X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=858ee0cb358f30cbe2cc8b1e9ecbd2e5d9ff29aa;hb=bafdfafe6c1b30607035fc4018c0405169b348e8;hp=fdbef674bcd86cbd0fbce27fd6916b24463b28c9;hpb=2fde1103e77a2448cce41d061781d0ec89ef239b;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index fdbef674..858ee0cb 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,10 +1,11 @@ // gdcmFile.cxx - +//----------------------------------------------------------------------------- #include "gdcmFile.h" #include "gdcmUtil.h" #include "jpeg/ljpg/jpegless.h" -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Constructor / Destructor /** * \ingroup gdcmFile * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant @@ -22,8 +23,7 @@ * @return */ -gdcmFile::gdcmFile(gdcmHeader *header) -{ +gdcmFile::gdcmFile(gdcmHeader *header) { Header=header; SelfHeader=false; @@ -31,7 +31,6 @@ gdcmFile::gdcmFile(gdcmHeader *header) SetPixelDataSizeFromHeader(); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant @@ -43,13 +42,10 @@ gdcmFile::gdcmFile(gdcmHeader *header) * This avoid a double parsing of public part of the header when * one sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). - * * @param filename file to be opened for parsing - * * @return */ -gdcmFile::gdcmFile(std::string & filename) -{ +gdcmFile::gdcmFile(std::string & filename) { Header=new gdcmHeader(filename.c_str()); SelfHeader=true; @@ -57,8 +53,7 @@ gdcmFile::gdcmFile(std::string & filename) SetPixelDataSizeFromHeader(); } -gdcmFile::gdcmFile(const char * filename) -{ +gdcmFile::gdcmFile(const char * filename) { Header=new gdcmHeader(filename); SelfHeader=true; @@ -66,52 +61,70 @@ gdcmFile::gdcmFile(const char * filename) SetPixelDataSizeFromHeader(); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief Destructor 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. + * \brief canonical destructor * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed * by the gdcmFile - * - * @param filename file to be opened for parsing - * - * @return */ -gdcmFile::~gdcmFile(void) -{ +gdcmFile::~gdcmFile(void) { if(SelfHeader) delete Header; Header=NULL; } +//----------------------------------------------------------------------------- +// Print +//----------------------------------------------------------------------------- +// Public /** * \ingroup gdcmFile * \brief * @return */ -gdcmHeader *gdcmFile::GetHeader(void) -{ +gdcmHeader *gdcmFile::GetHeader(void) { return(Header); } /** * \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) { + // 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] + int nb; std::string str_nb; - str_nb=Header->GetPubElValByNumber(0x0028,0x0100); + str_nb=Header->GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { @@ -121,7 +134,7 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize() * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel(); std::string str_PhotometricInterpretation = - Header->GetPubElValByNumber(0x0028,0x0004); + Header->GetEntryByNumber(0x0028,0x0004); /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ // pb when undealt Segmented Palette Color @@ -131,240 +144,27 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { } } - // see PS 3.3-2003 : C.7.6.3.2.1 - // - // MONOCHROME1 - // MONOCHROME2 - // PALETTE COLOR - // RGB - // HSV (Retired) - // ARGB (Retired) - // CMYK (Retired) - // YBR_FULL - // YBR_FULL_422 (no LUT, no Palette) - // YBR_PARTIAL_422 - // YBR_ICT - // YBR_RCT - - // LUT's - // ex : gdcm-US-ALOKA-16.dcm - // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data] - // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data] - // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data] - - // ex : OT-PAL-8-face.dcm - // 0028|1201 [US] [Red Palette Color Lookup Table Data] - // 0028|1202 [US] [Green Palette Color Lookup Table Data] - // 0028|1203 [US] [Blue Palette Color Lookup Table Data] - - -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * \brief Returns the size (in bytes) of required memory to hold - * \ the pixel data represented in this file, when user DOESN'T want - * \ to get RGB pixels image when it's stored as a PALETTE COLOR image - * \ - the (vtk) user is supposed to know how deal with LUTs - - * \ warning to be used with GetImagePixelsRaw() - * @return The size of pixel