X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=2defabdaebfcadf3c4ec6046467059cda33038c6;hb=00e89cde772e18e4f2baab2b01680330af909d59;hp=43d8c3a19f612626015becf4bf28cd2b8a86b343;hpb=5e17bc4d219d5136ce530159f182528d4f842eae;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 43d8c3a1..2defabda 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,981 +1,860 @@ -// gdcmFile.cxx - -//This is needed when compiling in debug mode -#ifdef _MSC_VER -// 'type' : forcing value to bool 'true' or 'false' (performance warning) -//#pragma warning ( disable : 4800 ) -// 'identifier' : class 'type' needs to have dll-interface to be used by -// clients of class 'type2' -#pragma warning ( disable : 4251 ) -// 'identifier' : identifier was truncated to 'number' characters in the -// debug information -#pragma warning ( disable : 4786 ) -#endif //_MSC_VER + /*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/10/08 17:24:54 $ + Version: $Revision: 1.137 $ + + 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.html 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 "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess +#include "gdcmDebug.h" +#include "gdcmPixelConvert.h" +#include "jpeg/ljpg/jpegless.h" -#define str2num(str, typeNum) *((typeNum *)(str)) +typedef std::pair IterHT; -///////////////////////////////////////////////////////////////// +//------------------------------------------------------------------------- +// Constructor / Destructor /** - * \ingroup gdcmFile - * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant - * file (see SetFileName, SetDcmTag and Write) + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (gdcmHeader only deals with the ... header) * 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 + * It will be up to the user to load the pixels into memory + * (see GetImageData, GetImageDataRaw) + * \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 + * user sets an a posteriori shadow dictionary (efficiency can be + * seen as a side effect). + * @param header already built gdcmHeader + */ +gdcmFile::gdcmFile(gdcmHeader *header) +{ + Header = header; + SelfHeader = false; + Initialise(); +} + +/** + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (gdcmHeader only deals with the ... header) + * Opens (in read only and when possible) an existing file and checks + * for DICOM compliance. Returns NULL on failure. + * It will be up to the user to load the pixels into memory + * (see GetImageData, GetImageDataRaw) + * \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) - :gdcmHeader(filename.c_str()) +gdcmFile::gdcmFile(std::string const & filename ) { - SetPixelDataSizeFromHeader(); + Header = new gdcmHeader( filename ); + SelfHeader = true; + Initialise(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) +/** + * \brief Factorization for various forms of constructors. + */ +void gdcmFile::Initialise() { - SetPixelDataSizeFromHeader(); + if ( Header->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( Header->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } + } + SaveInitialValues(); } /** - * \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 canonical destructor + * \note If the gdcmHeader was created by the gdcmFile constructor, + * it is destroyed by the gdcmFile */ -void gdcmFile::SetPixelDataSizeFromHeader(void) { - int nb; - std::string str_nb; - - str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; - } - lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel(); - - std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - if ( str_PhotometricInterpretation == "PALETTE COLOR " - || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !! - lgrTotale*=3; +gdcmFile::~gdcmFile() +{ + if( SelfHeader ) + { + delete Header; } - - // remaining to check : - // str_PhotometricInterpretation == "YBR_FULL" - // str_PhotometricInterpretation == "YBR_FULL_422" (no LUT, no Palette) - // -->and some more !! + Header = 0; + + DeleteInitialValues(); } -///////////////////////////////////////////////////////////////// /** - * \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. + * \brief Sets some initial values for the Constructor + * \warning not end user intended */ -size_t gdcmFile::GetImageDataSize(void) { - return (lgrTotale); +void gdcmFile::SaveInitialValues() +{ + + PixelRead = -1; // no ImageData read yet. + LastAllocatedPixelDataLength = 0; + Pixel_Data = 0; + + InitialSpp = ""; + InitialPhotInt = ""; + InitialPlanConfig = ""; + InitialBitsAllocated = ""; + InitialHighBit = ""; + + InitialRedLUTDescr = 0; + InitialGreenLUTDescr = 0; + InitialBlueLUTDescr = 0; + InitialRedLUTData = 0; + InitialGreenLUTData = 0; + InitialBlueLUTData = 0; + + if ( Header->IsReadable() ) + { + // the following values *may* be modified + // by