X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=20178169cf5a1c4f5e22c963a675335375a8b785;hb=9649936f884197f6f6260aae051d33729bce07d5;hp=f6cf79c91cb22a93595f09bc8690323514152f1b;hpb=1d7f7845726ab0b4e4630575f629a554d5707576;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index f6cf79c9..f044feb1 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,486 +1,716 @@ -// gdcmFile.cxx + /*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/10/28 03:10:58 $ + Version: $Revision: 1.150 $ + + 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 "gdcmDebug.h" +#include -static void _Swap(void* im, int swap, int lgr, int nb); +namespace gdcm +{ +typedef std::pair IterHT; + +//------------------------------------------------------------------------- +// Constructor / Destructor +/** + * \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 + * user sets an a posteriori shadow dictionary (efficiency can be + * seen as a side effect). + * @param header already built Header + */ +File::File(Header *header) +{ + HeaderInternal = header; + SelfHeader = false; + 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 (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 * seen as a side effect). - * * @param filename file to be opened for parsing - * - * @return */ - -gdcmFile::gdcmFile(string & filename) - :gdcmHeader(filename.c_str()) +File::File(std::string const & filename ) { + HeaderInternal = new Header( filename ); + SelfHeader = true; + Initialise(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) +/** + * \brief Factorization for various forms of constructors. + */ +void File::Initialise() { + if ( HeaderInternal->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( HeaderInternal->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } + + PixelConverter = new PixelConvert; + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + } + SaveInitialValues(); } - -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Renvoie la longueur 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 canonical destructor + * \note If the Header was created by the File constructor, + * it is destroyed by the File */ - -size_t gdcmFile::GetImageDataSize(void) { - int nbLignes, nbCol, nbFrames, nb; - string str_nbFrames, str_nb; - // Nombre de Lignes - nbLignes=atoi(gdcmHeader::GetPubElValByNumber(0x0028,0x0010).c_str()); - // Nombre de Colonnes - nbCol =atoi(gdcmHeader::GetPubElValByNumber(0x0028,0x0011).c_str()); - - // Nombre de Frames - str_nbFrames=gdcmHeader::GetPubElValByNumber(0x0028,0x0008); - - if (str_nbFrames == "gdcm::Unfound" ) { - nbFrames = 1; - } else { - nbFrames = atoi(str_nbFrames.c_str() ); - } - - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - - if (str_nb == "gdcm::Unfound" ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - } - - size_t lgrTotale = nbFrames*nbLignes*nbCol*(nb/8); - return (lgrTotale); +File::~File() +{ + if( SelfHeader ) + { + delete HeaderInternal; + } + HeaderInternal = 0; + + DeleteInitialValues(); } - - -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief TODO - * \warning WARNING - * + * \brief Sets some initial values for the Constructor + * \warning not end user intended */ -void * gdcmFile::GetImageData (void) { - char * _Pixels; - // Longueur en Octets des Pixels a lire - size_t taille = GetImageDataSize();// ne faudrait-il pas la stocker? - _Pixels = (char *) malloc(taille); - GetImageDataIntoVector(_Pixels, taille); - - // On l'affecte à un champ du dcmFile - Pixels = _Pixels; - lgrTotale = taille; - - // ca fait double emploi, il faudra nettoyer ça - - return(_Pixels); +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); + } } +/** + * \brief restores some initial values + * \warning not end user intended + */ +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 NON COMPRESSEE - * \Warning Aucun test n'est fait pour le moment sur le caractere compresse ou non de l'image - * - * @param destination - * @param MaxSize - * - * @return TODO JPR + * \brief delete initial values (il they were saved) + * of InitialLutDescriptors and InitialLutData */ +void File::DeleteInitialValues() +{ -int gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { - -// Question : -// dans quel cas la MaxSize sert-elle a quelque chose? -// que fait-on si la taille de l'image est + gde que Maxize? -// que fait-on si la taille de l'image est + petite que Maxize? - - - void * Pixels = destination; // pour garder le code identique avec GetImageData - - int nb, nbu, highBit, signe; - string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; - - unsigned short int mask = 0xffff; - - // Longueur en Octets des Pixels a lire - size_t _lgrTotale = GetImageDataSize(); // ne faudrait-il pas la stocker? - - // si lgrTotale < MaxSize ==> Gros pb - // -> on résoud à la goret - - if ( _lgrTotale < MaxSize ) MaxSize = _lgrTotale; - - GetPixels(MaxSize, destination); - - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb=gdcmHeader::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) { - int _sw = GetSwapCode(); - - _Swap (destination, _sw, _lgrTotale, nb); - } - - // On remet les Bits des Octets dans le bon ordre si besoin est - // - // ATTENTION : Jamais confronté a des pixels stockes sur 32 bits - // avec moins de 32 bits utilises - // et dont le bit de poids fort ne serait pas la ou on l'attend ... - // --> ne marchera pas dans ce cas - if (nbu!