data in bytes. - */ - -size_t gdcmFile::GetImageDataSizeRaw(void) { - return (lgrTotaleRaw); -} - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Returns the size (in bytes) of required memory to hold * the pixel data represented in this file. * @return The size of pixel data in bytes. */ - size_t gdcmFile::GetImageDataSize(void) { return (lgrTotale); } - -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Read pixel data from disk (optionaly decompressing) into the - * caller specified memory location. - * @param destination where the pixel data should be stored. - * + * \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. */ -bool gdcmFile::ReadPixelData(void* destination) { - - FILE *fp; - - if ( !(fp=Header->OpenFile())) - return false; - - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) { - Header->CloseFile(); - return false; - } - - - // ---------------------- Compacted File (12 Bits Per Pixel) - - /* unpack 12 Bits pixels into 16 Bits pixels */ - /* 2 pixels 12bit = [0xABCDEF] */ - /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */ - - if (Header->GetBitsAllocated()==12) { - int nbPixels = Header->GetXSize() * Header->GetYSize(); - unsigned char b0, b1, b2; - - unsigned short int* pdestination = (unsigned short int*)destination; - for(int p=0;p> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - /* A */ /* B */ /* D */ - *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - /* F */ /* C */ /* E */ - - // Troubles expected on Big-Endian processors ? - } - return(true); - } - - // ---------------------- Uncompressed File - - if ( !Header->IsDicomV3() || - Header->IsImplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - - if ( ItemRead != 1 ) { - Header->CloseFile(); - return false; - } else { - Header->CloseFile(); - return true; - } - } - - // ---------------------- Run Length Encoding - - if (Header->IsRLELossLessTransferSyntax()) { - bool res = (bool)gdcm_read_RLE_file (fp,destination); - return res; - } - - // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - - int nb; - std::string str_nb=Header->GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ? - } - - int nBytes= nb/8; - - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek - - bool jpg2000 = Header->IsJPEG2000(); - bool jpgLossless = Header->IsJPEGLossless(); - - bool res = true; - guint16 ItemTagGr,ItemTagEl; - int ln; - - // Position on begining of Jpeg Pixels - - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); - } - fread(&ln,4,1,fp); - if(Header->GetSwapCode()) - ln=Header->SwapLong(ln); // Basic Offset Table Item length - - if (ln != 0) { - // What is it used for ?!? - char *BasicOffsetTableItemValue = (char *)malloc(ln+1); - fread(BasicOffsetTableItemValue,ln,1,fp); - } - - // first Fragment initialisation - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); - } - - // parsing fragments until Sequence Delim. Tag found - - while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { - // --- for each Fragment - - fread(&ln,4,1,fp); - if(Header->GetSwapCode()) - ln=Header->SwapLong(ln); // Fragment Item length - - fragmentBegining=ftell(fp); - - if (jpg2000) { // JPEG 2000 : call to ??? - - res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written - - } // ------------------------------------- endif (JPEG2000) - - else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG - - JPEGLosslessDecodeImage (fp, // Reading Fragment pixels - (unsigned short *)destination, - Header->GetPixelSize()*8* Header->GetSamplesPerPixel(), - ln); - res=1; // in order not to break the loop - - } // ------------------------------------- endif (JPEGLossless) - - else { // JPEG Lossy : call to IJG 6b - - if (Header->GetBitsStored() == 8) { - res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels - } else { - res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels - } - } // ------------------------------------- endif (JPEGLossy) - - if (!res) break; - - destination = (char *)destination + taille * nBytes; // location in user's memory - // for next fragment (if any) - - fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start - fseek(fp,ln,SEEK_CUR); // at the begining of next fragment - - ItemTagGr = ItemTagEl =0; - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); - } - - } // endWhile parsing fragments