gdcmFile::GetImageDataIntoVectorRaw + // we save their initial value. + InitialSpp = Header->GetEntryByNumber(0x0028,0x0002); + InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004); + InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006); + + InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); + InitialHighBit = Header->GetEntryByNumber(0x0028,0x0102); + + // the following entries *may* be removed from the H table + // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw + // we keep a pointer on them. + InitialRedLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1101); + InitialGreenLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1102); + InitialBlueLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1103); + + InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201); + InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202); + InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203); + } } +/** + * \brief restores some initial values + * \warning not end user intended + */ +void gdcmFile::RestoreInitialValues() +{ + if ( Header->IsReadable() ) + { + // the following values *may* have been modified + // by gdcmFile::GetImageDataIntoVectorRaw + // we restore their initial value. + if ( InitialSpp != "") + Header->SetEntryByNumber(InitialSpp,0x0028,0x0002); + if ( InitialPhotInt != "") + Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); + if ( InitialPlanConfig != "") + + Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); + if ( InitialBitsAllocated != "") + Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); + if ( InitialHighBit != "") + Header->SetEntryByNumber(InitialHighBit,0x0028,0x0102); + + // the following entries *may* be have been removed from the H table + // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw + // we restore them. + + if (InitialRedLUTDescr) + Header->AddEntry(InitialRedLUTDescr); + if (InitialGreenLUTDescr) + Header->AddEntry(InitialGreenLUTDescr); + if (InitialBlueLUTDescr) + Header->AddEntry(InitialBlueLUTDescr); + + if (InitialRedLUTData) + Header->AddEntry(InitialBlueLUTDescr); + if (InitialGreenLUTData) + Header->AddEntry(InitialGreenLUTData); + if (InitialBlueLUTData) + Header->AddEntry(InitialBlueLUTData); + } +} -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Parse pixel data from disk and *prints* the result - * \ For multi-fragment Jpeg/Rle files checking purpose *only* - * \ Allows to 'see' if the file *does* conform - * \ (some of them do not) - * \ with Dicom Part 3, Annex A (PS 3.5-2003, page 58, page 85) - * + * \brief delete initial values (il they were saved) + * of InitialLutDescriptors and InitialLutData */ -bool gdcmFile::ParsePixelData(void) { +void gdcmFile::DeleteInitialValues() +{ - if ( !OpenFile()) - return false; +// InitialLutDescriptors and InitialLutData +// will have to be deleted if the don't belong any longer +// to the Header H table when the header is deleted... + + if ( InitialRedLUTDescr ) + delete InitialRedLUTDescr; + + if ( InitialGreenLUTDescr ) + delete InitialGreenLUTDescr; - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - return false; - } + if ( InitialBlueLUTDescr ) + delete InitialBlueLUTDescr; + + if ( InitialRedLUTData ) + delete InitialRedLUTData; - if ( !IsDicomV3() || - IsImplicitVRLittleEndianTransferSyntax() || - IsExplicitVRLittleEndianTransferSyntax() || - IsExplicitVRBigEndianTransferSyntax() || - IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - printf ("gdcmFile::ParsePixelData : non JPEG/RLE File\n"); - return 0; - } - - 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; - } - int nBytes= nb/8; - - //int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel(); - int taille = GetXSize() * GetYSize() * GetSamplesPerPixel(); - - printf ("Checking the Dicom-Jpeg/RLE Pixels\n"); + if ( InitialGreenLUTData != NULL) + delete InitialGreenLUTData; - guint16 ItemTagGr,ItemTagEl; - int ln; - long ftellRes; - char * destination = NULL; - - // ------------------------------- for Parsing : Position on begining of Jpeg/RLE Pixels + if ( InitialBlueLUTData != NULL) + delete InitialBlueLUTData; +} - if( !IsRLELossLessTransferSyntax()) { +//----------------------------------------------------------------------------- +// Print - // JPEG Image +//----------------------------------------------------------------------------- +// Public - std::cout << "JPEG image" << std::endl; - ftellRes=ftell(fp); - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Basic Offset Table Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Basic Offset Table Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n", - ftellRes,ItemTagGr,ItemTagEl ); - ftellRes=ftell(fp); - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Basic Offset Table Item Lentgh - printf("at %x : Basic Offset Table Item