X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=484cc6909b771923839065f92c52f157918b63ee;hb=3fd520b58c8d1939994de2c63cc038c3e7ac9522;hp=f72941973374dbb427afe0a31c817fa16c12c203;hpb=5fbbb82939b73f5de7695e5c388a33426a3b36f4;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index f7294197..484cc690 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,591 +1,1096 @@ -// gdcmFile.cxx +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/08/26 15:29:53 $ + Version: $Revision: 1.121 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ #include "gdcmFile.h" -#include "gdcmUtil.h" +#include "gdcmDebug.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. -#include "iddcmjpeg.h" -using namespace std; + 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()) +gdcmFile::gdcmFile(std::string const & filename ) { - SetPixelDataSizeFromHeader(); + Header = new gdcmHeader( filename ); + SelfHeader = true; + PixelRead = -1; // no ImageData read yet. + + if ( Header->IsReadable() ) + { + SetPixelDataSizeFromHeader(); + } } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) +/** + * \ingroup gdcmFile + * \brief canonical destructor + * \note If the gdcmHeader is created by the gdcmFile, it is destroyed + * by the gdcmFile + */ +gdcmFile::~gdcmFile() { - SetPixelDataSizeFromHeader(); + if( SelfHeader ) + { + delete Header; + } + Header = 0; } +//----------------------------------------------------------------------------- +// 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 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) { +void gdcmFile::SetPixelDataSizeFromHeader() +{ + // 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] + + // Number of "Bits Allocated" int nb; - string str_nb; + std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { + if ( str_nb == GDCM_UNFOUND ) + { nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; + } + else + { + nb = atoi( str_nb.c_str() ); + if (nb == 12) + { + nb =16; + } + } + ImageDataSize = ImageDataSizeRaw = 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() ) + { + ImageDataSize *= 3; } - lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();; } -///////////////////////////////////////////////////////////////// /** * \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); +size_t gdcmFile::GetImageDataSize() +{ + return ImageDataSize; } +/** + * \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() +{ + return ImageDataSizeRaw; +} -///////////////////////////////////////////////////////////////// /** * \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; - } - - 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; +void *gdcmFile::GetImageData() +{ + // FIXME + // I need to deallocate PixelData before doing any allocation: + PixelData = new uint8_t[ImageDataSize]; + if ( PixelData ) + { + GetImageDataIntoVector(PixelData, ImageDataSize); + GetHeader()->SetEntryVoidAreaByNumber( PixelData, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 0; // no PixelRaw + + 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); + GetImageDataIntoVectorRaw (destination, maxSize); + PixelRead = 0 ; // no PixelRaw + if ( !Header->HasLUT() ) + { + return ImageDataSize; + } + + // from Lut R + Lut G + Lut B + uint8_t *newDest = new uint8_t[ImageDataSize]; + uint8_t *a = (uint8_t *)destination; + uint8_t *lutRGBA = Header->GetLUTRGBA(); + + if ( lutRGBA ) + { + int j; + //int l = ImageDataSizeRaw; //loss of precision + // move Gray pixels to temp area + memmove(newDest, destination, ImageDataSizeRaw); + for (size_t i=0; iDataImg; - int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel(); - - switch (nBytes) { - case 1: - { - unsigned short *dest = (unsigned short *)destination; - 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 //why is there a 'else' when an allocation failed ? + { + // need to make RGB Pixels (?) + // from grey Pixels (?!) + // and Gray Lut (!?!) + // or Segmented xxx Palette Color Lookup Table Data and so on - // ------------------------------- JPEG Lossy : call to IJG 6b - - // TODO : faire qq chose d'intelligent pour limiter - // la duplication du code JPEG - // TODO : eplucher icelui pour traiter *egalement* bits=16 + // 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 ?!? - int nBS; - if ((nBS = GetBitsStored()) != 12) { - printf("Sorry, Bits Stored = %d not yet taken into account\n",nBS); - return false; - } - - int res = gdcm_read_JPEG_file (destination); - if (DEBUG) - printf ("res : %d\n",res); - return res; -} + std::string rgb = "MONOCHROME1 "; // Photometric Interpretation + Header->SetEntryByNumber(rgb,0x0028,0x0004); + } + + /// \todo Drop Palette Color out of the Header? + return ImageDataSize; +} /** * \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) { - PixelData = (void *) malloc(lgrTotale); - GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); +void * gdcmFile::GetImageDataRaw () +{ + size_t imgDataSize = ImageDataSize; + if ( Header->HasLUT() ) + { + /// \todo Let gdcmHeader user a chance to get the right value + imgDataSize = ImageDataSizeRaw; + } + + // FIXME + // I need to deallocate PixelData before doing any allocation: + PixelData = new uint8_t[imgDataSize]; + if ( PixelData ) + { + GetImageDataIntoVectorRaw(PixelData, ImageDataSize); + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 1; // PixelRaw + + 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 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 + * @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) { - - int nb, nbu, highBit, signe; - string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; +size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize) +{ + int nb, nbu, highBit, sign; + PixelRead = 1 ; // PixelRaw - if ( lgrTotale > MaxSize ) { + if ( ImageDataSize > maxSize ) + { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" "than caller's expected MaxSize"); - return (size_t)0; - } - - (void)ReadPixelData(destination); - - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - } - - // Nombre de Bits Utilises - str_nbu=GetPubElValByNumber(0x0028,0x0101); - if (str_nbu == "gdcm::Unfound" ) { - nbu = nb; - } else { - nbu = atoi(str_nbu.c_str() ); - } - - // Position du Bit de Poids Fort - str_highBit=GetPubElValByNumber(0x0028,0x0102); - if (str_highBit == "gdcm::Unfound" ) { - highBit = nb - 1; - } else { - highBit = atoi(str_highBit.c_str() ); - } - - // Signe des Pixels - str_signe=GetPubElValByNumber(0x0028,0x0103); - if (str_signe == "gdcm::Unfound" ) { - signe = 1; - } else { - signe = atoi(str_signe.c_str() ); - } - - // On remet les Octets dans le bon ordre si besoin est - if (nb != 8) - SwapZone(destination, GetSwapCode(), lgrTotale, nb); - - // On remet les Bits des Octets dans le bon ordre si besoin est - if (nbu != nb){ - int l = (int)lgrTotale / (nb/8); - if (nb == 16) { - guint16 mask = 0xffff; - mask = mask >> (nb-nbu); - guint16 *deb = (guint16 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; + return (size_t)0; + } + + ReadPixelData( destination ); + + // Number of Bits Allocated for storing a Pixel + std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); + if ( str_nb == GDCM_UNFOUND ) + { + nb = 16; + } + else + { + nb = atoi( str_nb.c_str() ); + // FIXME + // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated + // separately, correct ? + } + + // Number of Bits actually used + std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101); + if ( str_nbu == GDCM_UNFOUND ) + { + nbu = nb; + } + else + { + nbu = atoi( str_nbu.c_str() ); + } + + // High Bit Position + std::string 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 + std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103); + if ( str_sign == GDCM_UNFOUND ) + { + sign = 0; // default is unsigned + } + else + { + sign = atoi( str_sign.c_str() ); + } + + // re arange bytes inside the integer (processor endianity) + if ( nb != 8 ) + { + SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); + } + + // to avoid pb with some xmedcon breakers images + if ( nb == 16 && nbu < nb && sign == 0) + { + int l = (int)(ImageDataSize / (nb/8)); + uint16_t *deb = (uint16_t *)destination; + for(int i = 0; i> (nb-nbu); - guint32 *deb = (guint32 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; + uint16_t *deb = (uint16_t *)destination; + for(int i = 0; i> (nbu - highBit - 1)) & mask; + deb++; } - } else { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image"); - return (size_t)0; } - } - - // --- - string str_PlanarConfiguration = GetPubElValByNumber(0x0028,0x0006); - int PlanarConfiguration; - if (str_PlanarConfiguration == "gdcm::Unfound" ) { - PlanarConfiguration = 0; - } else { - PlanarConfiguration = atoi(str_PlanarConfiguration.c_str() ); - } - // --- - - // TODO : replace by - // if (GetPlanarConfiguration() == 1) { - // after unfreeze - - if (PlanarConfiguration == 1) { // need to make RGB Pixels - int l = lgrTotale/3 ; - - char * a = (char *)destination; - char * b = a + l; - char * c = b + l; - char * newDest = (char*) malloc(lgrTotale); - // TODO : - // any trick not to have to allocate temporary buffer is welcome ... - char *x = newDest; - for (int i=0;i> (nb - nbu); + uint32_t *deb = (uint32_t *)destination; + for(int i = 0; i> (nbu - highBit - 1)) & mask; + deb++; + } } - a = (char *)destination; - x = newDest; - for (int i=0;iGetEntryByNumber(0x0028,0x0004); -void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { -guint32 s32; -guint16 fort,faible; -int i; + if ( str_PhotometricInterpretation == "MONOCHROME1 " + || str_PhotometricInterpretation == "MONOCHROME2 " ) + { + return ImageDataSize; + } + + // Planar configuration = 0 : Pixels are already RGB + // Planar configuration = 1 : 3 planes : R, G, B + // Planar configuration = 2 : 1 gray Plane + 3 LUT -if(nb == 16) - switch(swap) { - case 0: - case 12: - case 1234: - break; - - case 21: - case 3412: - case 2143: - case 4321: - - for(i=0;i>8) - | ((((unsigned short int*)im)[i])<<8); - break; - - default: - printf("valeur de SWAP (16 bits) non autorisee : %d\n", swap); - } - -if( nb == 32 ) - switch (swap) { + // 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: - case 1234: + // 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(); - 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; + uint8_t* newDest = new uint8_t[ImageDataSize]; + uint8_t* x = newDest; + uint8_t* a = (uint8_t*)destination; + uint8_t* b = a + l; + uint8_t* 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; i < nbFrames; i++) + { + for (int j = 0; j < l; j++) + { + R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; + G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; + B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; + + if (R < 0.0) R = 0.0; + if (G < 0.0) G = 0.0; + if (B < 0.0) B = 0.0; + if (R > 255.0) R = 255.0; + if (G > 255.0) G = 255.0; + if (B > 255.0) B = 255.0; + + *(x++) = (uint8_t)R; + *(x++) = (uint8_t)G; + *(x++) = (uint8_t)B; + a++; b++; c++; + } + } + memmove(destination, newDest, ImageDataSize); + delete[] newDest; } - break; + 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(); - 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; + uint8_t *newDest = new uint8_t[ImageDataSize]; + uint8_t *x = newDest; + uint8_t *a = (uint8_t *)destination; + uint8_t *b = a + l; + uint8_t *c = b + l; + + for (int j = 0; j < l; j++) + { + *(x++) = *(a++); + *(x++) = *(b++); + *(x++) = *(c++); + } + memmove(destination, newDest, ImageDataSize); + delete[] newDest; } break; - - case 3412: - for(i=0;i>16; - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - default: - printf("valeur de SWAP (32 bits) non autorisee : %d\n", swap); - } -return; + case 2: + // Palettes were found + // Let the user deal with them ! + return ImageDataSize; + } + // now, it's an RGB image + // Lets's write it in the Header + + // CreateOrReplaceIfExist ? + + std::string spp = "3"; // Samples Per Pixel + std::string rgb = "RGB "; // Photometric Interpretation + std::string planConfig = "0"; // Planar Configuration + + Header->SetEntryByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(rgb,0x0028,0x0004); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); + + /// \todo Drop Palette Color out of the Header? + return ImageDataSize; } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief TODO JPR - * \warning doit-etre etre publique ? FIXME JPR - * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions - * - * @param inData TODO JPR - * @param ExpectedSize TODO JPR + * \brief performs a shalow 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 TODO JPR + * @return boolean */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(1); -} +bool gdcmFile::SetImageData(void *inData, size_t expectedSize) +{ + Header->SetImageDataSize( expectedSize ); + PixelData = inData; + ImageDataSize = expectedSize; + PixelRead = 1; + return true; +} -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief TODO JPR - * \ - * \warning WARNING doit-etre etre publique ? FIXME JPR - * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions - * - * @param ImageDataSize TODO JPR - * + * \brief Writes on disk A SINGLE Dicom file + * NO test is performed on processor "Endiannity". + * It's up to the user to call his Reader properly + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails */ -void gdcmFile::SetImageDataSize(size_t ImageDataSize) { +bool gdcmFile::WriteRawData(std::string