gdcmHeader */ gdcmFile::gdcmFile(gdcmHeader *header) { Header = header; SelfHeader = false; - PixelRead = -1; // no ImageData read yet. - - if (Header->IsReadable()) - { - SetPixelDataSizeFromHeader(); - } + Initialise(); } /** - * \ingroup gdcmFile - * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant - * file (see SetFileName, SetDcmTag and Write) + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (gdcmHeader 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 + * (see GetImageData, GetImageDataRaw) * \note the in-memory representation of all available tags found in * the DICOM header is post-poned to first header information access. * This avoid a double parsing of public part of the header when * one sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). * @param filename file to be opened for parsing - * @param exception_on_error whether we throw an exception or not - * @param ignore_shadow to allow skipping the shadow elements, - * to save memory space. */ -gdcmFile::gdcmFile(std::string const & filename, - bool exception_on_error, - bool ignore_shadow) +gdcmFile::gdcmFile(std::string const & filename ) { - Header = new gdcmHeader( filename, - exception_on_error, - ignore_shadow ); + Header = new gdcmHeader( filename ); SelfHeader = true; - PixelRead = -1; // no ImageData read yet. + Initialise(); +} +/** + * \brief Factorization for various forms of constructors. + */ +void gdcmFile::Initialise() +{ if ( Header->IsReadable() ) { - SetPixelDataSizeFromHeader(); + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( Header->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } } + SaveInitialValues(); } /** - * \ingroup gdcmFile * \brief canonical destructor - * \note If the gdcmHeader is created by the gdcmFile, it is destroyed - * by the gdcmFile + * \note If the gdcmHeader was created by the gdcmFile constructor, + * it is destroyed by the gdcmFile */ gdcmFile::~gdcmFile() -{ +{ if( SelfHeader ) { delete Header; } 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() ) + { + // 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); + } +} + +/** + * \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); + } +} + +/** + * \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; } //----------------------------------------------------------------------------- @@ -104,14 +232,12 @@ gdcmFile::~gdcmFile() // Public /** - * \ingroup gdcmFile - * \brief computes the length (in bytes) to ALLOCATE to receive the + * \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). - * @return length to allocate */ -void gdcmFile::SetPixelDataSizeFromHeader() +int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader() { // see PS 3.3-2003 : C.7.6.3.2.1 // @@ -140,92 +266,72 @@ void gdcmFile::SetPixelDataSizeFromHeader() // 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 = Header->GetBitsAllocated(); + 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 - - if ( Header->HasLUT() ) - { - ImageDataSize *= 3; - } -} - -/** - * \ingroup gdcmFile - * \brief Returns the size (in bytes) of required memory to hold - * the pixel data represented in this file. - * @return The size of pixel data in bytes. - */ -size_t gdcmFile::GetImageDataSize() -{ - return ImageDataSize; -} -/** - * \ingroup gdcmFile - * \brief Returns the size (in bytes) of required memory to hold - * the pixel data represented in this file, when user DOESN'T want - * to get RGB pixels image when it's stored as a PALETTE COLOR image - * -the (vtk) user is supposed to know how deal with LUTs- - * \warning to be used with GetImagePixelsRaw() - * @return The size of pixel data in bytes. - */ -size_t gdcmFile::GetImageDataSizeRaw() -{ - return ImageDataSizeRaw; + int DecompressedSize = Header->GetXSize() + * Header->GetYSize() + * Header->GetZSize() + * ( numberBitsAllocated / 8 ) + * Header->GetSamplesPerPixel(); + + return DecompressedSize; } /** - * \ingroup gdcmFile - * \brief Allocates necessary memory, copies the pixel data - * (image[s]/volume[s]) to newly allocated zone. - * Transforms YBR pixels into RGB pixels if any - * Transforms 3 planes R, G, B into a single RGB Plane - * Transforms single Grey plane + 3 Palettes into a RGB Plane + * \brief - Allocates necessary memory, + * - Reads the pixels from disk (uncompress if necessary), + * - Transforms YBR pixels, if any, into RGB pixels + * - Transforms 3 planes R, G, B, if any, into a single RGB Plane + * - Transforms single Grey plane + 3 Palettes into a RGB Plane + * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ -void *gdcmFile::GetImageData() +uint8_t* gdcmFile::GetImageData() { - // FIXME - // I need to deallocate PixelData before doing