X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=b91e7be504d581c816919563df8914326bffa773;hb=45c601b1fe996ebe3bf221541448f693a399173b;hp=c103e111bfe3711ef8e087351dd9e4e4507d0e1d;hpb=4a0c2407ec81e041c2e43781acec4c78c83fc487;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index c103e111..b91e7be5 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,431 +1,786 @@ -// gdcmFile.cxx + /*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/10/13 14:56:07 $ + Version: $Revision: 1.143 $ + + 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.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ #include "gdcmFile.h" -#include "gdcmUtil.h" -#include "iddcmjpeg.h" +#include "gdcmDebug.h" -///////////////////////////////////////////////////////////////// +namespace gdcm +{ +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 (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. - * \Note the in-memory representation of all available tags found in + * 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 filename file to be opened for parsing - * - * @return + * @param header already built Header */ - -gdcmFile::gdcmFile(string & filename) - :gdcmHeader(filename.c_str()) +File::File(Header *header) { - SetPixelDataSizeFromHeader(); + HeaderInternal = header; + SelfHeader = false; + Initialise(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) +/** + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * 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 + * (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 + */ +File::File(std::string const & filename ) { - SetPixelDataSizeFromHeader(); + HeaderInternal = new Header( filename ); + SelfHeader = true; + Initialise(); } - -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les - * pixels de l'image - * ou DES images dans le cas d'un multiframe - * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels - * (dans le cas d'images compressees, elle n'a pas de sens). - * - * @return longueur a allouer + * \brief Factorization for various forms of constructors. */ +void File::Initialise() +{ + if ( HeaderInternal->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( HeaderInternal->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } -void gdcmFile::SetPixelDataSizeFromHeader(void) { - int nb; - string str_nb; - str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; + + + // Just in case some access to a Header element requires disk access. + // Note: gdcmDocument::Fp is leaved open after OpenFile. + (void)HeaderInternal->OpenFile(); + // Number of Bits Allocated for storing a Pixel is defaulted to 16 + // when absent from the header. + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + if ( numberBitsAllocated == 0 ) + { + numberBitsAllocated = 16; + } + PixelConverter.SetBitsAllocated( numberBitsAllocated ); + + // Number of "Bits Stored" defaulted to number of "Bits Allocated" + // when absent from the header. + int numberBitsStored = HeaderInternal->GetBitsStored(); + if ( numberBitsStored == 0 ) + { + numberBitsStored = numberBitsAllocated; + } + PixelConverter.SetBitsStored( numberBitsStored ); + + // High Bit Position + int highBitPosition = HeaderInternal->GetHighBitPosition(); + if ( highBitPosition == 0 ) + { + highBitPosition = numberBitsAllocated - 1; + } + PixelConverter.SetHighBitPosition( highBitPosition ); + + + PixelConverter.SetXSize( HeaderInternal->GetXSize() ); + PixelConverter.SetYSize( HeaderInternal->GetYSize() ); + PixelConverter.SetZSize( HeaderInternal->GetZSize() ); + PixelConverter.SetSamplesPerPixel( HeaderInternal->GetSamplesPerPixel() ); + PixelConverter.SetPixelSize( HeaderInternal->GetPixelSize() ); + PixelConverter.SetPixelSign( HeaderInternal->IsSignedPixelData() ); + PixelConverter.SetSwapCode( HeaderInternal->GetSwapCode() ); + PixelConverter.SetIsUncompressed( + ! HeaderInternal->IsDicomV3() + || HeaderInternal->IsImplicitVRLittleEndianTransferSyntax() + || HeaderInternal->IsExplicitVRLittleEndianTransferSyntax() + || HeaderInternal->IsExplicitVRBigEndianTransferSyntax() + || HeaderInternal->IsDeflatedExplicitVRLittleEndianTransferSyntax() ); + PixelConverter.SetIsJPEG2000( HeaderInternal->IsJPEG2000() ); + PixelConverter.SetIsJPEGLossless( HeaderInternal->IsJPEGLossless() ); + PixelConverter.SetIsRLELossless( + HeaderInternal->IsRLELossLessTransferSyntax() ); + PixelConverter.SetPixelOffset( HeaderInternal->GetPixelOffset() ); + PixelConverter.SetPixelDataLength( HeaderInternal->GetPixelAreaLength() ); + PixelConverter.SetRLEInfo( &(HeaderInternal->RLEInfo) ); + PixelConverter.SetJPEGInfo( &(HeaderInternal->JPEGInfo) ); + PixelConverter.SetDecompressedSize( ImageDataSize ); + + PixelConverter.SetPlanarConfiguration( + HeaderInternal->GetPlanarConfiguration() ); + PixelConverter.SetIsMonochrome( HeaderInternal->IsMonochrome() ); + PixelConverter.SetIsPaletteColor( HeaderInternal->IsPaletteColor() ); + PixelConverter.SetIsYBRFull( HeaderInternal->IsYBRFull() ); + + HeaderInternal->CloseFile(); + } - lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8); + SaveInitialValues(); } /** - * \ingroup