until Sequence Delim. Tag found - - Header->CloseFile(); - return res; +size_t gdcmFile::GetImageDataSizeRaw(void) { + return (lgrTotaleRaw); } /** @@ -372,8 +172,8 @@ bool gdcmFile::ReadPixelData(void* destination) { * \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 + * 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 */ @@ -384,27 +184,6 @@ void * gdcmFile::GetImageData (void) { return(PixelData); } -/** - * \ingroup gdcmFile - * \brief Allocates necessary memory, copies the pixel data - * (image[s]/volume[s]) to newly allocated zone. - * Transforms YBR pixels into RGB pixels if any - Transforms 3 planes R, G, B into a single RGB Plane - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane - * @return Pointer to newly allocated pixel data. - * \ NULL if alloc fails - */ -void * gdcmFile::GetImageDataRaw (void) { - if (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) - GetImageDataIntoVectorRaw(PixelData, lgrTotale); - return(PixelData); -} - /** * \ingroup gdcmFile * \brief Copies at most MaxSize bytes of pixel data to caller's @@ -426,16 +205,13 @@ void * gdcmFile::GetImageDataRaw (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 l = GetImageDataIntoVectorRaw (destination, MaxSize); if (!Header->HasLUT()) return lgrTotale; - // from Lut R + Lut G + Lut B - + // 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(); @@ -457,36 +233,50 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // CreateOrReplaceIfExist ? std::string spp = "3"; // Samples Per Pixel - Header->SetPubElValByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(spp,0x0028,0x0002); std::string rgb= "RGB "; // Photometric Interpretation - Header->SetPubElValByNumber(rgb,0x0028,0x0004); + Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - Header->SetPubElValByNumber(planConfig,0x0028,0x0006); - - + 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 - - // Well . I'll wait till I find such an image - - // Oops! I get one (gdcm-US-ALOKA-16.dcm) - // No idea how to manage it - // It seems that *no Dicom Viewer* has any idea :-( - // Segmented xxx Palette Color are *more* than 65535 long ?!? + + // 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->SetPubElValByNumber(rgb,0x0028,0x0004); - - } - + 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::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) + GetImageDataIntoVectorRaw(PixelData, lgrTotale); + return(PixelData); +} /** * \ingroup gdcmFile @@ -500,7 +290,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { * (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) + * \warning DOES NOT transform the Grey Plane + Palette Color (if any) * into a single RGB Pixels Plane * the (VTK) user will manage the palettes * @@ -512,7 +302,6 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ - size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { int nb, nbu, highBit, signe; @@ -526,24 +315,22 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { (void)ReadPixelData(destination); - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = Header->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=Header->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=Header->GetPubElValByNumber(0x0028,0x0102); + } + // High Bit Position + str_highBit=Header->GetEntryByNumber(0x0028,0x0102); if (str_highBit == GDCM_UNFOUND ) { highBit = nb - 1; } else { @@ -552,14 +339,14 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // Pixel sign // 0 = Unsigned // 1 = Signed - str_signe=Header->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, Header->GetSwapCode(), lgrTotale, nb); @@ -598,9 +385,9 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { return (size_t)0; } } - +// DO NOT remove this code commented out. +// Nobody knows what's expecting you ... // Just to 'see' what was actually read on disk :-( -// Some troubles expected // FILE * f2; // f2 = fopen("SpuriousFile.raw","wb"); // fwrite(destination,lgrTotale,1,f2); @@ -610,7 +397,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // ------------------- std::string str_PhotometricInterpretation = - Header->GetPubElValByNumber(0x0028,0x0004); + Header->GetEntryByNumber(0x0028,0x0004); if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { @@ -643,10 +430,8 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { { if (str_PhotometricInterpretation == "YBR_FULL") { - // Warning : YBR_FULL_422 acts as RGB - // : we need to make RGB Pixels from Planes Y,cB,cR - // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - // for code optimisation + // 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 : @@ -661,11 +446,13 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { 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(); @@ -705,122 +492,34 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { *(x++) = *(a++); *(x++) = *(b++); *(x++) = *(c++); - } - + } memmove(destination,newDest,lgrTotale); free(newDest); - } - + } break; - } - + } case 2: // Palettes were found - // Let the user deal with them ! - return lgrTotale; + // Let the user deal with them ! + return lgrTotale; } - // now, it's an RGB image - // Lets's write it in the Header - - // CreateOrReplaceIfExist ? - + // now, it's an RGB image + // Lets's write it in the Header + // CreateOrReplaceIfExist ? std::string spp = "3"; // Samples Per Pixel - Header->SetPubElValByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(spp,0x0028,0x0002); std::string rgb="RGB "; // Photometric Interpretation - Header->SetPubElValByNumber(rgb,0x0028,0x0004); + Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - Header->SetPubElValByNumber(planConfig,0x0028,0x0006); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); // TODO : Drop Palette Color out of the Header? - return lgrTotale; } - - -/** - * \ingroup gdcmFile - * \brief Swap the bytes, according to swap code. - * \warning not end user intended - * @param im area to deal with - * @param swap swap code - * @param lgr Area Length - * @param nb Pixels Bit number - */ - -void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { -guint32 s32; -guint16 fort,faible; -int i; - -if(nb == 16) - switch(swap) { - case 0: - case 12: - case 1234: - break; - - case 21: - case 3412: - case 2143: - case 4321: - - for(i=0;i>8) - | ((((unsigned short int*)im)[i])<<8); - break; - - default: - printf("valeur de SWAP (16 bits) not allowed : %d\n", swap); - } - -if( nb == 32 ) - switch (swap) { - case 0: - case 1234: - break; - - case 4321: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - case 2143: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=fort; - ((unsigned long int*)im)[i]=(s32<<16)|faible; - } - break; - - case 3412: - for(i=0;i>16; - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - default: - printf(" SWAP value (32 bits) not allowed : %d\n", swap); - } -return; -} - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief TODO JPR @@ -830,17 +529,15 @@ return; * @param inData * @param ExpectedSize * - * @return integer acts as a boolean + * @return boolean */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { +bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { Header->SetImageDataSize(ExpectedSize); PixelData = inData; lgrTotale = ExpectedSize; - return(1); + return(true); } - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Ecrit sur disque les pixels d'UNE image @@ -848,23 +545,23 @@ int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { * Ca sera à l'utilisateur d'appeler son Reader correctement * (Equivalent a IdImaWriteRawFile) * - * @param fileName - * @return + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails */ -int gdcmFile::WriteRawData (std::string fileName) { +bool gdcmFile::WriteRawData (std::string fileName) { FILE * fp1; fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); - return (0); + return (false); } fwrite (PixelData,lgrTotale, 1, fp1); fclose (fp1); - return(1); + return(true); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Ecrit sur disque UNE image Dicom @@ -872,74 +569,76 @@ int gdcmFile::WriteRawData (std::string fileName) { * Ca fonctionnera correctement (?) sur processeur Intel * (Equivalent a IdDcmWrite) * - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmImplVR (std::string fileName) { +bool gdcmFile::WriteDcmImplVR (std::string fileName) { return WriteBase(fileName, ImplicitVR); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmImplVR (const char* fileName) { +bool gdcmFile::WriteDcmImplVR (const char* fileName) { return WriteDcmImplVR (std::string (fileName)); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmExplVR (std::string fileName) { +bool