X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=858ee0cb358f30cbe2cc8b1e9ecbd2e5d9ff29aa;hb=bafdfafe6c1b30607035fc4018c0405169b348e8;hp=af62cd8f545a8856958298eca0e2e1668bb5b47c;hpb=33413fc6fb41f4fd7efbce32083f943f252e8b6f;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index af62cd8f..858ee0cb 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,11 +1,11 @@ // gdcmFile.cxx - +//----------------------------------------------------------------------------- #include "gdcmFile.h" #include "gdcmUtil.h" -#include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess #include "jpeg/ljpg/jpegless.h" -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Constructor / Destructor /** * \ingroup gdcmFile * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant @@ -18,52 +18,84 @@ * one sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). * - * @param filename file to be opened for parsing + * @param header file to be opened for reading datas * * @return */ -gdcmFile::gdcmFile(std::string & filename) - :gdcmHeader(filename.c_str()) -{ - if (IsReadable()) - SetPixelDataSizeFromHeader(); +gdcmFile::gdcmFile(gdcmHeader *header) { + Header=header; + SelfHeader=false; + + if (Header->IsReadable()) + SetPixelDataSizeFromHeader(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) -{ - if (IsReadable()) +/** + * \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) { + Header=new gdcmHeader(filename.c_str()); + SelfHeader=true; + + if (Header->IsReadable()) + SetPixelDataSizeFromHeader(); +} + +gdcmFile::gdcmFile(const char * filename) { + Header=new gdcmHeader(filename); + SelfHeader=true; + + if (Header->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 + * \brief canonical destructor + * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed + * by the gdcmFile */ -void gdcmFile::SetPixelDataSizeFromHeader(void) { - int nb; - std::string str_nb; +gdcmFile::~gdcmFile(void) { + if(SelfHeader) + delete Header; + Header=NULL; +} - 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 = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - if ( str_PhotometricInterpretation == "PALETTE COLOR " ) { - lgrTotale*=3; - } +//----------------------------------------------------------------------------- +// Print + +//----------------------------------------------------------------------------- +// Public +/** + * \ingroup gdcmFile + * \brief + * @return + */ +gdcmHeader *gdcmFile::GetHeader(void) { + return(Header); } + +/** + * \ingroup gdcmFile + * \brief computes the length (in bytes) to ALLOCATE to receive the + * image(s) pixels (multiframes taken into account) + * \warning : it is NOT the group 7FE0 length + * (no interest for compressed images). + * @return length to allocate + */ +void gdcmFile::SetPixelDataSizeFromHeader(void) { // see PS 3.3-2003 : C.7.6.3.2.1 // // MONOCHROME1 @@ -79,226 +111,170 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { // 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 : US-PAL-8-10x-echo.dcm, 8BitsRunLengthColor.dcm - // 0028|1201 [OW] [Red Palette Color Lookup Table Data] - // 0028|1202 [OW] [Green Palette Color Lookup Table Data] - // 0028|1203 [OW] [Blue Palette Color Lookup Table Data] + // 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] + // 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 nb; + std::string str_nb; + str_nb=Header->GetEntryByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { + nb = 16; + } else { + nb = atoi(str_nb.c_str() ); + if (nb == 12) nb =16; + } + lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize() + * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel(); + std::string str_PhotometricInterpretation = + Header->GetEntryByNumber(0x0028,0x0004); + + /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ + // pb when undealt Segmented Palette Color + + if (Header->HasLUT()) { + lgrTotale*=3; + } +} -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Returns the size (in bytes) of required memory to hold * the pixel data represented in this file. * @return The size of pixel data in bytes. */ - size_t gdcmFile::GetImageDataSize(void) { return (lgrTotale); } +/** + * \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 Read pixel data from disk (optionaly decompressing) into the - * caller specified memory location. - * @param destination where the pixel data should be stored. - * + * \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 */ -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; - - for(int p=0;p> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - /* A */ /* B */ /* D */ - *((unsigned short int*)destination)++ = - ((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, lgrTotale, 1, fp); - if ( ItemRead != 1 ) { - CloseFile(); - return false; - } else { - CloseFile(); - return true; - } - } +void * gdcmFile::GetImageData (void) { + PixelData = (void *) malloc(lgrTotale); + if (PixelData) + GetImageDataIntoVector(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); -// ------------------------- 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); + if (!Header->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 = Header->GetLUTRGBA(); + if (lutRGBA) { + int l = lgrTotaleRaw; + memmove(newDest, destination, l);// move Gray pixels to temp area + int j; + for (int i=0;iSetEntryByNumber(spp,0x0028,0x0002); + std::string rgb= "RGB "; // Photometric Interpretation + Header->SetEntryByNumber(rgb,0x0028,0x0004); + std::string planConfig = "0"; // Planar Configuration + Header->SetEntryByNumber(planConfig,0x0028,0x0006); + + } else { + // need to make RGB Pixels (?) + // from grey Pixels (?!) + // and Gray Lut (!?!) + // or Segmented xxx Palette Color Lookup Table Data and so on + + // Oops! I get one (gdcm-US-ALOKA-16.dcm) + // No idea how to manage such an image + // It seems that *no Dicom Viewer* has any idea :-( + // Segmented xxx Palette Color are *more* than 65535 long ?!? + + std::string rgb= "MONOCHROME1 "; // Photometric Interpretation + Header->SetEntryByNumber(rgb,0x0028,0x0004); + } + // TODO : Drop Palette Color out of the Header? + return lgrTotale; +} /** * \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::GetImageData (void) { +void * gdcmFile::GetImageDataRaw (void) { + if (Header->HasLUT()) + lgrTotale /= 3; // TODO Let gdcmHeadar user a chance + // to get the right value + // Create a member lgrTotaleRaw ??? PixelData = (void *) malloc(lgrTotale); if (PixelData) - GetImageDataIntoVector(PixelData, lgrTotale); + GetImageDataIntoVectorRaw(PixelData, lgrTotale); return(PixelData); } @@ -306,6 +282,18 @@ void * gdcmFile::GetImageData (void) { * \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 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 @@ -314,8 +302,7 @@ void * gdcmFile::GetImageData (void) { * @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 gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { int nb, nbu, highBit, signe; std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; @@ -328,42 +315,52 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { (void)ReadPixelData(destination); - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = GetPubElValByNumber(0x0028,0x0100); + // Number of Bits Allocated for storing a Pixel + str_nb = Header->GetEntryByNumber(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); + } + // Number of Bits actually used + str_nbu=Header->GetEntryByNumber(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); + } + // High Bit Position + str_highBit=Header->GetEntryByNumber(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); + } + // Pixel sign + // 0 = Unsigned + // 1 = Signed + str_signe=Header->GetEntryByNumber(0x0028,0x0103); if (str_signe == GDCM_UNFOUND ) { - signe = 1; + signe = 0; // default is unsigned } else { signe = atoi(str_signe.c_str() ); } - // re arange bytes inside the integer + // re arange bytes inside the integer (processor endianity) if (nb != 8) - SwapZone(destination, GetSwapCode(), lgrTotale, nb); - + SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb); + + // to avoid pb with some xmedcon breakers images + if (nb==16 && nbuGetEntryByNumber(0x0028,0x0004); if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { @@ -412,7 +413,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( - int planConf=GetPlanarConfiguration(); + int planConf=Header->GetPlanarConfiguration(); // 0028,0006 // Whatever Planar Configuration is, // "PALETTE COLOR " implies that we deal with the palette. @@ -427,25 +428,31 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { 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(); + if (str_PhotometricInterpretation == "YBR_FULL") { + + // Warning : YBR_FULL_422 acts as RGB + // : we need to make RGB Pixels from Planes Y,cB,cR + + // to see the tricks about YBR_FULL, YBR_FULL_422, + // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : + // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf + // and be *very* affraid + // + int l = Header->GetXSize()*Header->GetYSize(); + int nbFrames = Header->GetZSize(); 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 + // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf + // for code optimisation + for (int i=0;iGetXSize()*Header->GetYSize()*Header->GetZSize(); char * newDest = (char*) malloc(lgrTotale); - char *x = newDest; + char * x = newDest; char * a = (char *)destination; char * b = a + l; char * c = b + l; - // TODO : - // any trick not to have to allocate temporary buffer is welcome ... - - for (int i=0;iSetEntryByNumber(spp,0x0028,0x0002); + std::string rgb="RGB "; // Photometric Interpretation + Header->SetEntryByNumber(rgb,0x0028,0x0004); + std::string planConfig = "0"; // Planar Configuration - gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); - // + Drop Palette Color ? - + // TODO : Drop Palette Color out of the Header? return lgrTotale; } -// -// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs -// - -/** - * \ingroup gdcmFile - * \brief Swap the bytes, according to swap code. - * \warning not end user intended - * @param im area to deal with - * @param swap swap code - * @param lgr Area Length - * @param nb Pixels Bit number - */ - -void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { -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) 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 @@ -661,46 +529,15 @@ return; * @param inData * @param ExpectedSize * - * @return integer acts as a boolean + * @return boolean */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); +bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { + Header->SetImageDataSize(ExpectedSize); PixelData = inData; lgrTotale = ExpectedSize; - return(1); + return(true); } - -///////////////////////////////////////////////////////////////// -/** - * \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 @@ -708,23 +545,23 @@ void gdcmFile::SetImageDataSize(size_t ImageDataSize) { * Ca sera à l'utilisateur d'appeler son Reader correctement * (Equivalent a IdImaWriteRawFile) * - * @param fileName - * @return + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails */ -int gdcmFile::WriteRawData (std::string fileName) { +bool 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); + return (false); } fwrite (PixelData,lgrTotale, 1, fp1); fclose (fp1); - return(1); + return(true); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Ecrit sur disque UNE image Dicom @@ -732,74 +569,76 @@ int gdcmFile::WriteRawData (std::string fileName) { * Ca fonctionnera correctement (?) sur processeur Intel * (Equivalent a IdDcmWrite) * - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmImplVR (std::string fileName) { +bool gdcmFile::WriteDcmImplVR (std::string