=nb){ - mask = mask >> (nb-nbu); - int l=(int)MaxSize/(nb/8); - unsigned short *deb = (unsigned short *)Pixels; - for(int i=0;i> (nbu-highBit-1)) & mask; - deb ++; - } - } - - // VOIR s'il ne faudrait pas l'affecter à un champ du dcmHeader - - return 1; +// 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; } +//----------------------------------------------------------------------------- +// Print -// -// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs -// - -static void _Swap(void* im, int swap, int lgr, int nb) { -guint32 s32; -guint16 fort,faible; -int i; - -if(nb == 16) - - 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; +//----------------------------------------------------------------------------- +// Public + +/** + * \brief computes the length (in bytes) we must ALLOCATE to receive the + * image(s) pixels (multiframes taken into account) + * \warning : it is NOT the group 7FE0 length + * (no interest for compressed images). + */ +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; } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief TODO JPR - * \warning doit-etre etre publique ? FIXME JPR - * - * @param Data TODO JPR - * @param ExpectedSize TODO JPR - * - * @return TODO JPR + * \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 */ -int gdcmFile::SetImageData(void * Data, size_t ExpectedSize) { - - SetImageDataSize(ExpectedSize); - - Pixels = Data; - lgrTotale = ExpectedSize; - - return(1); +uint8_t* File::GetImageData() +{ + if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + uint8_t* pixelData; + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + pixelData = PixelConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the decompressed + pixelData = PixelConverter->GetDecompressed(); + } + +// PIXELCONVERT CLEANME + // 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(); + } + if ( PixelConverter->GetRGB() ) + { + // now, it's an RGB image + // Lets's write it in the Header + 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); + PixelRead = 0; // no PixelRaw + } + else + { + if ( HeaderInternal->HasLUT() ) + { + // The LUT interpretation failed + std::string photometricInterpretation = "MONOCHROME1 "; + HeaderInternal->SetEntryByNumber( photometricInterpretation, + 0x0028, 0x0004 ); + PixelRead = 0; // no PixelRaw + } + else + { + if ( PixelConverter->IsDecompressedRGB() ) + { + /////////////////////////////////////////////////// + // 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); + } + PixelRead = 1; // PixelRaw + } + } + + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // Will be 7fe0, 0010 in standard case + GetHeader()->SetEntryBinAreaByNumber( pixelData, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); +// END PIXELCONVERT CLEANME + + return pixelData; } +/** + * \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. + */ +size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) +{ + if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + if ( PixelConverter->GetRGBSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memmove( destination, + (void*)PixelConverter->GetRGB(), + PixelConverter->GetRGBSize() ); + return PixelConverter->GetRGBSize(); + } + + // Either no LUT conversion necessary or LUT conversion failed + if ( PixelConverter->GetDecompressedSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memmove( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + return PixelConverter->GetDecompressedSize(); +} -///////////////////////////////////////////////////////////////// /** - * \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 () +{ + uint8_t* decompressed = GetDecompressed(); + if ( ! decompressed ) + { + return 0; + } + +// PIXELCONVERT CLEANME + // 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(); + } + if ( PixelConverter->IsDecompressedRGB() ) + { + /////////////////////////////////////////////////// + // 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); + } + + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // will be 7fe0, 0010 in standard cases + GetHeader()->SetEntryBinAreaByNumber( decompressed, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + PixelRead = 1; // PixelRaw +// END PIXELCONVERT CLEANME -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 