X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=ffb3d848027124d12c7a97f93e5e25448d7522e7;hb=54ce6e928bccc91bb12601c782b92c833678de40;hp=69fba75867b02e30d7db4318657454647e97c8d6;hpb=ec5c97e570cd68bd66ccf41b61e96d11c87bbd5b;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 69fba758..ffb3d848 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 @@ -17,25 +18,86 @@ * one sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). * - * @param filename file to be opened for parsing + * @param header file to be opened for reading datas * * @return */ -gdcmFile::gdcmFile(std::string & filename) - :gdcmHeader(filename.c_str()) +gdcmFile::gdcmFile(gdcmHeader *header) { - if (IsReadable()) - SetPixelDataSizeFromHeader(); + Header=header; + SelfHeader=false; + + if (Header->IsReadable()) + SetPixelDataSizeFromHeader(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) +/** + * \ingroup gdcmFile + * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant + * file (see SetFileName, SetDcmTag and Write) + * Opens (in read only and when possible) an existing file and checks + * for DICOM compliance. Returns NULL on failure. + * \Note the in-memory representation of all available tags found in + * the DICOM header is post-poned to first header information access. + * This avoid a double parsing of public part of the header when + * one sets an a posteriori shadow dictionary (efficiency can be + * seen as a side effect). + * + * @param filename file to be opened for parsing + * + * @return + */ +gdcmFile::gdcmFile(std::string & filename) { - if (IsReadable()) + Header=new gdcmHeader(filename.c_str()); + SelfHeader=true; + + if (Header->IsReadable()) SetPixelDataSizeFromHeader(); } +gdcmFile::gdcmFile(const char * filename) +{ + Header=new gdcmHeader(filename); + SelfHeader=true; + + if (Header->IsReadable()) + SetPixelDataSizeFromHeader(); +} + +/** + * \ingroup gdcmFile + * \brief 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. + * \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 + * @return + */ +gdcmHeader *gdcmFile::GetHeader(void) +{ + return(Header); +} + /** * \ingroup gdcmFile * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les @@ -47,28 +109,6 @@ gdcmFile::gdcmFile(const char * filename) * @return longueur a allouer */ void gdcmFile::SetPixelDataSizeFromHeader(void) { - int nb; - std::string str_nb; - str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; - } - lgrTotale = lgrTotaleRaw = GetXSize() * GetYSize() * GetZSize() - * (nb/8)* GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = - gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - - /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ - // pb when undealt Segmented Palette Color - - if (HasLUT()) { - lgrTotale*=3; - } -} - // see PS 3.3-2003 : C.7.6.3.2.1 // // MONOCHROME1 @@ -84,222 +124,61 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { // YBR_ICT // YBR_RCT - // LUT's - // ex : gdcm-US-ALOKA-16.dcm - // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data] - // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data] - // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data] - - // ex : 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] - + // 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] -///////////////////////////////////////////////////////////////// -/** - * \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. - */ + // 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] -size_t gdcmFile::GetImageDataSizeRaw(void) { - return (lgrTotaleRaw); + int nb; + std::string str_nb; + str_nb=Header->GetPubEntryByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { + nb = 16; + } else { + nb = atoi(str_nb.c_str() ); + if (nb == 12) nb =16; + } + lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize() + * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel(); + std::string str_PhotometricInterpretation = + Header->GetPubEntryByNumber(0x0028,0x0004); + + /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ + // pb when undealt Segmented Palette Color + + if (Header->HasLUT()) { + lgrTotale*=3; + } } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Returns the size (in bytes) of required memory to hold * the pixel data represented in this file. * @return The size of pixel data in bytes. */ - size_t gdcmFile::GetImageDataSize(void) { return (lgrTotale); } - -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief 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) { - - if ( !OpenFile()) - return false; - - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - return false; - } - - - // ---------------------- Compacted File (12 Bits Per Pixel) - - /* unpack 12 Bits pixels into 16 Bits pixels */ - /* 2 pixels 12bit = [0xABCDEF] */ - /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */ - - if (GetBitsAllocated()==12) { - int nbPixels = GetXSize()*GetYSize(); - unsigned char b0, b1, b2; - - 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 ( !IsDicomV3() || - IsImplicitVRLittleEndianTransferSyntax() || - IsExplicitVRLittleEndianTransferSyntax() || - IsExplicitVRBigEndianTransferSyntax() || - IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - size_t ItemRead = fread(destination, GetPixelAreaLength(), 1, fp); - - if ( ItemRead != 1 ) { - CloseFile(); - return false; - } else { - CloseFile(); - return true; - } - } - - // ---------------------- Run Length Encoding - - if (gdcmHeader::IsRLELossLessTransferSyntax()) { - int res = (bool)gdcm_read_RLE_file (destination); - return res; - } - - // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - - int nb; - std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ? - } - int nBytes= nb/8; - - int taille = GetXSize() * GetYSize() * GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek - - bool jpg2000 = IsJPEG2000(); - bool jpgLossless = IsJPEGLossless(); - - bool res = true; - guint16 ItemTagGr,ItemTagEl; - int ln; - - // Position on begining of Jpeg Pixels - - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Basic Offset Table Item length - - if (ln != 0) { - // What is it used for ?!? - char *BasicOffsetTableItemValue = (char *)malloc(ln+1); - fread(BasicOffsetTableItemValue,ln,1,fp); - } - - // first Fragment initialisation - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - - // parsing fragments until Sequence Delim. Tag found - - while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { - - // --- for each Fragment - - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Fragment Item length - - fragmentBegining=ftell(fp); - - if (jpg2000) { // JPEG 2000 : call to ??? - - res = (bool)gdcm_read_JPEG2000_file (destination); // Not Yet written - - } // ------------------------------------- endif (JPEG2000) - - else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG - - JPEGLosslessDecodeImage (fp, // Reading Fragment pixels - (unsigned short *)destination, - GetPixelSize()*8* GetSamplesPerPixel(), - ln); - res=1; // in order not to break the loop - - } // ------------------------------------- endif (JPEGLossless) - - else { // JPEG Lossy : call to IJG 6b - - if (GetBitsStored() == 8) { - res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels - } else { - res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels - } - } // ------------------------------------- endif (JPEGLossy) - - if (!res) break; - - destination = (char *)destination + taille * nBytes; // location in user's memory - // for next fragment (if any) - - fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start - fseek(fp,ln,SEEK_CUR); // at the begining of next fragment - - ItemTagGr = ItemTagEl =0; - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - - } // endWhile parsing fragments until Sequence Delim. Tag found - - return res; -} +size_t gdcmFile::GetImageDataSizeRaw(void) { + return (lgrTotaleRaw); +} /** * \ingroup gdcmFile @@ -318,27 +197,6 @@ 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 (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 @@ -360,19 +218,16 @@ 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 (!HasLUT()) + 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 = GetLUTRGBA(); + unsigned char * lutRGBA = Header->GetLUTRGBA(); if (lutRGBA) { int l = lgrTotaleRaw; memmove(newDest, destination, l);// move Gray pixels to temp area @@ -391,13 +246,12 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // CreateOrReplaceIfExist ? std::string spp = "3"; // Samples Per Pixel - gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002); + Header->SetPubEntryByNumber(spp,0x0028,0x0002); std::string rgb= "RGB "; // Photometric Interpretation - gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004); + Header->SetPubEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006); - - + Header->SetPubEntryByNumber(planConfig,0x0028,0x0006); + } else { // need to make RGB Pixels (?) // from grey Pixels (?!) @@ -412,7 +266,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // Segmented xxx Palette Color are *more* than 65535 long ?!? std::string rgb= "MONOCHROME1 "; // Photometric Interpretation - gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004); + Header->SetPubEntryByNumber(rgb,0x0028,0x0004); } @@ -420,7 +274,26 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { 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 @@ -434,7 +307,7 @@ 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 * @@ -446,7 +319,6 @@ 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; @@ -461,7 +333,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { (void)ReadPixelData(destination); // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = GetPubElValByNumber(0x0028,0x0100); + str_nb = Header->GetPubEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { @@ -469,7 +341,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { } // Nombre de Bits Utilises - str_nbu=GetPubElValByNumber(0x0028,0x0101); + str_nbu=Header->GetPubEntryByNumber(0x0028,0x0101); if (str_nbu == GDCM_UNFOUND ) { nbu = nb; } else { @@ -477,7 +349,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { } // Position du Bit de Poids Fort - str_highBit=GetPubElValByNumber(0x0028,0x0102); + str_highBit=Header->GetPubEntryByNumber(0x0028,0x0102); if (str_highBit == GDCM_UNFOUND ) { highBit = nb - 1; } else { @@ -486,7 +358,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // Pixel sign // 0 = Unsigned // 1 = Signed - str_signe=GetPubElValByNumber(0x0028,0x0103); + str_signe=Header->GetPubEntryByNumber(0x0028,0x0103); if (str_signe == GDCM_UNFOUND ) { signe = 0; // default is unsigned } else { @@ -495,7 +367,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // re arange bytes inside the integer if (nb != 8) - SwapZone(destination, GetSwapCode(), lgrTotale, nb); + SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb); // to avoid pb with some xmedcon breakers images if (nb==16 && nbuGetPubEntryByNumber(0x0028,0x0004); if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { @@ -560,7 +432,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( - int planConf=GetPlanarConfiguration(); // 0028,0006 + int planConf=Header->GetPlanarConfiguration(); // 0028,0006 // Whatever Planar Configuration is, // "PALETTE COLOR " implies that we deal with the