fileName) { return WriteBase(fileName, ImplicitVR); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmImplVR (const char* fileName) { +bool gdcmFile::WriteDcmImplVR (const char* fileName) { return WriteDcmImplVR (std::string (fileName)); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmExplVR (std::string fileName) { +bool 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. + * \warning if a DICOM_V3 header is supplied, + * groups < 0x0008 and shadow groups are ignored) + * \warning NO TEST is performed on processor "Endiannity". * Ca fonctionnera correctement (?) sur processeur Intel * (Equivalent a IdDcmWrite) * - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteAcr (std::string fileName) { +bool gdcmFile::WriteAcr (std::string fileName) { return WriteBase(fileName, ACR); } -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Protected /** * \ingroup gdcmFile * - * @param FileName - * @param type - * - * @return int acts as a boolean +* @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 */ -int gdcmFile::WriteBase (std::string FileName, FileType type) { +bool gdcmFile::WriteBase (std::string fileName, FileType type) { FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); + fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); - return (0); + printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); + return (false); } if ( (type == ImplicitVR) || (type == ExplicitVR) ) { @@ -818,15 +657,15 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // 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); + if ( Header->GetFileType() == ACR_LIBIDO){ + rows = Header->GetEntryByNumber(0x0028, 0x0010); + columns = Header->GetEntryByNumber(0x0028, 0x0011); + Header->SetEntryByNumber(columns, 0x0028, 0x0010); + Header->SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- - gdcmHeader::Write(fp1, type); + Header->Write(fp1, type); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -834,13 +673,268 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // ...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); + if (Header->GetFileType() == ACR_LIBIDO){ + Header->SetEntryByNumber(rows , 0x0028, 0x0010); + Header->SetEntryByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- fwrite(PixelData, lgrTotale, 1, fp1); fclose (fp1); - return(1); + return(true); +} + +//----------------------------------------------------------------------------- +// Private +/** + * \ingroup gdcmFile + * \brief Swap the bytes, according to swap code. + * \warning not end user intended + * @param im area to deal with + * @param swap swap code + * @param lgr Area Length + * @param nb Pixels Bit number + */ +void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { +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("SWAP value (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 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) { + + FILE *fp; + + if ( !(fp=Header->OpenFile())) + return false; + + if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) { + Header->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 (Header->GetBitsAllocated()==12) { + int nbPixels = Header->GetXSize() * Header->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 ( !Header->IsDicomV3() || + Header->IsImplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRBigEndianTransferSyntax() || + Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { + + size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); + + if ( ItemRead != 1 ) { + Header->CloseFile(); + return false; + } else { + Header->CloseFile(); + return true; + } + } + + // ---------------------- Run Length Encoding + if (Header->IsRLELossLessTransferSyntax()) { + bool res = (bool)gdcm_read_RLE_file (fp,destination); + return res; + } + + // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 + int nb; + std::string str_nb=Header->GetEntryByNumber(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 = Header->GetXSize() * Header->GetYSize() + * Header->GetSamplesPerPixel(); + long fragmentBegining; // for ftell, fseek + + bool jpg2000 = Header->IsJPEG2000(); + bool jpgLossless = Header->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(Header->GetSwapCode()) { + ItemTagGr=Header->SwapShort(ItemTagGr); + ItemTagEl=Header->SwapShort(ItemTagEl); + } + fread(&ln,4,1,fp); + if(Header->GetSwapCode()) + ln=Header->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(Header->GetSwapCode()) { + ItemTagGr=Header->SwapShort(ItemTagGr); + ItemTagEl=Header->SwapShort(ItemTagEl); + } + + // parsing fragments until Sequence Delim. Tag found + while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { + // --- for each Fragment + + fread(&ln,4,1,fp); + if(Header->GetSwapCode()) + ln=Header->SwapLong(ln); // Fragment Item length + + fragmentBegining=ftell(fp); + + if (jpg2000) { // JPEG 2000 : call to ??? + + res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written + + } // ------------------------------------- endif (JPEG2000) + + else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG + + JPEGLosslessDecodeImage (fp, // Reading Fragment pixels + (unsigned short *)destination, + Header->GetPixelSize()*8* Header->GetSamplesPerPixel(), + ln); + res=1; // in order not to break the loop + + } // ------------------------------------- endif (JPEGLossless) + + else { // JPEG Lossy : call to IJG 6b + + if (Header->GetBitsStored() == 8) { + res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels + } else { + res = (bool)gdcm_read_JPEG_file12 (fp,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(Header->GetSwapCode()) { + ItemTagGr=Header->SwapShort(ItemTagGr); + ItemTagEl=Header->SwapShort(ItemTagEl); + } + + } // endWhile parsing fragments until Sequence Delim. Tag found + + Header->CloseFile(); + return res; } +//-----------------------------------------------------------------------------