// gdcmFile.cxx #include "gdcmFile.h" #include "gdcmUtil.h" #include "jpeg/ljpg/jpegless.h" ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant * file (see SetFileName, SetDcmTag and Write) * 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 * 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(std::string & filename) :gdcmHeader(filename.c_str()) { if (IsReadable()) SetPixelDataSizeFromHeader(); } gdcmFile::gdcmFile(const char * filename) :gdcmHeader(filename) { if (IsReadable()) SetPixelDataSizeFromHeader(); } /** * \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 */ void gdcmFile::SetPixelDataSizeFromHeader(void) { int nb; std::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; } lgrTotale = lgrTotaleRaw = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel(); std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ // pb when undealt Segmented Palette Color if (HasLUT()) { lgrTotale*=3; } } // 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] ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Returns the size (in bytes) of required memory to hold * \ the pixel data represented in this file, when user DOESN'T want * \ to get RGB pixels image when it's stored as a PALETTE COLOR image * \ - the (vtk) user is supposed to know how deal with LUTs - * \ warning to be used with GetImagePixelsRaw() * @return The size of pixel data in bytes. */ size_t gdcmFile::GetImageDataSizeRaw(void) { return (lgrTotaleRaw); } ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Returns the size (in bytes) of required memory to hold * the pixel data represented in this file. * @return The size of pixel data in bytes. */ size_t gdcmFile::GetImageDataSize(void) { return (lgrTotale); } ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Read pixel data from disk (optionaly decompressing) into the * caller specified memory location. * @param destination where the pixel data should be stored. * */ bool gdcmFile::ReadPixelData(void* destination) { if ( !OpenFile()) return false; if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { CloseFile(); return false; } // ---------------------- Compacted File (12 Bits Per Pixel) /* unpack 12 Bits pixels into 16 Bits pixels */ /* 2 pixels 12bit = [0xABCDEF] */ /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */ if (GetBitsAllocated()==12) { int nbPixels = GetXSize()*GetYSize(); unsigned char b0, b1, b2; unsigned short int* pdestination = (unsigned short int*)destination; for(int p=0;p> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); /* A */ /* B */ /* D */ *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); /* F */ /* C */ /* E */ // Troubles expected on Big-Endian processors ? } return(true); } // ---------------------- Uncompressed File if ( !IsDicomV3() || IsImplicitVRLittleEndianTransferSyntax() || IsExplicitVRLittleEndianTransferSyntax() || IsExplicitVRBigEndianTransferSyntax() || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { size_t ItemRead = fread(destination, GetPixelAreaLength(), 1, fp); if ( ItemRead != 1 ) { CloseFile(); return false; } else { CloseFile(); return true; } } // ---------------------- Run Length Encoding if (gdcmHeader::IsRLELossLessTransferSyntax()) { int res = (bool)gdcm_read_RLE_file (destination); return res; } // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 int nb; std::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; // ?? 12 should be ACR-NEMA only ? } int nBytes= nb/8; int taille = GetXSize() * GetYSize() * GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek bool jpg2000 = IsJPEG2000(); bool jpgLossless = IsJPEGLossless(); bool res = true; guint16 ItemTagGr,ItemTagEl; int ln; // Position on begining of Jpeg Pixels fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El if(GetSwapCode()) { ItemTagGr=SwapShort(ItemTagGr); ItemTagEl=SwapShort(ItemTagEl); } fread(&ln,4,1,fp); if(GetSwapCode()) ln=SwapLong(ln); // Basic Offset Table Item length if (ln != 0) { // What is it used for ?!? char *BasicOffsetTableItemValue = (char *)malloc(ln+1); fread(BasicOffsetTableItemValue,ln,1,fp); } // first Fragment initialisation fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El if(GetSwapCode()) { ItemTagGr=SwapShort(ItemTagGr); ItemTagEl=SwapShort(ItemTagEl); } // parsing fragments until Sequence Delim. Tag found while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { // --- for each Fragment fread(&ln,4,1,fp); if(GetSwapCode()) ln=SwapLong(ln); // Fragment Item length fragmentBegining=ftell(fp); if (jpg2000) { // JPEG 2000 : call to ??? res = (bool)gdcm_read_JPEG2000_file (destination); // Not Yet written } // ------------------------------------- endif (JPEG2000) else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG JPEGLosslessDecodeImage (fp, // Reading Fragment pixels (unsigned short *)destination, GetPixelSize()*8* GetSamplesPerPixel(), ln); res=1; // in order not to break the loop } // ------------------------------------- endif (JPEGLossless) else { // JPEG Lossy : call to IJG 6b if (GetBitsStored() == 8) { res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels } else { res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels } } // ------------------------------------- endif (JPEGLossy) if (!res) break; destination = (char *)destination + taille * nBytes; // location in user's memory // for next fragment (if any) fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start fseek(fp,ln,SEEK_CUR); // at the begining of next fragment ItemTagGr = ItemTagEl =0; fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El if(GetSwapCode()) { ItemTagGr=SwapShort(ItemTagGr); ItemTagEl=SwapShort(ItemTagEl); } } // endWhile parsing fragments until Sequence Delim. Tag found return res; } /** * \ingroup gdcmFile * \brief Allocates necessary memory, copies the pixel data * (image[s]/volume[s]) to newly allocated zone. * Transforms YBR pixels into RGB pixels if any Transforms 3 planes R, G, B into a single RGB Plane Transforms single Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ void * gdcmFile::GetImageData (void) { PixelData = (void *) malloc(lgrTotale); if (PixelData) GetImageDataIntoVector(PixelData, lgrTotale); return(PixelData); } /** * \ingroup gdcmFile * \brief Allocates necessary memory, copies the pixel data * (image[s]/volume[s]) to newly allocated zone. * Transforms YBR pixels into RGB pixels if any Transforms 3 planes R, G, B into a single RGB Plane DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ void * gdcmFile::GetImageDataRaw (void) { if (HasLUT()) lgrTotale /= 3; // TODO Let gdcmHeadar user a chance // to get the right value // Create a member lgrTotaleRaw ??? PixelData = (void *) malloc(lgrTotale); if (PixelData) GetImageDataIntoVectorRaw(PixelData, lgrTotale); return(PixelData); } /** * \ingroup gdcmFile * \brief Copies at most MaxSize bytes of pixel data to caller's * memory space. * \warning This function was designed to avoid people that want to build * 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 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 gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { size_t l = GetImageDataIntoVectorRaw (destination, MaxSize); if (!HasLUT()) return lgrTotale; // from Lut R + Lut G + Lut B unsigned char * newDest = (unsigned char *)malloc(lgrTotale); unsigned char * a = (unsigned char *)destination; unsigned char * lutRGBA = (unsigned char *)GetLUTRGBA(); if (lutRGBA) { int l = lgrTotale/3; memmove(newDest, destination, l);// move Gray pixels to temp area int j; for (int i=0;i 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() ); } // Pixel sign // 0 = Unsigned // 1 = Signed str_signe=GetPubElValByNumber(0x0028,0x0103); if (str_signe == GDCM_UNFOUND ) { signe = 0; // default is unsigned } else { signe = atoi(str_signe.c_str() ); } // re arange bytes inside the integer if (nb != 8) SwapZone(destination, GetSwapCode(), lgrTotale, nb); // to avoid pb with some xmedcon breakers images if (nb==16 && nbu> (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; } } // Just to 'see' what was actually read on disk :-( // Some troubles expected // FILE * f2; // f2 = fopen("SpuriousFile.raw","wb"); // fwrite(destination,lgrTotale,1,f2); // fclose(f2); // Deal with the color // ------------------- std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { return lgrTotale; } // Planar configuration = 0 : Pixels are already RGB // Planar configuration = 1 : 3 planes : R, G, B // Planar configuration = 2 : 1 gray Plane + 3 LUT // Well ... supposed to be ! // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0, // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( int planConf=GetPlanarConfiguration(); // 0028,0006 // Whatever Planar Configuration is, // "PALETTE COLOR " implies that we deal with the palette. if (str_PhotometricInterpretation == "PALETTE COLOR ") planConf=2; switch (planConf) { case 0: // Pixels are already RGB break; case 1: { if (str_PhotometricInterpretation == "YBR_FULL") { // Warning : YBR_FULL_422 acts as RGB // need to make RGB Pixels from Planes Y,cB,cR // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf // for code optimisation