palette. @@ -577,18 +449,18 @@ 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 + // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf + // for code optimisation // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : + // 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 = GetXSize()*GetYSize(); - int nbFrames = GetZSize(); + int l = Header->GetXSize()*Header->GetYSize(); + int nbFrames = Header->GetZSize(); unsigned char * newDest = (unsigned char*) malloc(lgrTotale); unsigned char *x = newDest; @@ -625,9 +497,9 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { } else { // need to make RGB Pixels from R,G,B Planes - // (all the Frames at a time) + // (all the Frames at a time) - int l = GetXSize()*GetYSize()*GetZSize(); + int l = Header->GetXSize()*Header->GetYSize()*Header->GetZSize(); char * newDest = (char*) malloc(lgrTotale); char * x = newDest; @@ -650,111 +522,26 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { 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 - gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002); + Header->SetPubEntryByNumber(spp,0x0028,0x0002); std::string rgb="RGB "; // Photometric Interpretation - gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004); + Header->SetPubEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006); + Header->SetPubEntryByNumber(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 @@ -766,44 +553,13 @@ return; * * @return integer acts as a boolean */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); +bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { + Header->SetImageDataSize(ExpectedSize); PixelData = inData; lgrTotale = ExpectedSize; - return(1); -} - - -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * \brief Sets the Pixel Area size in the Header - * --> not-for-rats function - * - * \warning WARNING doit-etre etre publique ? - * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions - * - * @param ImageDataSize new Pixel Area Size - * warning : nothing else is checked - */ - -void gdcmFile::SetImageDataSize(size_t ImageDataSize) { - std::string content1; - char car[20]; - // Assumes ElValue (0x7fe0, 0x0010) exists ... - sprintf(car,"%d",ImageDataSize); - - gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010); - a->SetLength(ImageDataSize); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetPubElValByNumber(content1, 0x7fe0, 0x0000); + return(true); } - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief Ecrit sur disque les pixels d'UNE image @@ -815,19 +571,18 @@ void gdcmFile::SetImageDataSize(size_t ImageDataSize) { * @return */ -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 @@ -839,11 +594,10 @@ int gdcmFile::WriteRawData (std::string fileName) { * @return int acts as a boolean */ -int gdcmFile::WriteDcmImplVR (std::string fileName) { +bool gdcmFile::WriteDcmImplVR (std::string fileName) { return WriteBase(fileName, ImplicitVR); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief @@ -851,11 +605,10 @@ int gdcmFile::WriteDcmImplVR (std::string fileName) { * @return int acts as a boolean */ -int gdcmFile::WriteDcmImplVR (const char* fileName) { +bool gdcmFile::WriteDcmImplVR (const char* fileName) { return WriteDcmImplVR (std::string (fileName)); } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile * \brief @@ -863,11 +616,10 @@ int gdcmFile::WriteDcmImplVR (const char* fileName) { * @return int acts as a boolean */ -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 @@ -883,11 +635,12 @@ int gdcmFile::WriteDcmExplVR (std::string fileName) { * @return int acts as a boolean */ -int gdcmFile::WriteAcr (std::string fileName) { +bool gdcmFile::WriteAcr (std::string fileName) { return WriteBase(fileName, ACR); } -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Protected /** * \ingroup gdcmFile * @@ -896,13 +649,13 @@ int gdcmFile::WriteAcr (std::string fileName) { * * @return int acts as a boolean */ -int gdcmFile::WriteBase (std::string FileName, FileType type) { +bool gdcmFile::WriteBase (std::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); + return (false); } if ( (type == ImplicitVR) || (type == ExplicitVR) ) { @@ -921,15 +674,15 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // just before writting ... std::string rows, columns; - if ( filetype == ACR_LIBIDO){ - rows = GetPubElValByNumber(0x0028, 0x0010); - columns = GetPubElValByNumber(0x0028, 0x0011); - SetPubElValByNumber(columns, 0x0028, 0x0010); - SetPubElValByNumber(rows , 0x0028, 0x0011); + if ( Header->GetFileType() == ACR_LIBIDO){ + rows = Header->GetPubEntryByNumber(0x0028, 0x0010); + columns = Header->GetPubEntryByNumber(0x0028, 0x0011); + Header->SetPubEntryByNumber(columns, 0x0028, 0x0010); + Header->SetPubEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- - gdcmHeader::Write(fp1, type); + Header->Write(fp1, type); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -937,13 +690,268 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // ...and we restore the Header to be Dicom Compliant again // just after writting - if (filetype == ACR_LIBIDO){ - SetPubElValByNumber(rows , 0x0028, 0x0010); - SetPubElValByNumber(columns, 0x0028, 0x0011); + if (Header->GetFileType() == ACR_LIBIDO){ + Header->SetPubEntryByNumber(rows , 0x0028, 0x0010); + Header->SetPubEntryByNumber(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("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 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->GetPubEntryByNumber(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; } +//-----------------------------------------------------------------------------