gdcmFile::WriteDcmExplVR (std::string fileName) { return WriteBase(fileName, ExplicitVR); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels * (a l'attention des logiciels cliniques * qui ne prennent en entrée QUE des images ACR ... - * \warning si un header DICOM est fourni en entree, - * les groupes < 0x0008 et les groupes impairs sont ignores) - * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur. + * \warning if a DICOM_V3 header is supplied, + * groups < 0x0008 and shadow groups are ignored) + * \warning NO TEST is performed on processor "Endiannity". * Ca fonctionnera correctement (?) sur processeur Intel * (Equivalent a IdDcmWrite) * - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteAcr (std::string fileName) { +bool gdcmFile::WriteAcr (std::string fileName) { return WriteBase(fileName, ACR); } -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Protected /** * \ingroup gdcmFile * - * @param FileName - * @param type - * - * @return int acts as a boolean +* @param fileName name of the file to be created + * (any already existing file is overwritten) + * @param type file type (ExplicitVR, ImplicitVR, ...) + * @return false if write fails */ -int gdcmFile::WriteBase (std::string FileName, FileType type) { +bool gdcmFile::WriteBase (std::string fileName, FileType type) { FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); + fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); - return (0); + printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); + return (false); } if ( (type == ImplicitVR) || (type == ExplicitVR) ) { @@ -959,10 +658,10 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { std::string rows, columns; if ( Header->GetFileType() == ACR_LIBIDO){ - rows = Header->GetPubElValByNumber(0x0028, 0x0010); - columns = Header->GetPubElValByNumber(0x0028, 0x0011); - Header->SetPubElValByNumber(columns, 0x0028, 0x0010); - Header->SetPubElValByNumber(rows , 0x0028, 0x0011); + rows = Header->GetEntryByNumber(0x0028, 0x0010); + columns = Header->GetEntryByNumber(0x0028, 0x0011); + Header->SetEntryByNumber(columns, 0x0028, 0x0010); + Header->SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- @@ -975,12 +674,267 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // just after writting if (Header->GetFileType() == ACR_LIBIDO){ - Header->SetPubElValByNumber(rows , 0x0028, 0x0010); - Header->SetPubElValByNumber(columns, 0x0028, 0x0011); + Header->SetEntryByNumber(rows , 0x0028, 0x0010); + Header->SetEntryByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- fwrite(PixelData, lgrTotale, 1, fp1); fclose (fp1); - return(1); + return(true); +} + +//----------------------------------------------------------------------------- +// Private +/** + * \ingroup gdcmFile + * \brief Swap the bytes, according to swap code. + * \warning not end user intended + * @param im area to deal with + * @param swap swap code + * @param lgr Area Length + * @param nb Pixels Bit number + */ +void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { +guint32 s32; +guint16 fort,faible; +int i; + +if(nb == 16) + switch(swap) { + case 0: + case 12: + case 1234: + break; + + case 21: + case 3412: + case 2143: + case 4321: + + for(i=0;i>8) + | ((((unsigned short int*)im)[i])<<8); + break; + + default: + printf("SWAP value (16 bits) not allowed : %d\n", swap); + } + +if( nb == 32 ) + switch (swap) { + case 0: + case 1234: + break; + + case 4321: + for(i=0;i>16; + fort= (fort>>8) | (fort<<8); + faible=(faible>>8) | (faible<<8); + s32=faible; + ((unsigned long int*)im)[i]=(s32<<16)|fort; + } + break; + + case 2143: + for(i=0;i>16; + fort= (fort>>8) | (fort<<8); + faible=(faible>>8) | (faible<<8); + s32=fort; + ((unsigned long int*)im)[i]=(s32<<16)|faible; + } + break; + + case 3412: + for(i=0;i>16; + s32=faible; + ((unsigned long int*)im)[i]=(s32<<16)|fort; + } + break; + + default: + printf("SWAP value (32 bits) not allowed : %d\n", swap); + } +return; +} + +/** + * \ingroup gdcmFile + * \brief Read pixel data from disk (optionaly decompressing) into the + * caller specified memory location. + * @param destination where the pixel data should be stored. + * + */ +bool gdcmFile::ReadPixelData(void* destination) { + + FILE *fp; + + if ( !