any allocation: - PixelData = new uint8_t[ImageDataSize]; - if ( PixelData ) + // 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 ) { - GetImageDataIntoVector(PixelData, ImageDataSize); - GetHeader()->SetEntryVoidAreaByNumber( PixelData, + 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 - return PixelData; + return Pixel_Data; } /** - * \ingroup gdcmFile - * \brief Copies at most MaxSize bytes of pixel data to caller's + * \brief + * Read the pixels from disk (uncompress if necessary), + * Transforms YBR pixels, if any, into RGB pixels + * Transforms 3 planes R, G, B, if any, into a single RGB Plane + * Transforms single Grey plane + 3 Palettes into a RGB Plane + * Copies at most MaxSize bytes of pixel data to caller allocated * 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 + * \warning This function allows people that want to build a volume + * from an image stack *not to* have, 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 @@ -243,9 +349,8 @@ void *gdcmFile::GetImageData() */ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) { - //size_t l = GetImageDataIntoVectorRaw (destination, maxSize); GetImageDataIntoVectorRaw (destination, maxSize); - PixelRead = 0 ; // no PixelRaw + PixelRead = 0 ; // =0 : no ImageDataRaw if ( !Header->HasLUT() ) { return ImageDataSize; @@ -259,7 +364,6 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) if ( lutRGBA ) { int j; - //int l = ImageDataSizeRaw; //loss of precision // move Gray pixels to temp area memmove(newDest, destination, ImageDataSizeRaw); for (size_t i=0; iSetEntryByNumber(spp,0x0028,0x0002); - std::string rgb = "RGB "; // Photometric Interpretation + std::string rgb = "RGB "; // Photometric Interpretation Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration Header->SetEntryByNumber(planConfig,0x0028,0x0006); } - else //why is there a 'else' when an allocation failed ? - { - // need to make RGB Pixels (?) - // from grey Pixels (?!) - // and Gray Lut (!?!) - // or Segmented xxx Palette Color Lookup Table Data and so on - - // Oops! I get one (gdcm-US-ALOKA-16.dcm) - // No idea how to manage such an image + 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 :-( - // Segmented xxx Palette Color are *more* than 65535 long ?!? - - std::string rgb = "MONOCHROME1 "; // Photometric Interpretation - Header->SetEntryByNumber(rgb,0x0028,0x0004); + + std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation + Header->SetEntryByNumber(photomInterp,0x0028,0x0004); } /// \todo Drop Palette Color out of the Header? @@ -306,40 +406,53 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) } /** - * \ingroup gdcmFile - * \brief Allocates necessary memory, copies the pixel data - * (image[s]/volume[s]) to newly allocated zone. - * Transforms YBR pixels into RGB pixels if any - * Transforms 3 planes R, G, B into a single RGB Plane + * \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 + * Copies the pixel data (image[s]/volume[s]) to newly allocated zone. * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -void * gdcmFile::GetImageDataRaw () +uint8_t* gdcmFile::GetImageDataRaw () { - size_t imgDataSize = ImageDataSize; + 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]; - // FIXME - // I need to deallocate PixelData before doing any allocation: - PixelData = new uint8_t[imgDataSize]; - if ( PixelData ) + if ( Pixel_Data ) { - GetImageDataIntoVectorRaw(PixelData, ImageDataSize); - GetHeader()->SetEntryVoidAreaByNumber(PixelData, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + 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 PixelData; + return Pixel_Data; } /** - * \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 @@ -362,11 +475,19 @@ 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) +size_t gdcmFile::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 "read" before + { + RestoreInitialValues(); + } + PixelRead = 1 ; // PixelRaw - + if ( ImageDataSize > maxSize ) { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" @@ -377,270 +498,262 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize) ReadPixelData( destination ); // Number of Bits Allocated for storing a Pixel - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( numberBitsAllocated == 0 ) { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - // FIXME - // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated - // separately, correct ? + numberBitsAllocated = 16; } // Number of Bits actually used - std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101); - if ( str_nbu == GDCM_UNFOUND ) + int numberBitsStored = Header->GetBitsStored(); + if ( numberBitsStored == 0 ) { - nbu = nb; - } - else - { - nbu = atoi( str_nbu.c_str() ); + numberBitsStored = numberBitsAllocated; } // High Bit Position - std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102); - if ( str_highBit == GDCM_UNFOUND ) + int highBitPosition = Header->GetHighBitPosition(); + if ( highBitPosition == 0 ) { - highBit = nb - 1; + highBitPosition = numberBitsAllocated - 1; } - 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 + bool signedPixel = Header->IsSignedPixelData(); + + gdcmPixelConvert::ConvertReorderEndianity( + (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + Header->GetSwapCode(), + signedPixel ); + + ConvertReArrangeBits( (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + highBitPosition ); + +#ifdef GDCM_DEBUG + FILE* DebugFile; + DebugFile = fopen( "SpuriousFile.RAW", "wb" ); + fwrite( PixelConvertor.GetUncompressed(), + PixelConvertor.GetUncompressedsSize(), + 1, DebugFile ); + fclose( DebugFile ); +#endif //GDCM_DEBUG + +// SPLIT ME +////////////////////////////////// +// Deal with the color + + // Monochrome pictures don't require color intervention + if ( Header->IsMonochrome() ) { - sign = atoi( str_sign.c_str() ); + 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 :-( - // re arange bytes inside the integer (processor endianity) - if ( nb != 8 ) + 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() ) { - SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); + return ImageDataSize; } - - // to avoid pb with some xmedcon breakers images - if ( nb == 16 && nbu < nb && sign == 0) + + // When planConf is 0, pixels are allready in RGB + + if ( planConf == 1 ) { - int l = (int)(ImageDataSize / (nb/8)); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; iIsYBRFull() ) { - if( *deb == 0xffff ) - { - *deb = 0; - } - deb++; + ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest); + } + else + { + ConvertRGBPlanesToRGBPixels((uint8_t*)destination, newDest); } + memmove(destination, newDest, ImageDataSize); + delete[] newDest; } - // re arange bits inside the bytes - if ( nbu != nb ) +/////////////////////////////////////////////////// + // 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; +} + +/** + * \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 / (nb/8)); - if ( nb == 16 ) + int l = (int)(imageDataSize / (numberBitsAllocated/8)); + if ( numberBitsAllocated == 16 ) { uint16_t mask = 0xffff; - mask = mask >> (nb-nbu); - uint16_t *deb = (uint16_t *)destination; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint16_t* deb = (uint16_t*)pixelZone; for(int i = 0; i> (nbu - highBit - 1)) & mask; + *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask; deb++; } } - else if ( nb == 32 ) + else if ( numberBitsAllocated == 32 ) { uint32_t mask = 0xffffffff; - mask = mask >> (nb - nbu); - uint32_t *deb = (uint32_t *)destination; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint32_t* deb = (uint32_t*)pixelZone; for(int i = 0; i> (nbu - highBit - 1)) & mask; + *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask; deb++; } } else { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); - return 0; + dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image"); + throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()", + "weird image !?" ); } } -// 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 " ) +/** + * \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) +{ + // 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++) { - return ImageDataSize; + 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; + + *(destination++) = (uint8_t)R; + *(destination++) = (uint8_t)G; + *(destination++) = (uint8_t)B; + a++; + b++; + c++; + } } - - // 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 +/** + * \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(); - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if ( str_PhotometricInterpretation == "PALETTE COLOR ") - { - planConf = 2; - } + uint8_t* a = source; + uint8_t* b = source + l; + uint8_t* c = source + l + l; - switch ( planConf ) + for (int j = 0; j < l; j++) { - 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; + *(destination++) = *(a++); + *(destination++) = *(b++); + *(destination++) = *(c++); } - // now, it's an RGB image - // Lets's write it in the Header - - // CreateOrReplaceIfExist ? - - std::string spp = "3"; // Samples Per Pixel - std::string rgb = "RGB "; // Photometric Interpretation - std::string planConfig = "0"; // Planar Configuration - - Header->SetEntryByNumber(spp,0x0028,0x0002); - Header->SetEntryByNumber(rgb,0x0028,0x0004); - Header->SetEntryByNumber(planConfig,0x0028,0x0006); - - /// \todo Drop Palette Color out of the Header? - return