X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=035e25c3d5935b736cd172d9be5fe46558427c41;hb=abac16617f1453f5db19618ccb45e821efa867b6;hp=b47418923c9edb0a8c2d5f781172085faff5477e;hpb=7589d23967892c94462e22a49ec50fcd225c5c38;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index b4741892..035e25c3 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,579 +1,802 @@ -// gdcmFile.cxx + /*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/11/30 14:17:52 $ + Version: $Revision: 1.167 $ + + 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 "gdcmDocument.h" +#include "gdcmDebug.h" #include "gdcmUtil.h" +#include "gdcmBinEntry.h" +#include +namespace gdcm +{ +typedef std::pair IterHT; -// TODO : remove DEBUG -#define DEBUG 0 - - -#include "iddcmjpeg.h" -using namespace std; +//------------------------------------------------------------------------- +// 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 ) { - SetPixelDataSizeFromHeader(); + HeaderInternal = new Header( filename ); + SelfHeader = true; + Initialise(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) +/** + * \brief Factorization for various forms of constructors. + */ +void File::Initialise() { - SetPixelDataSizeFromHeader(); + WriteMode = WMODE_DECOMPRESSED; + WriteType = WTYPE_IMPL_VR; + + PixelConverter = new PixelConvert; + Archive = new DocEntryArchive( HeaderInternal ); + + if ( HeaderInternal->IsReadable() ) + { + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + } + + Pixel_Data = 0; + ImageDataSize = 0; } /** - * \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 canonical destructor + * \note If the Header was created by the File constructor, + * it is destroyed by the File */ -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; +File::~File() +{ + if( PixelConverter ) + { + delete PixelConverter; + } + if( Archive ) + { + delete Archive; + } + + if( SelfHeader ) + { + delete HeaderInternal; } - lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();; + HeaderInternal = 0; } -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Print + +//----------------------------------------------------------------------------- +// Public /** - * \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. + * \brief Get the size of the image data + * + * If the image can be RGB (with a lut or by default), the size + * corresponds to the RGB image + * @return The image size */ -size_t gdcmFile::GetImageDataSize(void) { - return (lgrTotale); +size_t File::GetImageDataSize() +{ + return PixelConverter->GetRGBSize(); } - -///////////////////////////////////////////////////////////////// /** - * \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 Get the size of the image data + * + * If the image can be RGB by transformation in a LUT, this + * transformation isn't considered + * @return The raw image size */ -bool gdcmFile::ReadPixelData(void* destination) { - if ( !OpenFile()) - return false; - - printf("GetPixelOffset() %d\n",GetPixelOffset() ); - - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - return false; - } - - if ( !IsDicomV3() || - IsImplicitVRLittleEndianTransferSyntax() || - IsExplicitVRLittleEndianTransferSyntax() || - IsExplicitVRBigEndianTransferSyntax() || - IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - size_t ItemRead = fread(destination, lgrTotale, 1, fp); - if ( ItemRead != 1 ) { - CloseFile(); - return false; - } else { - CloseFile(); - return true; - } - } - - // ------------------------------- Position on begining of Jpeg Pixels - - int ln; - fseek(fp,4,SEEK_CUR); - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); - if (DEBUG) - printf ("ln %d\n",ln); - fseek(fp,ln,SEEK_CUR); - fseek(fp,4,SEEK_CUR); - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); - if (DEBUG) - printf ("ln image comprimée %d\n",ln); - - - // ------------------------------- JPEG LossLess : call to Jpeg Libido - - if (IsJPEGLossless()) { - - ClbJpeg* jpg = _IdDcmJpegRead(fp); - if(jpg == NULL) { - CloseFile(); - return false; - } - // Gros soucis : - // jpg->DataImg est alloue en int32 systematiquement : - // il faut le copier pixel par pixel dans destination ... - // ... qui est un void * - // --> du CAST sportif a faire ... - - // memcpy(destination,jpg->DataImg,lgrTotale); - - // Bon ... - // ... y'a p't etre + ruse (?) - - int nb; - string 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; - } - int nBytes= nb/8; - int * dataJpg = jpg->DataImg; - int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel(); - - switch (nBytes) { - - case 1: - { - unsigned short *dest = (unsigned short *)destination; - for (int i=0; i255) printf("data %d\n",*(dataJpg +i) ); - *((unsigned char *)dest+i) = *(dataJpg +i); - } - } - break; - - case 