int l = GetXSize()*GetYSize(); int nbFrames = GetZSize(); unsigned char * newDest = (unsigned char*) malloc(lgrTotale); unsigned char *x = newDest; unsigned char * a = (unsigned char *)destination; unsigned char * b = a + l; unsigned char * c = b + l; double R,G,B; // TODO : Replace by the 'well known' // integer computation counterpart for (int i=0;i255.0) R=255.0; if (G>255.0) G=255.0; if (B>255.0) B=255.0; *(x++) = (unsigned char)R; *(x++) = (unsigned char)G; *(x++) = (unsigned char)B; a++; b++; c++; } } memmove(destination,newDest,lgrTotale); free(newDest); } else { // need to make RGB Pixels from R,G,B Planes // (all the Frames at a time) int l = GetXSize()*GetYSize()*GetZSize(); char * newDest = (char*) malloc(lgrTotale); char * x = newDest; char * a = (char *)destination; char * b = a + l; char * c = b + l; for (int j=0;j>8) | ((((unsigned short int*)im)[i])<<8); break; default: printf("valeur de SWAP (16 bits) not allowed : %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(" SWAP value (32 bits) not allowed : %d\n", swap); } return; } ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief TODO JPR * \warning doit-etre etre publique ? * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions * * @param inData * @param ExpectedSize * * @return integer acts as a boolean */ int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { SetImageDataSize(ExpectedSize); PixelData = inData; lgrTotale = ExpectedSize; return(1); } ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Sets the Pixel Area size in the Header * --> not-for-rats function * * \warning WARNING doit-etre etre publique ? * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions * * @param ImageDataSize new Pixel Area Size * warning : nothing else is checked */ void gdcmFile::SetImageDataSize(size_t ImageDataSize) { std::string content1; char car[20]; // Assumes ElValue (0x7fe0, 0x0010) exists ... sprintf(car,"%d",ImageDataSize); gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010); a->SetLength(ImageDataSize); ImageDataSize+=8; sprintf(car,"%d",ImageDataSize); content1=car; SetPubElValByNumber(content1, 0x7fe0, 0x0000); } ///////////////////////////////////////////////////////////////// /** * \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) * * @param fileName * @return */ int gdcmFile::WriteRawData (std::string fileName) { FILE * fp1; fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); return (0); } fwrite (PixelData,lgrTotale, 1, fp1); fclose (fp1); return(1); } ///////////////////////////////////////////////////////////////// /** * \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) * * @param fileName * @return int acts as a boolean */ int gdcmFile::WriteDcmImplVR (std::string fileName) { return WriteBase(fileName, ImplicitVR); } ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief * @param fileName * @return int acts as a boolean */ int gdcmFile::WriteDcmImplVR (const char* fileName) { return WriteDcmImplVR (std::string (fileName)); } ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief * @param fileName * @return int acts as a boolean */ int gdcmFile::WriteDcmExplVR (std::string fileName) { return WriteBase(fileName, ExplicitVR); } ///////////////////////////////////////////////////////////////// /** * \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 fileName * @return int acts as a boolean */ int gdcmFile::WriteAcr (std::string fileName) { return WriteBase(fileName, ACR); } ///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * * @param FileName * @param type * * @return int acts as a boolean */ int gdcmFile::WriteBase (std::string FileName, FileType type) { FILE * fp1; fp1 = fopen(FileName.c_str(),"wb"); if (fp1 == NULL) { printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); return (0); } if ( (type == ImplicitVR) || (type == ExplicitVR) ) { char * filePreamble; // writing Dicom File Preamble filePreamble=(char*)calloc(128,1); fwrite(filePreamble,128,1,fp1); fwrite("DICM",4,1,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 ... std::string rows, columns; if ( filetype == ACR_LIBIDO){ rows = GetPubElValByNumber(0x0028, 0x0010); columns = GetPubElValByNumber(0x0028, 0x0011); SetPubElValByNumber(columns, 0x0028, 0x0010); SetPubElValByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- gdcmHeader::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 (filetype == ACR_LIBIDO){ SetPubElValByNumber(rows , 0x0028, 0x0010); SetPubElValByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- fwrite(PixelData, lgrTotale, 1, fp1); fclose (fp1); return(1); }