ImageDataSize; } /** - * \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 : lane 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 gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize) { Header->SetImageDataSize( expectedSize ); - PixelData = inData; - ImageDataSize = expectedSize; +// FIXME : if already allocated, memory leak ! + Pixel_Data = inData; + ImageDataSize = ImageDataSizeRaw = expectedSize; PixelRead = 1; - +// FIXME : 7fe0, 0010 IS NOT set ... return true; } /** - * \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 @@ -651,20 +764,19 @@ bool gdcmFile::SetImageData(void *inData, size_t expectedSize) bool gdcmFile::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()); return false; } - fwrite (PixelData, ImageDataSize, 1, fp1); + fwrite (Pixel_Data, ImageDataSize, 1, fp1); fclose (fp1); return true; } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the Implicit Value Representation convention * NO test is performed on processor "Endiannity". @@ -679,7 +791,6 @@ bool gdcmFile::WriteDcmImplVR (std::string const & fileName) } /** - * \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 @@ -693,7 +804,6 @@ bool gdcmFile::WriteDcmExplVR (std::string const & fileName) } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the ACR-NEMA convention * NO test is performed on processor "Endiannity". @@ -715,7 +825,6 @@ bool gdcmFile::WriteAcr (std::string const & fileName) //----------------------------------------------------------------------------- // 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 @@ -730,7 +839,7 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) 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()); @@ -801,7 +910,7 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) } // ----------------- End of Special Patch ---------------- - // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now + // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); return true; @@ -810,99 +919,14 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) //----------------------------------------------------------------------------- // 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 - */ -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; - } - } -} - -/** - * \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) +bool gdcmFile::ReadPixelData(void* destination) { - FILE *fp = Header->OpenFile(); + FILE* fp = Header->OpenFile(); if ( !fp ) { @@ -914,32 +938,13 @@ bool gdcmFile::ReadPixelData(void *destination) return false; } - // ---------------------- 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 ? - } - + gdcmPixelConvert::ConvertDecompress12BitsTo16Bits( + (uint8_t*)destination, + Header->GetXSize(), + Header->GetYSize(), + fp); Header->CloseFile(); return true; } @@ -966,28 +971,25 @@ bool gdcmFile::ReadPixelData(void *destination) // ---------------------- Run Length Encoding if ( Header->IsRLELossLessTransferSyntax() ) { - bool res = gdcm_read_RLE_file (fp,destination); + bool res = gdcmPixelConvert::gdcm_read_RLE_file ( destination, + Header->GetXSize(), + Header->GetYSize(), + Header->GetZSize(), + Header->GetBitsAllocated(), + &(Header->RLEInfo), + fp ); Header->CloseFile(); return res; } // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - if ( nb == 12 ) - { - nb = 16; // ?? 12 should be ACR-NEMA only - } + numberBitsAllocated = 16; } - int nBytes= nb/8; + int nBytes= numberBitsAllocated/8; int taille = Header->GetXSize() * Header->GetYSize() * Header->GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek @@ -1046,7 +1048,7 @@ bool gdcmFile::ReadPixelData(void *destination) if ( jpg2000 ) { // JPEG 2000 : call to ??? - res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written + res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written // ------------------------------------- endif (JPEG2000) } else if (jpgLossless) @@ -1064,12 +1066,18 @@ bool gdcmFile::ReadPixelData(void *destination) if ( Header->GetBitsStored() == 8) { // Reading Fragment pixels - res = (bool)gdcm_read_JPEG_file (fp,destination); + res = gdcm_read_JPEG_file (fp,destination); } - else + else if ( Header->GetBitsStored() == 12) { // Reading Fragment pixels - res = (bool)gdcm_read_JPEG_file12 (fp,destination); + res = gdcm_read_JPEG_file12 (fp,destination); + } + else + { + // other JPEG lossy not supported + dbg.Error(" gdcmFile::ReadPixelData : unknown jpeg lossy compression"); + return 0; } // ------------------------------------- endif (JPEGLossy) } @@ -1100,4 +1108,4 @@ bool gdcmFile::ReadPixelData(void *destination) Header->CloseFile(); return res; } -//----------------------------------------------------------------------------- +