2: - { - unsigned short *dest = (unsigned short *)destination; - - // etonnant (?) - // la ligne commentee ci-dessous fait passer l'exec de 0.15 sec a 5.5 sec - // pour la meme image 512*512 ... - // optimiseur pas mis en oeuvre (?) - //for (int i=0; i - // TODO : eplucher icelui pour traiter *egalement* bits=16 - int nBS; - if ((nBS = GetBitsStored()) != 12) { - printf("Sorry, Bits Stored = %d not yet taken into account\n",nBS); - return false; - } - - int res = gdcm_read_JPEG_file (destination); - if (DEBUG) - printf ("res : %d\n",res); - return res; - -} +size_t File::GetImageDataRawSize() +{ + return PixelConverter->GetDecompressedSize(); +} /** - * \ingroup gdcmFile - * \brief Allocates necessary memory, copies the pixel data - * (image[s]/volume[s]) to newly allocated zone. - * @return Pointer to newly allocated pixel data. + * \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 (void) { - PixelData = (void *) malloc(lgrTotale); - GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); +uint8_t* File::GetImageData() +{ + if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + return PixelConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the decompressed + return PixelConverter->GetDecompressed(); + } } /** - * \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 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 + * @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; + } -size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + if ( PixelConverter->GetRGBSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memcpy( destination, + (void*)PixelConverter->GetRGB(), + PixelConverter->GetRGBSize() ); + return PixelConverter->GetRGBSize(); + } - 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" + // 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 (size_t)0; + return 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; + memcpy( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + return PixelConverter->GetDecompressedSize(); +} + +/** + * \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 () +{ + return GetDecompressed(); +} + +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 ); + if(fp) + HeaderInternal->CloseFile(); + + decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + dbg.Verbose(0, "File::GetDecompressed: read/decompress of " + "pixel data apparently went wrong."); + return 0; } } - return lgrTotale; -} - - -// -// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs -// - -void gdcmFile::SwapZone(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; -} - -///////////////////////////////////////////////////////////////// + + return decompressed; +} + /** - * \ingroup gdcmFile - * \brief TODO JPR - * \warning doit-etre etre publique ? FIXME JPR - * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions - * - * @param inData TODO JPR - * @param ExpectedSize TODO 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 * - * @return TODO JPR + * @return boolean */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - - - return(1); +bool File::SetImageData(uint8_t* inData, size_t expectedSize) +{ +// FIXME : if already allocated, memory leak ! + Pixel_Data = inData; + ImageDataSize = expectedSize; +// FIXME : 7fe0, 0010 IS NOT set ... + return true; } - -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief TODO JPR - * \ - * \warning WARNING doit-etre etre publique ? FIXME JPR - * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions - * - * @param ImageDataSize TODO JPR - * + * \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 */ -void gdcmFile::SetImageDataSize(size_t ImageDataSize) { +bool File::WriteRawData(std::string const & fileName) +{ + std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); + if (!fp1) + { + dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); + return false; + } + fp1.write((char*)Pixel_Data, ImageDataSize); + fp1.close(); - string content1; - char car[20]; - - // suppose que le ElValue (0x7fe0, 0x0010) existe ... - - sprintf(car,"%d",ImageDataSize); - - gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010); - a->SetLength(ImageDataSize); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetPubElValByNumber(content1, 0x7fe0, 0x0000); + return true; } - -///////////////////////////////////////////////////////////////// /** - * \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 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::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); +bool File::WriteDcmImplVR (std::string const & fileName) +{ + SetWriteTypeToDcmImplVR(); + return Write(fileName); } +/** +* \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 + */ +bool File::WriteDcmExplVR (std::string const & fileName) +{ + SetWriteTypeToDcmExplVR(); + return Write(fileName); +} -///////////////////////////////////////////////////////////////// /** - * \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 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 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::WriteDcmImplVR (string nomFichier) { - return WriteBase(nomFichier, ImplicitVR); +bool File::WriteAcr (std::string const & fileName) +{ + SetWriteTypeToAcr(); + return Write(fileName); +} + +bool File::Write(std::string const& fileName) +{ + switch(WriteType) + { + case WTYPE_IMPL_VR: + return WriteBase(fileName,ImplicitVR); + case WTYPE_EXPL_VR: + return WriteBase(fileName,ExplicitVR); + case WTYPE_ACR: + return WriteBase(fileName,ACR); + } + return(false); } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \brief Access to the underlying \ref PixelConverter RGBA LUT */ - -int gdcmFile::WriteDcmImplVR (const char* nomFichier) { - return WriteDcmImplVR (string (nomFichier)); +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); } - -///////////////////////////////////////////////////////////////// + +//----------------------------------------------------------------------------- +// Protected /** - * \ingroup gdcmFile - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \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) +{ + switch(type) + { + case ImplicitVR: + SetWriteFileTypeToImplicitVR(); + break; + case ExplicitVR: + SetWriteFileTypeToExplicitVR(); + break; + case ACR: + case ACR_LIBIDO: + SetWriteFileTypeToACR(); + break; + default: + SetWriteFileTypeToExplicitVR(); + } + + if( type == ACR_LIBIDO ) + { + SetWriteToLibido(); + } + else + { + SetWriteToNoLibido(); + } + + switch(WriteMode) + { + case WMODE_NATIVE : + SetWriteToNative(); + break; + case WMODE_DECOMPRESSED : + SetWriteToDecompressed(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; + } -int gdcmFile::WriteDcmExplVR (string nomFichier) { - return WriteBase(nomFichier, ExplicitVR); + // -------------------------------------------------------------- + // 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 +/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO) + { + SetWriteToLibido(); + }*/ + // ----------------- End of Special Patch ---------------- + + bool check = CheckWriteIntegrity(); + if(check) + { + check = HeaderInternal->Write(fileName,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 ) + { + RestoreWriteFromLibido(); + }*/ + // ----------------- End of Special Patch ---------------- + + RestoreWrite(); + RestoreWriteFileType(); + RestoreWriteOfLibido(); + + return check; } - -///////////////////////////////////////////////////////////////// + /** - * \ingroup gdcmFile - * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels - * (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 + * \brief Check the write integrity * - * @return TODO JPR + * The tests made are : + * - verify the size of the image to write with the possible write + * when the user set an image data + * @return true if the check successfulls */ +bool File::CheckWriteIntegrity() +{ + if(Pixel_Data) + { + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) + { + numberBitsAllocated = 16; + } + + size_t decSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + size_t rgbSize = decSize; + if( HeaderInternal->HasLUT() ) + rgbSize = decSize * 3; + + switch(WriteMode) + { + case WMODE_NATIVE : + break; + case WMODE_DECOMPRESSED : + if( decSize!=ImageDataSize ) + { + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); + //std::cerr<<"Dec : "<GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + + Archive->Push(pixel); + } } -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * - * @param FileName TODO JPR - * @param type TODO JPR - * - * @return TODO JPR - */ -int gdcmFile::WriteBase (string FileName, FileType type) { +void File::SetWriteToDecompressed() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + { + SetWriteToRGB(); + } + else + { + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + if(HeaderInternal->HasLUT()) + { + photInt->SetValue("PALETTE COLOR "); + photInt->SetLength(14); + } + else + { + photInt->SetValue("MONOCHROME1 "); + photInt->SetLength(12); + } + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + if(Pixel_Data) + { + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + } + else + { + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); + } - FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); - return (0); + Archive->Push(photInt); + Archive->Push(pixel); } +} - 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); +void File::SetWriteToRGB() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3) + { + PixelConverter->BuildRGBImage(); + + ValEntry* spp = CopyValEntry(0x0028,0x0002); + spp->SetValue("3 "); + spp->SetLength(2); + + ValEntry* planConfig = CopyValEntry(0x0028,0x0006); + planConfig->SetValue("0 "); + planConfig->SetLength(2); + + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("RGB "); + photInt->SetLength(4); + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + if(Pixel_Data) + { + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + } + else if(PixelConverter->GetRGB()) + { + pixel->SetBinArea(PixelConverter->GetRGB(),false); + pixel->SetLength(PixelConverter->GetRGBSize()); + } + else // Decompressed data + { + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); + } + + Archive->Push(spp); + Archive->Push(planConfig); + Archive->Push(photInt); + Archive->Push(pixel); + + // Remove any LUT + Archive->Push(0x0028,0x1101); + Archive->Push(0x0028,0x1102); + Archive->Push(0x0028,0x1103); + Archive->Push(0x0028,0x1201); + Archive->Push(0x0028,0x1202); + Archive->Push(0x0028,0x1203); + + // For old ACR-NEMA + // Thus, we have a RGB image and the bits allocated = 24 and + // samples per pixels = 1 (in the read file) + if(HeaderInternal->GetBitsAllocated()==24) + { + ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100); + bitsAlloc->SetValue("8 "); + bitsAlloc->SetLength(2); + + ValEntry* bitsStored = CopyValEntry(0x0028,0x0101); + bitsStored->SetValue("8 "); + bitsStored->SetLength(2); + + ValEntry* highBit = CopyValEntry(0x0028,0x0102); + highBit->SetValue("7 "); + highBit->SetLength(2); + + Archive->Push(bitsAlloc); + Archive->Push(bitsStored); + Archive->Push(highBit); + } } + else + { + SetWriteToDecompressed(); + } +} - gdcmHeader::Write(fp1, type); - fwrite(PixelData, lgrTotale, 1, fp1); - fclose (fp1); - return(1); +void File::RestoreWrite() +{ + Archive->Restore(0x0028,0x0002); + Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); + Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + + // For old ACR-NEMA (24 bits problem) + Archive->Restore(0x0028,0x0100); + Archive->Restore(0x0028,0x0101); + Archive->Restore(0x0028,0x0102); + + // For the LUT + Archive->Restore(0x0028,0x1101); + Archive->Restore(0x0028,0x1102); + Archive->Restore(0x0028,0x1103); + Archive->Restore(0x0028,0x1201); + Archive->Restore(0x0028,0x1202); + Archive->Restore(0x0028,0x1203); } + +void File::SetWriteFileTypeToACR() +{ + Archive->Push(0x0002,0x0010); +} + +void File::SetWriteFileTypeToExplicitVR() +{ + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() ); + + ValEntry* tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + tss->SetLength(ts.length()); + + Archive->Push(tss); +} + +void File::SetWriteFileTypeToImplicitVR() +{ + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() ); + + ValEntry* tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + tss->SetLength(ts.length()); +} + +void File::RestoreWriteFileType() +{ + Archive->Restore(0x0002,0x0010); +} + +void File::SetWriteToLibido() +{ + ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); + ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); + + if( oldRow && oldCol ) + { + std::string rows, columns; + + ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); + ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + + newRow->Copy(oldCol); + newCol->Copy(oldRow); + + newRow->SetValue(oldCol->GetValue()); + newCol->SetValue(oldRow->GetValue()); + + Archive->Push(newRow); + Archive->Push(newCol); + } + + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue("ACRNEMA_LIBIDO_1.1"); + libidoCode->SetLength(10); + Archive->Push(libidoCode); +} + +void File::SetWriteToNoLibido() +{ + ValEntry *recCode = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0008,0x0010)); + if( recCode ) + { + if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + { + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue(""); + libidoCode->SetLength(0); + Archive->Push(libidoCode); + } + } +} + +void File::RestoreWriteOfLibido() +{ + Archive->Restore(0x0028,0x0010); + Archive->Restore(0x0028,0x0011); + Archive->Restore(0x0008,0x0010); +} + +ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + ValEntry* newE; + + if(oldE) + { + newE = new ValEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewValEntryByNumber(group,element); + } + + return(newE); +} + +BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + BinEntry* newE; + + if(oldE) + { + newE = new BinEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewBinEntryByNumber(group,element); + } + + + return(newE); +} + +//----------------------------------------------------------------------------- +// Private + +//----------------------------------------------------------------------------- +} // end namespace gdcm +