Lentgh (??) %d x(%08x)\n", - ftellRes,ln,ln); - if (ln != 0) { - // What is it used for ?? - char * BasicOffsetTableItemValue= (char *)malloc(ln+1); - fread(BasicOffsetTableItemValue,ln,1,fp); - guint32 a; - for (int i=0;iGetBitsAllocated(); + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) + { + numberBitsAllocated = 16; + } - ftellRes=ftell(fp); - 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); - } - printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", - ftellRes,ItemTagGr,ItemTagEl ); - - // while 'Sequence Delimiter Item' (fffe,e0dd) not found - while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { - // Parse fragments of the current Fragment (Frame) - ftellRes=ftell(fp); - fread(&fragmentLength,4,1,fp); - if(GetSwapCode()) - fragmentLength=SwapLong(fragmentLength); // length - printf(" at %x : 'fragment' length %d x(%08x)\n", - ftellRes, fragmentLength,fragmentLength); - -// destination += taille * nBytes; // location in user's memory -// printf (" Destination will be x(%x) = %d \n", -// destination,destination ); - - //------------------ scanning (not reading) fragment pixels - - fread(&nbRleSegments,4,1,fp); // Reading : Number of RLE Segments - if(GetSwapCode()) - nbRleSegments=SwapLong(nbRleSegments); - printf(" Nb of RLE Segments : %d\n",nbRleSegments); - - for(int k=1; k<=15; k++) { // Reading RLE Segments Offset Table - ftellRes=ftell(fp); - fread(&RleSegmentOffsetTable[k],4,1,fp); - if(GetSwapCode()) - RleSegmentOffsetTable[k]=SwapLong(RleSegmentOffsetTable[k]); - printf(" at : %x Offset Segment %d : %d (%x)\n", - ftellRes,k,RleSegmentOffsetTable[k],RleSegmentOffsetTable[k]); - } - if (nbRleSegments>1) { - for(int k=1; k<=nbRleSegments-1; k++) { // skipping (not reading) RLE Segments - RleSegmentLength[k]=RleSegmentOffsetTable[k+1]-RleSegmentOffsetTable[k]; - ftellRes=ftell(fp); - printf (" Segment %d : Length = %d Start at %x\n", - k,RleSegmentLength[k], ftellRes); - fseek(fp,RleSegmentLength[k],SEEK_CUR); - } - } - RleSegmentLength[nbRleSegments] = fragmentLength - RleSegmentOffsetTable[nbRleSegments] ; - // TODO : Check the value - ftellRes=ftell(fp); - printf (" Segment %d : Length = %d Start at %x\n", - nbRleSegments,RleSegmentLength[nbRleSegments],ftellRes); - - fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR); - - // ------------------ end of scanning fragment pixels - - ftellRes=ftell(fp); - 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); - } - printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", - ftellRes,ItemTagGr,ItemTagEl ); - } - } - return 1; + int DecompressedSize = Header->GetXSize() + * Header->GetYSize() + * Header->GetZSize() + * ( numberBitsAllocated / 8 ) + * Header->GetSamplesPerPixel(); + + return DecompressedSize; } -///////////////////////////////////////////////////////////////// /** - * \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, + * - Reads the pixels from disk (uncompress if necessary), + * - Transforms YBR pixels, if any, into RGB pixels + * - Transforms 3 planes R, G, B, if any, into a single RGB Plane + * - Transforms single Grey plane + 3 Palettes into a RGB Plane + * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. + * @return Pointer to newly allocated pixel data. + * NULL if alloc fails */ -bool gdcmFile::ReadPixelData(void* destination) { +uint8_t* gdcmFile::GetImageData() +{ + // FIXME (Mathieu) + // I need to deallocate Pixel_Data before doing any allocation: + + if ( Pixel_Data ) + if ( LastAllocatedPixelDataLength != ImageDataSize ) + free(Pixel_Data); + if ( !Pixel_Data ) + Pixel_Data = new uint8_t[ImageDataSize]; + + if ( Pixel_Data ) + { + LastAllocatedPixelDataLength = ImageDataSize; - if ( !OpenFile()) - return false; - - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - return false; - } + // we load the pixels (and transform grey level + LUT into RGB) + GetImageDataIntoVector(Pixel_Data, ImageDataSize); -// ------------------------- Uncompressed File - - if ( !IsDicomV3() || - IsImplicitVRLittleEndianTransferSyntax() || - IsExplicitVRLittleEndianTransferSyntax() || - IsExplicitVRBigEndianTransferSyntax() || - IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - size_t ItemRead = fread(destination, lgrTotale, 1, fp); - if ( ItemRead != 1 ) { - CloseFile(); - return false; - } else { - CloseFile(); - return true; + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // Will be 7fe0, 0010 in standard case + GetHeader()->SetEntryBinAreaByNumber( Pixel_Data, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 0; // no PixelRaw + + return Pixel_Data; +} + +/** + * \brief + * Read the pixels from disk (uncompress if necessary), + * Transforms YBR pixels, if any, into RGB pixels + * Transforms 3 planes R, G, B, if any, into a single RGB Plane + * Transforms single Grey plane + 3 