gdcmFile - * \brief Accessor + * \brief canonical destructor + * \note If the Header was created by the File constructor, + * it is destroyed by the File */ -size_t gdcmFile::GetImageDataSize(void) { - return (lgrTotale); -} +File::~File() +{ + if( SelfHeader ) + { + delete HeaderInternal; + } + HeaderInternal = 0; + DeleteInitialValues(); +} /** - * \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. - * + * \brief Sets some initial values for the Constructor + * \warning not end user intended */ -bool gdcmFile::ReadPixelData(void* destination) { - if ( !OpenFile()) - return false; - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - return false; - } - if (IsJPEGLossless()) { - destination = _IdDcmJpegRead(fp); - } else { - size_t ItemRead = fread(destination, lgrTotale, 1, fp); - if ( ItemRead != 1 ) { - CloseFile(); - return false; - } +void File::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 ( HeaderInternal->IsReadable() ) + { + // the following values *may* be modified + // by File::GetImageDataIntoVectorRaw + // we save their initial value. + 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 File::GetImageDataIntoVectorRaw + // we keep a pointer on them. + 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); } - CloseFile(); - return true; -} +} -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Allocates necessary memory, copies the pixel data - * (image[s]/volume[s]) to newly allocated zone and return a - * pointer to it: + * \brief restores some initial values + * \warning not end user intended */ -void * gdcmFile::GetImageData (void) { - PixelData = (void *) malloc(lgrTotale); - GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); +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); + } } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief amene en mémoire dans une zone précisee par l'utilisateur - * les Pixels d'une image - * - * @param destination - * @param MaxSize - * - * @return The number of bytes actually copied. + * \brief delete initial values (il they were saved) + * of InitialLutDescriptors and InitialLutData */ +void File::DeleteInitialValues() +{ -size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { +// 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... - int nb, nbu, highBit, signe; - string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; - - if ( lgrTotale > MaxSize ) { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return (size_t)0; - } - - (void)ReadPixelData(destination); - - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - } - - // Nombre de Bits Utilises - str_nbu=GetPubElValByNumber(0x0028,0x0101); - if (str_nbu == "gdcm::Unfound" ) { - nbu = nb; - } else { - nbu = atoi(str_nbu.c_str() ); - } - - // Position du Bit de Poids Fort - str_highBit=GetPubElValByNumber(0x0028,0x0102); - if (str_highBit == "gdcm::Unfound" ) { - highBit = nb - 1; - } else { - highBit = atoi(str_highBit.c_str() ); - } - - // Signe des Pixels - str_signe=GetPubElValByNumber(0x0028,0x0103); - if (str_signe == "gdcm::Unfound" ) { - signe = 1; - } else { - signe = atoi(str_signe.c_str() ); - } - - // On remet les Octets dans le bon ordre si besoin est - if (nb != 8) - SwapZone(destination, GetSwapCode(), lgrTotale, nb); - - // On remet les Bits des Octets dans le bon ordre si besoin est - if (nbu != nb){ - int l = (int)lgrTotale / (nb/8); - if (nb == 16) { - guint16 mask = 0xffff; - mask = mask >> (nb-nbu); - guint16 *deb = (guint16 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; - } - } else if (nb == 32 ) { - guint32 mask = 0xffffffff; - mask = mask >> (nb-nbu); - guint32 *deb = (guint32 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; - } - } else { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image"); - return (size_t)0; - } - } - return lgrTotale; + 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; } +//----------------------------------------------------------------------------- +// Print -// -// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs -// +//----------------------------------------------------------------------------- +// Public -void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { -guint32 s32; -guint16 fort,faible; -int i; +/** + * \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). + */ +int File::ComputeDecompressedPixelDataSizeFromHeader() +{ + // 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] + + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + // Number of "Bits Allocated" is fixed to 16 when: + // - it is not defined (i.e. it's value is 0) + // - it's 12, since we will expand the image to 16 bits (see + // PixelConvert::ConvertDecompress12BitsTo16Bits() ) + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) + { + numberBitsAllocated = 16; + } + + int DecompressedSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + + return DecompressedSize; +} -if(nb == 16) +/** + * \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 + */ +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]; - switch(swap) { - case 0: - case 12: - case 1234: - break; - - case 21: - case 3412: - case 2143: - case 4321: - - for(i=0;i>8) - | ((((unsigned short int*)im)[i])<<8); - break; - - default: - printf("valeur de SWAP (16 bits) non autorisee : %d\n", swap); - } - -if( nb == 32 ) - - switch (swap) { - case 0: - case 1234: - break; - - case 4321: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - case 2143: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=fort; - ((unsigned long int*)im)[i]=(s32<<16)|faible; - } - break; - - case 3412: - for(i=0;i>16; - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - default: - printf("valeur de SWAP (32 bits) non autorisee : %d\n", swap); - } -return; + if ( Pixel_Data ) + { + 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 Pixel_Data; } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief TODO JPR - * \warning doit-etre etre publique ? FIXME JPR - * - * @param Data TODO JPR - * @param ExpectedSize TODO JPR - * - * @return TODO JPR + * \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 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 + * (for some axis related reasons?). Hence he will have + * to load the image line by line, starting from the end. + * VTK users have to call GetImageData + * + * @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. */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(1); -} +size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) +{ + GetImageDataIntoVectorRaw (destination, maxSize); + PixelRead = 0 ; // =0 : no ImageDataRaw + 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 = HeaderInternal->GetLUTRGBA(); + + if ( lutRGBA ) + { + int j; + // 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 + HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004); + std::string planConfig = "0"; // Planar Configuration + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); + } + 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 + HeaderInternal->SetEntryByNumber(photomInterp,0x0028,0x0004); + } + + /// \todo Drop Palette Color out of the Header? + return ImageDataSize; +} -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief TODO JPR - * \ - * \warning WARNING doit-etre etre publique ? FIXME JPR - * - * @param ImageDataSize TODO JPR - * + * \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 */ +uint8_t* File::GetImageDataRaw () +{ + size_t imgDataSize; + if ( HeaderInternal->HasLUT() ) + /// \todo Let Header 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 -void gdcmFile::SetImageDataSize(size_t ImageDataSize) { - - string content1; - string content2; - char car[20]; - - // suppose que le ElValue (0x7fe0, 0x0010) existe ... - - sprintf(car,"%d",ImageDataSize); - content2=car; - SetPubElValByNumber(content2, 0x7fe0, 0x0010); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetPubElValByNumber(content1, 0x7fe0, 0x0000); + return Pixel_Data; } - -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Ecrit sur disque les pixels d'UNE image - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca sera à l'utilisateur d'appeler son Reader correctement - * (Equivalent a IdImaWriteRawFile) FIXME JPR - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \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. */ +void File::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) +{ + // we save the initial values of the following + // in order to be able to restore the header in a disk-consistent state + // (if user asks twice to get the pixels from disk) -int gdcmFile::WriteRawData (string nomFichier) { - - FILE * fp1; - fp1 = fopen(nomFichier.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str()); - return (0); - } - - fwrite (PixelData,lgrTotale, 1, fp1); - fclose (fp1); - return(1); -} + if ( PixelRead != -1 ) // File was "read" before + { + RestoreInitialValues(); + } + + PixelRead = 1 ; // PixelRaw + + if ( ImageDataSize > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return; + } + FILE* fp = HeaderInternal->OpenFile(); + PixelConverter.ReadAndDecompressPixelData( destination, fp ); + HeaderInternal->CloseFile(); + + if ( ! PixelConverter.HandleColor( (uint8_t*)destination ) ) + { + return; + } +/////////////////////////////////////////////////// + // now, it's an RGB image + // Lets's write it in the Header + + // Droping Palette Color out of the Header + // has been moved to the Write process. + + // TODO : move 'values' modification to the write process + // : save also (in order to be able to restore) + // : 'high bit' -when not equal to 'bits stored' + 1 + // : 'bits allocated', when it's equal to 12 ?! + + std::string spp = "3"; // Samples Per Pixel + std::string photInt = "RGB "; // Photometric Interpretation + std::string planConfig = "0"; // Planar Configuration + + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); + + return; +} -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Ecrit sur disque UNE image Dicom - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) FIXME JPR + * \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 * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * @return boolean + */ +bool File::SetImageData(uint8_t* inData, size_t expectedSize) +{ + HeaderInternal->SetImageDataSize( expectedSize ); +// FIXME : if already allocated, memory leak ! + Pixel_Data = inData; + ImageDataSize = ImageDataSizeRaw = expectedSize; + PixelRead = 1; +// FIXME : 7fe0, 0010 IS NOT set ... + return true; +} + +/** + * \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 + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails */ -int gdcmFile::WriteDcmImplVR (string nomFichier) { - return WriteBase(nomFichier, ImplicitVR); +bool File::WriteRawData(std::string const & fileName) +{ + FILE* fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Fail to open (write) file [%s] \n", fileName.c_str()); + return false; + } + fwrite (Pixel_Data, ImageDataSize, 1, fp1); + fclose (fp1); + + return true; } -int gdcmFile::WriteDcmImplVR (const char* nomFichier) { - return WriteDcmImplVR (string (nomFichier)); +/** + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention + * NO test is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails + */ + +bool File::WriteDcmImplVR (std::string const & fileName) +{ + return WriteBase(fileName, ImplicitVR); } - -///////////////////////////////////////////////////////////////// + /** - * \ingroup gdcmFile - * - * @param nomFichier TODO JPR - * - * @return TODO JPR +* \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 + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmExplVR (string nomFichier) { - return WriteBase(nomFichier, ExplicitVR); +bool File::WriteDcmExplVR (std::string const & fileName) +{ + return WriteBase(fileName, ExplicitVR); } - -///////////////////////////////////////////////////////////////// + /** - * \ingroup gdcmFile - * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels + * \brief Writes on disk A SINGLE Dicom file, + * using the ACR-NEMA convention + * NO test is performed on processor "Endiannity". * (a l'attention des logiciels cliniques * qui ne prennent en entrée QUE des images ACR ... - * \warning si un header DICOM est fourni en entree, - * les groupes < 0x0008 et les groupes impairs sont ignores) - * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \warning if a DICOM_V3 header is supplied, + * groups < 0x0008 and shadow groups are ignored + * \warning NO TEST is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteAcr (string nomFichier) { - return WriteBase(nomFichier, ACR); +bool File::WriteAcr (std::string const & fileName) +{ + return WriteBase(fileName, ACR); } -int gdcmFile::WriteBase (string nomFichier, FileType type) { +//----------------------------------------------------------------------------- +// Protected +/** + * \brief NOT a end user inteded function + * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @param type file type (ExplicitVR, ImplicitVR, ...) + * @return false if write fails + */ +bool File::WriteBase (std::string const & fileName, FileType type) +{ + if ( PixelRead == -1 && type != ExplicitVR) + { + return false; + } - FILE * fp1; - fp1 = fopen(nomFichier.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str()); - return (0); + 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 == ImplicitVR) || (type == ExplicitVR) ) { - char * filePreamble; - // Ecriture Dicom File Preamble - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); + if ( type == ImplicitVR || type == ExplicitVR ) + { + // 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; } - gdcmHeader::Write(fp1, type); - fwrite(PixelData, lgrTotale, 1, fp1); + // -------------------------------------------------------------- + // Special Patch to allow gdcm to re-write ACR-LibIDO formated images + // + // 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 ( HeaderInternal->GetFileType() == ACR_LIBIDO) + { + rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010); + columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011); + + HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0010); + HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- + + uint16_t grPixel = HeaderInternal->GetGrPixel(); + uint16_t numPixel = HeaderInternal->GetNumPixel();; + + DocEntry* PixelElement = + GetHeader()->GetDocEntryByNumber(grPixel, numPixel); + + if ( PixelRead == 1 ) + { + // we read pixel 'as is' (no tranformation LUT -> RGB) + PixelElement->SetLength( ImageDataSizeRaw ); + } + else if ( PixelRead == 0 ) + { + // we tranformed GrayLevel pixels + LUT into RGB Pixel + PixelElement->SetLength( ImageDataSize ); + } + + HeaderInternal->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 ( HeaderInternal->GetFileType() == ACR_LIBIDO ) + { + HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010); + HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- + + // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); - return(1); + + return true; } + +} // end namespace gdcm +