const & fileName) +{ + FILE *fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Fail to open (write) file [%s] \n", fileName.c_str()); + return false; + } + fwrite (PixelData, ImageDataSize, 1, fp1); + fclose (fp1); - string content1; - char car[20]; - - // suppose que le ElValue (0x7fe0, 0x0010) existe ... - - sprintf(car,"%d",ImageDataSize); - - gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010); - a->SetLength(ImageDataSize); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetPubElValByNumber(content1, 0x7fe0, 0x0000); + return true; } - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief Ecrit sur disque les pixels d'UNE image - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca sera à l'utilisateur d'appeler son Reader correctement - * (Equivalent a IdImaWriteRawFile) FIXME JPR - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention + * NO test is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteRawData (string nomFichier) { - - FILE * fp1; - fp1 = fopen(nomFichier.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",nomFichier.c_str()); - return (0); - } - - fwrite (PixelData,lgrTotale, 1, fp1); - fclose (fp1); - return(1); +bool gdcmFile::WriteDcmImplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmImplicitVR); } - - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief Ecrit sur disque UNE image Dicom - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) FIXME JPR - * - * @param nomFichier TODO JPR - * - * @return TODO JPR +* \brief Writes on disk A SINGLE Dicom file, + * using the 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 */ -int gdcmFile::WriteDcmImplVR (string nomFichier) { - return WriteBase(nomFichier, ImplicitVR); +bool gdcmFile::WriteDcmExplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmExplicitVR); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \brief Writes on disk A SINGLE Dicom file, + * using the ACR-NEMA convention + * NO test is performed on processor "Endiannity". + * (a l'attention des logiciels cliniques + * qui ne prennent en entrée QUE des images ACR ... + * \warning if a DICOM_V3 header is supplied, + * groups < 0x0008 and shadow groups are ignored + * \warning NO TEST is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ - -int gdcmFile::WriteDcmImplVR (const char* nomFichier) { - return WriteDcmImplVR (string (nomFichier)); + +bool gdcmFile::WriteAcr (std::string const & fileName) +{ + return WriteBase(fileName, gdcmACR); } - -///////////////////////////////////////////////////////////////// + +//----------------------------------------------------------------------------- +// Protected /** * \ingroup gdcmFile - * - * @param nomFichier TODO JPR - * - * @return TODO JPR + * \brief NOT a end user inteded function + * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @param type file type (ExplicitVR, ImplicitVR, ...) + * @return false if write fails */ +bool gdcmFile::WriteBase (std::string const & fileName, FileType type) +{ + if ( PixelRead == -1 && type != gdcmExplicitVR) + { + return false; + } -int gdcmFile::WriteDcmExplVR (string nomFichier) { - return WriteBase(nomFichier, ExplicitVR); + FILE *fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Failed to open (write) File [%s] \n", fileName.c_str()); + return false; + } + + if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + { + // writing Dicom File Preamble + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble, 128, 1, fp1); + fwrite("DICM", 4, 1, fp1); + + delete[] 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() == gdcmACR_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 ---------------- + + uint16_t grPixel = Header->GetGrPixel(); + uint16_t numPixel = Header->GetNumPixel();; + + gdcmDocEntry* PixelElement = + GetHeader()->GetDocEntryByNumber(grPixel, numPixel); + + if ( PixelRead == 1 ) + { + // we read pixel 'as is' (no tranformation LUT -> RGB) + PixelElement->SetLength( ImageDataSizeRaw ); + } + else if ( PixelRead == 0 ) + { + // we tranformed GrayLevel pixels + LUT into RGB Pixel + PixelElement->SetLength( ImageDataSize ); + } + + 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() == gdcmACR_LIBIDO ) + { + Header->SetEntryByNumber(rows , 0x0028, 0x0010); + Header->SetEntryByNumber(columns, 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- + + // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now + fclose (fp1); + + return