Palettes into a RGB Plane + * Copies at most MaxSize bytes of pixel data to caller allocated + * memory space. + * \warning This function allows people that want to build a volume + * from an image stack *not to* have, 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) +{ + GetImageDataIntoVectorRaw (destination, maxSize); + PixelRead = 0 ; // =0 : no ImageDataRaw + 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; + // move Gray pixels to temp area + memmove(newDest, destination, ImageDataSizeRaw); + for (size_t i=0; iDataImg; - - switch (nBytes) { - case 1: - { - unsigned short *dest = (unsigned short *)destination; - for (int i=0; iDataImg; - unsigned short *dest = (unsigned short *)destination; - switch (nBytes) { - case 1: - { - 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 // GetLUTRGBA() failed + { + // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color + // that are *more* than 65535 long ?!? + // No idea how to manage such an image ! + // Need to make RGB Pixels (?) from grey Pixels (?!) and Gray Lut (!?!) + // It seems that *no Dicom Viewer* has any idea :-( + + std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation + Header->SetEntryByNumber(photomInterp,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. + * \brief Allocates necessary memory, + * Transforms YBR pixels (if any) into RGB pixels + * Transforms 3 planes R, G, B (if any) into a single RGB Plane + * Copies the pixel data (image[s]/volume[s]) to newly allocated zone. + * 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); - if (PixelData) - GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); +uint8_t* gdcmFile::GetImageDataRaw () +{ + size_t imgDataSize; + if ( Header->HasLUT() ) + /// \todo Let gdcmHeader user a chance to get the right value + imgDataSize = ImageDataSizeRaw; + else + imgDataSize = ImageDataSize; + + // FIXME (Mathieu) + // I need to deallocate Pixel_Data before doing any allocation: + + if ( Pixel_Data ) + if ( LastAllocatedPixelDataLength != imgDataSize ) + free(Pixel_Data); + if ( !Pixel_Data ) + Pixel_Data = new uint8_t[imgDataSize]; + + if ( Pixel_Data ) + { + LastAllocatedPixelDataLength = imgDataSize; + + // we load the pixels ( grey level or RGB, but NO transformation) + GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize); + + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // will be 7fe0, 0010 in standard cases + GetHeader()->SetEntryBinAreaByNumber(Pixel_Data, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 1; // PixelRaw + + return Pixel_Data; } /** - * \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::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) +{ + // we save the initial values of the following + // in order to be able to restore the header in a disk-consistent state + // (if user asks twice to get the pixels from disk) -size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { - - int nb, nbu, highBit, signe; - std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; - - if ( lgrTotale > MaxSize ) { + if ( PixelRead != -1 ) // File was "read" before + { + RestoreInitialValues(); + } + + PixelRead = 1 ; // PixelRaw + + 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() ); - } - - // re arange bytes inside the integer - if (nb != 8) - SwapZone(destination, GetSwapCode(), lgrTotale, nb); - - // re arange bits inside the bytes - 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 ++; - } - } else if (nb == 32 ) { - guint32 mask = 0xffffffff; - mask = mask >> (nb-nbu); - guint32 *deb = (guint32 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; - } - } else { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image"); - return (size_t)0; - } - } - - // Try to deal with the color - // -------------------------- - - std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - - if ( (str_PhotometricInterpretation == "MONOCHROME1 ") - || (str_PhotometricInterpretation == "MONOCHROME2 ") - || (str_PhotometricInterpretation == "RGB")) { - return lgrTotale; + return (size_t)0; } - - switch ( GetPlanarConfiguration() ) { - case 0: - // Pixels are already RGB - break; + + ReadPixelData( destination ); + + // Number of Bits Allocated for storing a Pixel + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( numberBitsAllocated == 0 ) + { + numberBitsAllocated = 16; + } + + // Number of Bits actually used + int numberBitsStored = Header->GetBitsStored(); + if ( numberBitsStored == 0 ) + { + numberBitsStored = numberBitsAllocated; + } + + // High Bit Position + int highBitPosition = Header->GetHighBitPosition(); + if ( highBitPosition == 0 ) + { + highBitPosition = numberBitsAllocated - 1; + } + + bool signedPixel = Header->IsSignedPixelData(); + + gdcmPixelConvert::ConvertReorderEndianity( + (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + Header->GetSwapCode(), + signedPixel ); + + ConvertReArrangeBits( (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + highBitPosition ); + +#ifdef GDCM_DEBUG + FILE* DebugFile; + DebugFile = fopen( "SpuriousFile.RAW", "wb" ); + fwrite( PixelConvertor.GetUncompressed(), + PixelConvertor.GetUncompressedsSize(), + 1, DebugFile ); + fclose( DebugFile ); +#endif //GDCM_DEBUG + +// SPLIT ME +////////////////////////////////// +// Deal with the color - case 1: - // need to make RGB Pixels from Planes R,G,B + // Monochrome pictures don't require color intervention + if ( Header->IsMonochrome() ) + { + 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 + + // 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(); + + // Planar configuration = 2 ==> 1 gray Plane + 3 LUT + // ...and... + // whatever the Planar Configuration might be, "PALETTE COLOR " + // implies that we deal with the palette. + if ( ( planConf == 2 ) || Header->IsPaletteColor() ) + { + return ImageDataSize; + } + + // When planConf is 0, pixels are allready in RGB + + if ( planConf == 1 ) + { + uint8_t* newDest = new uint8_t[ImageDataSize]; + // Warning : YBR_FULL_422 acts as RGB + if ( Header->IsYBRFull() ) { - 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 j=0;j>8) - | ((((unsigned short int*)im)[i])<<8); - break; - - default: - printf("valeur de SWAP (16 bits) not allowed : %d\n", swap); - } + std::string spp = "3"; // Samples Per Pixel + std::string photInt = "RGB "; // Photometric Interpretation + std::string planConfig = "0"; // Planar Configuration + + Header->SetEntryByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(photInt,0x0028,0x0004); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); -if( nb == 32 ) - switch (swap) { - case 0: - case 1234: - break; + return ImageDataSize; +} - 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; +/** + * \brief Re-arrange the bits within the bytes. + */ +void gdcmFile::ConvertReArrangeBits( uint8_t* pixelZone, + size_t imageDataSize, + int numberBitsStored, + int numberBitsAllocated, + int highBitPosition) + throw ( gdcmFormatError ) +{ + if ( numberBitsStored != numberBitsAllocated ) + { + int l = (int)(imageDataSize / (numberBitsAllocated/8)); + if ( numberBitsAllocated == 16 ) + { + uint16_t mask = 0xffff; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint16_t* deb = (uint16_t*)pixelZone; + for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; + deb++; } - 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; + } + else if ( numberBitsAllocated == 32 ) + { + uint32_t mask = 0xffffffff; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint32_t* deb = (uint32_t*)pixelZone; + for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; + deb++; } - 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; + } + else + { + dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image"); + throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()", + "weird image !?" ); + } + } } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief TODO JPR - * \warning doit-etre etre publique ? - * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions - * - * @param inData - * @param ExpectedSize - * - * @return integer acts as a boolean + * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels + * \warning Works on all the frames at a time */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(1); +void gdcmFile::ConvertYcBcRPlanesToRGBPixels(uint8_t* source, + uint8_t* destination) +{ + // 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(); + + uint8_t* a = source; + uint8_t* b = source + l; + uint8_t* c = source + l + l; + double R, G, B; + + /// \todo : Replace by the 'well known' integer computation + /// counterpart. Refer to + /// 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; + + *(destination++) = (uint8_t)R; + *(destination++) = (uint8_t)G; + *(destination++) = (uint8_t)B; + a++; + b++; + c++; + } + } } - -///////////////////////////////////////////////////////////////// /** - * \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 + * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels + * \warning Works on all the frames at a time */ +void gdcmFile::ConvertRGBPlanesToRGBPixels(uint8_t* source, + uint8_t* destination) +{ + int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); -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); -} + uint8_t* a = source; + uint8_t* b = source + l; + uint8_t* c = source + l + l; + for (int j = 0; j < l; j++) + { + *(destination++) = *(a++); + *(destination++) = *(b++); + *(destination++) = *(c++); + } +} -///////////////////////////////////////////////////////////////// /** - * \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) + * \brief Points the internal Pixel_Data pointer to the callers