X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=176b2c8c1b66abcc018d415854cc048593b3b88a;hb=eb835becc89cc1b8a1dc1f122f54b7659a6127be;hp=da30b3d0c4663eb998e0b942ac013b8547a49393;hpb=83215515e2daebf8680f227829e16515f6441311;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index da30b3d0..176b2c8c 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,70 +1,116 @@ // gdcmFile.cxx - +//----------------------------------------------------------------------------- #include "gdcmFile.h" #include "gdcmUtil.h" #include "jpeg/ljpg/jpegless.h" -///////////////////////////////////////////////////////////////// +typedef std::pair IterHT; + +//----------------------------------------------------------------------------- +// Constructor / Destructor /** * \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 + * \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 - * + * @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; + PixelRead=-1; // no ImageData read yet. + + 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 + */ +gdcmFile::gdcmFile(std::string & filename) { + Header=new gdcmHeader(filename.c_str()); + SelfHeader=true; + PixelRead=-1; // no ImageData read yet. + + 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 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 */ -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 = GetXSize() * GetYSize() * GetZSize() - * (nb/8)* GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = - gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - if ( str_PhotometricInterpretation == "PALETTE COLOR " ) { - lgrTotale*=3; - } + gdcmFile::gdcmFile(const char * filename) { + Header=new gdcmHeader(filename); + SelfHeader=true; + PixelRead=-1; // no ImageData read yet. + + if (Header->IsReadable()) + SetPixelDataSizeFromHeader(); } +/** + * \ingroup gdcmFile + * \brief canonical destructor + * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed + * by the gdcmFile + */ +gdcmFile::~gdcmFile(void) { + if(SelfHeader) + delete Header; + Header=NULL; +} + +//----------------------------------------------------------------------------- +// Print + +//----------------------------------------------------------------------------- +// Public +/** + * \ingroup gdcmFile + * \brief returns the gdcmHeader *Header + * @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 @@ -80,219 +126,172 @@ 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] + // 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] */ +void * gdcmFile::GetImageData (void) { + PixelData = (void *) malloc(lgrTotale); + if (PixelData) + GetImageDataIntoVector(PixelData, lgrTotale); + PixelRead=0; // no PixelRaw + return(PixelData); +} - 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 ? +/** + * \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); + PixelRead=0 ; // no PixelRaw + 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); - } // ------------------------------------- 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; -} + } 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); + PixelRead=1; // PixelRaw return(PixelData); } @@ -303,11 +302,14 @@ void * gdcmFile::GetImageData (void) { * \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 VTK users since vtk chooses + * 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 @@ -317,11 +319,11 @@ 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; + PixelRead=1 ; // PixelRaw if ( lgrTotale > MaxSize ) { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" @@ -330,25 +332,23 @@ 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 { @@ -357,16 +357,16 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // Pixel sign // 0 = Unsigned // 1 = Signed - str_signe=GetPubElValByNumber(0x0028,0x0103); + str_signe=Header->GetEntryByNumber(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 + // 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 ") ) { @@ -431,7 +432,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( - int planConf=GetPlanarConfiguration(); // 0028,0006 + int planConf=Header->GetPlanarConfiguration(); // 0028,0006 // Whatever Planar Configuration is, // "PALETTE COLOR " implies that we deal with the palette. @@ -448,24 +449,29 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { { 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(); + // 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; @@ -505,77 +511,241 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { *(x++) = *(a++); *(x++) = *(b++); *(x++) = *(c++); - } - + } memmove(destination,newDest,lgrTotale); free(newDest); - } - + } break; - } - + } case 2: - // 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;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); // TODO : Drop Palette Color out of the Header? - return lgrTotale; } +/** + * \ingroup gdcmFile + * \brief performs a shadow copy (not a deep copy) of the user given + * pixel area. + * 'image' Pixels are presented as C-like 2D arrays : line per line. + * 'volume'Pixels are presented as C-like 3D arrays : lane per plane + * \warning user is kindly requested NOT TO 'free' the Pixel area + * @param inData user supplied pixel area + * @param ExpectedSize total image size, in Bytes + * + * @return boolean + */ +bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { + Header->SetImageDataSize(ExpectedSize); + PixelData = inData; + lgrTotale = ExpectedSize; + return(true); +} + +/** + * \ingroup gdcmFile + * \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 gdcmFile::WriteRawData (std::string fileName) { + FILE * fp1; + fp1 = fopen(fileName.c_str(),"wb"); + if (fp1 == NULL) { + printf("Fail to open (write) file [%s] \n",fileName.c_str()); + return (false); + } + fwrite (PixelData,lgrTotale, 1, fp1); + fclose (fp1); + return(true); +} + +/** + * \ingroup gdcmFile + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention + * NO test is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails + */ + +bool gdcmFile::WriteDcmImplVR (std::string fileName) { + return WriteBase(fileName, ImplicitVR); +} + +/** + * \ingroup gdcmFile + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention + * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails + */ + +bool gdcmFile::WriteDcmImplVR (const char* fileName) { + return WriteDcmImplVR (std::string (fileName)); +} + +/** + * \ingroup gdcmFile +* \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 gdcmFile::WriteDcmExplVR (std::string fileName) { + return WriteBase(fileName, ExplicitVR); +} + +/** + * \ingroup gdcmFile + * \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 + */ + +bool gdcmFile::WriteAcr (std::string fileName) { + return WriteBase(fileName, ACR); +} +//----------------------------------------------------------------------------- +// Protected +/** + * \ingroup gdcmFile + * \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, DICOMDIR, ...) + * @return false if write fails + */ +bool gdcmFile::WriteBase (std::string fileName, FileType type) { + + FILE * fp1; + + if (PixelRead==-1 && type != DICOMDIR) { +/* std::cout << "U never Read the pixels; U cannot write the file" + << std::endl;*/ + return false; + } + + fp1 = fopen(fileName.c_str(),"wb"); + if (fp1 == NULL) { + printf("Failed to open (write) File [%s] \n",fileName.c_str()); + return (false); + } + + if ( (type == ImplicitVR) || (type == ExplicitVR) ) { + char * filePreamble; + // writing Dicom File Preamble + filePreamble=(char*)calloc(128,1); + fwrite(filePreamble,128,1,fp1); + fwrite("DICM",4,1,fp1); + free (filePreamble); + } + + // -------------------------------------------------------------- + // 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 ( 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 ---------------- + + // TODO : get the grPixel, numPixel values (for some ACR-NEMA images only) + + guint16 grPixel =Header->GetGrPixel(); + guint16 numPixel=Header->GetNumPixel();; + + // Update Pixel Data Length + // the *last* of the (GrPixel, NumPixel), if many. + + TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel); + TagHeaderEntryHT::iterator p2; + gdcmHeaderEntry * PixelElement; + + IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym + + if (Header->GetEntry().count(key) == 1) // only the first is significant + p2=it.first; // iterator on the first (unique) synonym + else + p2=it.second;// iterator on the last synonym + + PixelElement=p2->second; // H Table target column (2-nd col) + // PixelElement->SetPrintLevel(2); + // PixelElement->Print(); + + if (PixelRead==1) + PixelElement->SetLength(lgrTotaleRaw); + else if (PixelRead==0) + PixelElement->SetLength(lgrTotale); + + //PixelElement->SetPrintLevel(2); + //PixelElement->Print(); + + Header->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 (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(true); +} + +//----------------------------------------------------------------------------- +// Private /** * \ingroup gdcmFile * \brief Swap the bytes, according to swap code. @@ -585,7 +755,6 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { * @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; @@ -609,7 +778,7 @@ if(nb == 16) break; default: - printf("valeur de SWAP (16 bits) not allowed : %d\n", swap); + printf("SWAP value (16 bits) not allowed : %d\n", swap); } if( nb == 32 ) @@ -650,201 +819,182 @@ if( nb == 32 ) break; default: - printf(" SWAP value (32 bits) not allowed : %d\n", swap); + 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) + * \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. * - * @param fileName - * @return */ +bool gdcmFile::ReadPixelData(void* destination) { -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); -} + FILE *fp; -///////////////////////////////////////////////////////////////// -/** - * \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 - */ + 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 ? + } -int gdcmFile::WriteDcmImplVR (std::string fileName) { - return WriteBase(fileName, ImplicitVR); -} + Header->CloseFile(); + return(true); + } -///////////////////////////////////////////////////////////////// -/** - * \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 - */ + // ---------------------- Uncompressed File + if ( !Header->IsDicomV3() || + Header->IsImplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRBigEndianTransferSyntax() || + Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { -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 - */ + size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); + if ( ItemRead != 1 ) { + Header->CloseFile(); + return false; + } else { + Header->CloseFile(); + return true; + } + } -int gdcmFile::WriteAcr (std::string fileName) { - return WriteBase(fileName, ACR); -} + // ---------------------- Run Length Encoding + if (Header->IsRLELossLessTransferSyntax()) { + bool res = (bool)gdcm_read_RLE_file (fp,destination); + Header->CloseFile(); + 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 ? + } -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * - * @param FileName - * @param type - * - * @return int acts as a boolean - */ -int gdcmFile::WriteBase (std::string FileName, FileType type) { + int nBytes= nb/8; + + int taille = Header->GetXSize() * Header->GetYSize() + * Header->GetSamplesPerPixel(); + long fragmentBegining; // for ftell, fseek - FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); - return (0); + 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); } - - 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); + 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 - // -------------------------------------------------------------- - // 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); + fread(&ln,4,1,fp); + if(Header->GetSwapCode()) + ln=Header->SwapLong(ln); // Fragment Item length + + fragmentBegining=ftell(fp); - // -------------------------------------------------------------- - // 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 (jpg2000) { // JPEG 2000 : call to ??? + + res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written - if (filetype == ACR_LIBIDO){ - SetPubElValByNumber(rows , 0x0028, 0x0010); - SetPubElValByNumber(columns, 0x0028, 0x0011); - } - // ----------------- End of Special Patch ---------------- + } // ------------------------------------- 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 - fwrite(PixelData, lgrTotale, 1, fp1); - fclose (fp1); - return(1); + 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; } +//-----------------------------------------------------------------------------