true; } - -///////////////////////////////////////////////////////////////// + +//----------------------------------------------------------------------------- +// Private /** - * \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 + * \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) +{ + int i; -int gdcmFile::WriteAcr (string nomFichier) { - return WriteBase(nomFichier, ACR); + if( nb == 16 ) + { + uint16_t* im16 = (uint16_t*)im; + switch( swap ) + { + case 0: + case 12: + case 1234: + break; + case 21: + case 3412: + case 2143: + case 4321: + for(i=0; i < lgr/2; i++) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } + break; + default: + std::cout << "SWAP value (16 bits) not allowed :i" << swap << + std::endl; + } + } + else if( nb == 32 ) + { + uint32_t s32; + uint16_t fort, faible; + uint32_t* im32 = (uint32_t*)im; + switch ( swap ) + { + case 0: + case 1234: + break; + case 4321: + for(i = 0; i < lgr/4; i++) + { + faible = im32[i] & 0x0000ffff; // 4321 + fort = im32[i] >> 16; + fort = ( fort >> 8 ) | ( fort << 8 ); + faible = ( faible >> 8 ) | ( faible << 8); + s32 = faible; + im32[i] = ( s32 << 16 ) | fort; + } + break; + case 2143: + for(i = 0; i < lgr/4; i++) + { + faible = im32[i] & 0x0000ffff; // 2143 + fort = im32[i] >> 16; + fort = ( fort >> 8 ) | ( fort << 8 ); + faible = ( faible >> 8) | ( faible << 8); + s32 = fort; + im32[i] = ( s32 << 16 ) | faible; + } + break; + case 3412: + for(i = 0; i < lgr/4; i++) + { + faible = im32[i] & 0x0000ffff; // 3412 + fort = im32[i] >> 16; + s32 = faible; + im32[i] = ( s32 << 16 ) | fort; + } + break; + default: + std::cout << "SWAP value (32 bits) not allowed : " << swap << + std::endl; + } + } } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * - * @param FileName TODO JPR - * @param type 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. * - * @return TODO JPR */ -int gdcmFile::WriteBase (string FileName, FileType type) { +bool gdcmFile::ReadPixelData(void *destination) +{ + FILE *fp = Header->OpenFile(); - FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); - return (0); + if ( !fp ) + { + 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(); + uint8_t b0, b1, b2; + + uint16_t* pdestination = (uint16_t*)destination; + for(int p = 0; p < nbPixels; p += 2 ) + { + fread(&b0,1,1,fp); + fread(&b1,1,1,fp); + fread(&b2,1,1,fp); - 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); + //Two steps is necessary to please VC++ + *pdestination++ = ((b0 >> 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 ? + } + + Header->CloseFile(); + return true; } - gdcmHeader::Write(fp1, type); - fwrite(PixelData, lgrTotale, 1, fp1); - fclose (fp1); - return(1); + // ---------------------- Uncompressed File + if ( !Header->IsDicomV3() || + Header->IsImplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRBigEndianTransferSyntax() || + Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) + { + size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); + Header->CloseFile(); + if ( ItemRead != 1 ) + { + return false; + } + else + { + return true; + } + } + + // ---------------------- Run Length Encoding + if ( Header->IsRLELossLessTransferSyntax() ) + { + bool res = 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 + + bool jpg2000 = Header->IsJPEG2000(); + bool jpgLossless = Header->IsJPEGLossless(); + + bool res = true; + uint16_t 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 ?!? + uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1]; + fread(BasicOffsetTableItemValue,ln,1,fp); + //delete[] BasicOffsetTableItemValue; + } + + // 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 = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written + // ------------------------------------- endif (JPEG2000) + } + else if (jpgLossless) + { + // JPEG LossLess : call to xmedcom Lossless JPEG + // Reading Fragment pixels + JPEGLosslessDecodeImage (fp, (uint16_t*)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) + { + // Reading Fragment pixels + res = gdcm_read_JPEG_file (fp,destination); + } + else + { + // Reading Fragment pixels + res = gdcm_read_JPEG_file12 (fp,destination); + } + // ------------------------------------- endif (JPEGLossy) + } + + if ( !res ) + { + break; + } + + // location in user's memory + // for next fragment (if any) + destination = (uint8_t*)destination + taille * nBytes; + + 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; } +//-----------------------------------------------------------------------------