X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=176b2c8c1b66abcc018d415854cc048593b3b88a;hb=eb835becc89cc1b8a1dc1f122f54b7659a6127be;hp=94f86cb7e88c62d58d9f0eff77e2c7e45b7014b9;hpb=9f643008e8a960617fb30ed9dcd454612657e5d2;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 94f86cb7..176b2c8c 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,71 +1,164 @@ // gdcmFile.cxx - +//----------------------------------------------------------------------------- #include "gdcmFile.h" #include "gdcmUtil.h" +#include "jpeg/ljpg/jpegless.h" +typedef std::pair IterHT; -// TODO : remove DEBUG -#define DEBUG 0 +//----------------------------------------------------------------------------- +// 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 + * 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 header file to be opened for reading datas + * @return + */ + +gdcmFile::gdcmFile(gdcmHeader *header) { + Header=header; + SelfHeader=false; + PixelRead=-1; // no ImageData read yet. + if (Header->IsReadable()) + SetPixelDataSizeFromHeader(); +} -#include "iddcmjpeg.h" -using namespace std; +/** + * \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 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 - * - * @return */ - -gdcmFile::gdcmFile(string & filename) - :gdcmHeader(filename.c_str()) -{ - SetPixelDataSizeFromHeader(); + gdcmFile::gdcmFile(const char * filename) { + Header=new gdcmHeader(filename); + SelfHeader=true; + PixelRead=-1; // no ImageData read yet. + + if (Header->IsReadable()) + SetPixelDataSizeFromHeader(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) -{ - 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 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 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) { - int nb; - string str_nb; + // 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] - str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { + 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 = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();; + 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 @@ -76,139 +169,129 @@ 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; - - 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; - } +void * gdcmFile::GetImageData (void) { + PixelData = (void *) malloc(lgrTotale); + if (PixelData) + GetImageDataIntoVector(PixelData, lgrTotale); + PixelRead=0; // no PixelRaw + return(PixelData); +} - 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; 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; +/** + * \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); + + } 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. - * @return Pointer to newly allocated pixel data. + * 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); - GetImageDataIntoVector(PixelData, lgrTotale); + if (PixelData) + GetImageDataIntoVectorRaw(PixelData, lgrTotale); + PixelRead=1; // PixelRaw return(PixelData); } @@ -216,6 +299,18 @@ 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 @@ -224,11 +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; - string str_nbFrames, str_nb, str_nbu, str_highBit, str_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" @@ -236,45 +331,55 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t 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() ); - } + (void)ReadPixelData(destination); - // 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 + // 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() ); + } + // 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() ); + } + // High Bit Position + str_highBit=Header->GetEntryByNumber(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=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 (processor endianity) if (nb != 8) - SwapZone(destination, GetSwapCode(), lgrTotale, nb); - - // On remet les Bits des Octets dans le bon ordre si besoin est + 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 ") ) { + return lgrTotale; } - free(newDest); - } + + // 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=Header->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 + // : 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;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 = Header->GetXSize()*Header->GetYSize()*Header->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;jSetEntryByNumber(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); + + // 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 + */ -// -// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs -// +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. + * \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; @@ -366,7 +778,7 @@ if(nb == 16) break; default: - printf("valeur de SWAP (16 bits) non autorisee : %d\n", swap); + printf("SWAP value (16 bits) not allowed : %d\n", swap); } if( nb == 32 ) @@ -407,183 +819,182 @@ if( nb == 32 ) break; default: - printf("valeur de SWAP (32 bits) non autorisee : %d\n", swap); + printf("SWAP value (32 bits) not allowed : %d\n", swap); } return; } -///////////////////////////////////////////////////////////////// -/** - * \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 - * - * @return TODO JPR - */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(1); -} - - -///////////////////////////////////////////////////////////////// /** - * \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 + * \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) { -void gdcmFile::SetImageDataSize(size_t ImageDataSize) { - - 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); -} + 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 ? + } -///////////////////////////////////////////////////////////////// -/** - * \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 - */ + Header->CloseFile(); + return(true); + } -int gdcmFile::WriteRawData (string nomFichier) { + // ---------------------- Uncompressed File + if ( !Header->IsDicomV3() || + Header->IsImplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRBigEndianTransferSyntax() || + Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - FILE * fp1; - fp1 = fopen(nomFichier.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str()); - return (0); + size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); + if ( ItemRead != 1 ) { + Header->CloseFile(); + return false; + } else { + Header->CloseFile(); + return true; + } } - - fwrite (PixelData,lgrTotale, 1, fp1); - fclose (fp1); - return(1); -} + // ---------------------- 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 ? + } + int nBytes= nb/8; + + int taille = Header->GetXSize() * Header->GetYSize() + * Header->GetSamplesPerPixel(); + long fragmentBegining; // for ftell, fseek -///////////////////////////////////////////////////////////////// -/** - * \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 - */ + 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 -int gdcmFile::WriteDcmImplVR (string nomFichier) { - return WriteBase(nomFichier, ImplicitVR); -} + fread(&ln,4,1,fp); + if(Header->GetSwapCode()) + ln=Header->SwapLong(ln); // Fragment Item length + + fragmentBegining=ftell(fp); -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * - * @param nomFichier TODO JPR - * - * @return TODO JPR - */ + if (jpg2000) { // JPEG 2000 : call to ??? -int gdcmFile::WriteDcmImplVR (const char* nomFichier) { - return WriteDcmImplVR (string (nomFichier)); -} - -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * - * @param nomFichier TODO JPR - * - * @return TODO JPR - */ + res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written -int gdcmFile::WriteDcmExplVR (string nomFichier) { - return WriteBase(nomFichier, ExplicitVR); -} + } // ------------------------------------- endif (JPEG2000) -///////////////////////////////////////////////////////////////// -/** - * \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 - * - * @return TODO JPR - */ - -int gdcmFile::WriteAcr (string nomFichier) { - return WriteBase(nomFichier, ACR); -} - -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * - * @param FileName TODO JPR - * @param type TODO JPR - * - * @return TODO JPR - */ -int gdcmFile::WriteBase (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; - // Ecriture Dicom File Preamble - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - } - - gdcmHeader::Write(fp1, type); - fwrite(PixelData, lgrTotale, 1, fp1); - fclose (fp1); - return(1); + 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; } +//-----------------------------------------------------------------------------