(fp=Header->OpenFile())) + return false; + + if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) { + Header->CloseFile(); + return false; + } + + + // ---------------------- Compacted File (12 Bits Per Pixel) + /* unpack 12 Bits pixels into 16 Bits pixels */ + /* 2 pixels 12bit = [0xABCDEF] */ + /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */ + if (Header->GetBitsAllocated()==12) { + int nbPixels = Header->GetXSize() * Header->GetYSize(); + unsigned char b0, b1, b2; + + unsigned short int* pdestination = (unsigned short int*)destination; + for(int p=0;p> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); + /* A */ /* B */ /* D */ + *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); + /* F */ /* C */ /* E */ + + // Troubles expected on Big-Endian processors ? + } + return(true); + } + + // ---------------------- Uncompressed File + if ( !Header->IsDicomV3() || + Header->IsImplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRBigEndianTransferSyntax() || + Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { + + size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); + + if ( ItemRead != 1 ) { + Header->CloseFile(); + return false; + } else { + Header->CloseFile(); + return true; + } + } + + // ---------------------- Run Length Encoding + if (Header->IsRLELossLessTransferSyntax()) { + bool res = (bool)gdcm_read_RLE_file (fp,destination); + return res; + } + + // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 + int nb; + std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { + nb = 16; + } else { + nb = atoi(str_nb.c_str() ); + if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ? + } + + int nBytes= nb/8; + + int taille = Header->GetXSize() * Header->GetYSize() + * Header->GetSamplesPerPixel(); + long fragmentBegining; // for ftell, fseek + + bool jpg2000 = Header->IsJPEG2000(); + bool jpgLossless = Header->IsJPEGLossless(); + + bool res = true; + guint16 ItemTagGr,ItemTagEl; + int ln; + + // Position on begining of Jpeg Pixels + + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if(Header->GetSwapCode()) { + ItemTagGr=Header->SwapShort(ItemTagGr); + ItemTagEl=Header->SwapShort(ItemTagEl); + } + fread(&ln,4,1,fp); + if(Header->GetSwapCode()) + ln=Header->SwapLong(ln); // Basic Offset Table Item length + + if (ln != 0) { + // What is it used for ?!? + char *BasicOffsetTableItemValue = (char *)malloc(ln+1); + fread(BasicOffsetTableItemValue,ln,1,fp); + } + + // first Fragment initialisation + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if(Header->GetSwapCode()) { + ItemTagGr=Header->SwapShort(ItemTagGr); + ItemTagEl=Header->SwapShort(ItemTagEl); + } + + // parsing fragments until Sequence Delim. Tag found + while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { + // --- for each Fragment + + fread(&ln,4,1,fp); + if(Header->GetSwapCode()) + ln=Header->SwapLong(ln); // Fragment Item length + + fragmentBegining=ftell(fp); + + if (jpg2000) { // JPEG 2000 : call to ??? + + res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written + + } // ------------------------------------- endif (JPEG2000) + + else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG + + JPEGLosslessDecodeImage (fp, // Reading Fragment pixels + (unsigned short *)destination, + Header->GetPixelSize()*8* Header->GetSamplesPerPixel(), + ln); + res=1; // in order not to break the loop + + } // ------------------------------------- endif (JPEGLossless) + + else { // JPEG Lossy : call to IJG 6b + + if (Header->GetBitsStored() == 8) { + res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels + } else { + res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels + } + } // ------------------------------------- endif (JPEGLossy) + + if (!res) break; + + destination = (char *)destination + taille * nBytes; // location in user's memory + // for next fragment (if any) + + fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start + fseek(fp,ln,SEEK_CUR); // at the begining of next fragment + + ItemTagGr = ItemTagEl =0; + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if(Header->GetSwapCode()) { + ItemTagGr=Header->SwapShort(ItemTagGr); + ItemTagEl=Header->SwapShort(ItemTagEl); + } + + } // endWhile parsing fragments until Sequence Delim. Tag found + + Header->CloseFile(); + return res; } +//-----------------------------------------------------------------------------