decompressed; } +uint8_t* File::GetDecompressed() +{ + uint8_t* decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + // The decompressed image migth not be loaded yet: + std::ifstream* fp = HeaderInternal->OpenFile(); + PixelConverter->ReadAndDecompressPixelData( fp ); + HeaderInternal->CloseFile(); + decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + dbg.Verbose(0, "File::GetDecompressed: read/decompress of " + "pixel data apparently went wrong."); + return 0; + } + } + + return decompressed; +} -///////////////////////////////////////////////////////////////// /** - * \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 + * \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 */ - -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 (Pixels,lgrTotale, 1, fp1); - fclose (fp1); - return(1); +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 + */ +bool File::WriteRawData(std::string const & fileName) +{ + std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); + if (!fp1) + { + printf("Fail to open (write) file [%s] \n", fileName.c_str()); + return false; + } + fp1.write((char*)Pixel_Data, ImageDataSize); + fp1.close(); + + return true; +} -///////////////////////////////////////////////////////////////// /** - * \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 - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \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 */ -int gdcmFile::WriteDcm (string nomFichier) { - -// ATTENTION : fonction non terminée (commitée a titre de precaution) - - FILE * fp1; - char* filePreamble; - fp1 = fopen(nomFichier.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str()); - return (0); - } - - // Ecriture Dicom File Preamble - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - - // un accesseur de + est obligatoire ??? - // pourtant le gdcmElValSet contenu dans le gdcmHeader - // ne devrait pas être visible par l'utilisateur final (?) - - GetPubElValSet().Write(fp1); - - fwrite(Pixels, lgrTotale, 1, fp1); - - fclose (fp1); - return(1); +bool File::WriteDcmImplVR (std::string const & fileName) +{ + return WriteBase(fileName, ImplicitVR); } -int gdcmFile::WriteDcm (const char* nomFichier) { - WriteDcm (string (nomFichier)); -} - - -///////////////////////////////////////////////////////////////// /** - * \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) { - -// ATTENTION : fonction non terminée (commitée a titre de precaution) - - FILE * fp1; - char* filePreamble; - fp1 = fopen(nomFichier.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str()); - return (0); - } - - // Ecriture Dicom File Preamble - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - - // un accesseur de + est obligatoire ??? - // pourtant le gdcmElValSet contenu dans le gdcmHeader - // ne devrait pas être visible par l'utilisateur final (?) - - GetPubElValSet().WriteExplVR(fp1); - - fwrite(Pixels, lgrTotale, 1, fp1); - - fclose (fp1); - return(1); +bool File::WriteDcmExplVR (std::string const & fileName) +{ + return WriteBase(fileName, ExplicitVR); } - -///////////////////////////////////////////////////////////////// + /** - * \ingroup gdcmFile - * \brief Ecrit sur disque UNE image ACR-NEMA + * \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 ... - * si un header DICOM est fourni en entree, - * les groupes < 0x0008 et les groupes impairs sont ignores) - * 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) { +bool File::WriteAcr (std::string const & fileName) +{ + return WriteBase(fileName, ACR); +} -// ATTENTION : fonction non terminée (commitée a titre de precaution) +//----------------------------------------------------------------------------- +// 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; + } + + std::ofstream* fp1 = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (fp1 == NULL) + { + printf("Failed to open (write) File [%s] \n", fileName.c_str()); + return false; + } + + if ( type == ImplicitVR || type == ExplicitVR ) + { + // writing Dicom File Preamble + uint8_t filePreamble[128]; + memset(filePreamble, 0, 128); + fp1->write((char*)filePreamble, 128); + fp1->write("DICM", 4); + } + + // -------------------------------------------------------------- + // 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 ---------------- + fp1->close (); + + return true; +} - FILE * fp1; - fp1 = fopen(nomFichier.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str()); - return (0); - } +/** + * \brief Access to the underlying \ref PixelConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); +} - // un accesseur de + est obligatoire ??? - // pourtant le gdcmElValSet contenu dans le gdcmHeader - // ne devrait pas être visible par l'utilisateur final (?) - - GetPubElValSet().WriteAcr(fp1); - - fwrite(Pixels, lgrTotale, 1, fp1); +} // end namespace gdcm - fclose (fp1); - return(1); -}