inData + * image representation, BUT WITHOUT COPYING THE DATA. + * 'image' Pixels are presented as C-like 2D arrays : line per line. + * 'volume'Pixels are presented as C-like 3D arrays : plane per plane + * \warning Since the pixels are not copied, it is the caller's responsability + * not to deallocate it's data before gdcm uses them (e.g. with + * the Write() method. + * @param inData user supplied pixel area + * @param expectedSize total image size, in Bytes * - * @param fileName - * @return + * @return boolean */ - -int gdcmFile::WriteRawData (std::string fileName) { - FILE * fp1; - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); - return (0); - } - fwrite (PixelData,lgrTotale, 1, fp1); - fclose (fp1); - return(1); +bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize) +{ + Header->SetImageDataSize( expectedSize ); +// FIXME : if already allocated, memory leak ! + Pixel_Data = inData; + ImageDataSize = ImageDataSizeRaw = expectedSize; + PixelRead = 1; +// FIXME : 7fe0, 0010 IS NOT set ... + return true; } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Ecrit sur disque UNE image Dicom - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * - * @param fileName - * @return int acts as a boolean + * \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 */ -int gdcmFile::WriteDcmImplVR (std::string fileName) { - return WriteBase(fileName, ImplicitVR); +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 (Pixel_Data, ImageDataSize, 1, fp1); + fclose (fp1); + + return true; } -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief - * @param fileName - * @return int acts as a boolean + * \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::WriteDcmImplVR (const char* fileName) { - return WriteDcmImplVR (std::string (fileName)); + +bool gdcmFile::WriteDcmImplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmImplicitVR); } - -///////////////////////////////////////////////////////////////// + /** - * \ingroup gdcmFile - * \brief - * @param fileName - * @return int acts as a boolean +* \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::WriteDcmExplVR (std::string fileName) { - return WriteBase(fileName, ExplicitVR); +bool gdcmFile::WriteDcmExplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmExplicitVR); } - -///////////////////////////////////////////////////////////////// + /** - * \ingroup gdcmFile - * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels + * \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 si un header DICOM est fourni en entree, - * les groupes < 0x0008 et les groupes impairs sont ignores) - * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * - * @param fileName - * @return int acts as a boolean + * \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::WriteAcr (std::string fileName) { - return WriteBase(fileName, ACR); +bool gdcmFile::WriteAcr (std::string const & fileName) +{ + return WriteBase(fileName, gdcmACR); } -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Protected /** - * \ingroup gdcmFile - * - * @param FileName - * @param type - * - * @return int acts as a boolean + * \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 */ -int gdcmFile::WriteBase (std::string FileName, FileType type) { +bool gdcmFile::WriteBase (std::string const & fileName, FileType type) +{ + if ( PixelRead == -1 && type != gdcmExplicitVR) + { + return false; + } - FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); - return (0); + 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 == ImplicitVR) || (type == ExplicitVR) ) { - char * filePreamble; + if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + { // writing Dicom File Preamble - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble, 128, 1, fp1); + fwrite("DICM", 4, 1, fp1); + + delete[] filePreamble; } // -------------------------------------------------------------- @@ -984,17 +863,39 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // 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 ( filetype == ACR_LIBIDO){ - rows = GetPubElValByNumber(0x0028, 0x0010); - columns = GetPubElValByNumber(0x0028, 0x0011); - SetPubElValByNumber(columns, 0x0028, 0x0010); - SetPubElValByNumber(rows , 0x0028, 0x0011); - } - // ----------------- End of Special Patch ---------------- + if ( Header->GetFileType() == gdcmACR_LIBIDO) + { + rows = Header->GetEntryByNumber(0x0028, 0x0010); + columns = Header->GetEntryByNumber(0x0028, 0x0011); - gdcmHeader::Write(fp1, type); + 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 @@ -1002,13 +903,209 @@ 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() == gdcmACR_LIBIDO ) + { + Header->SetEntryByNumber(rows , 0x0028, 0x0010); + Header->SetEntryByNumber(columns, 0x0028, 0x0011); + } // ----------------- End of Special Patch ---------------- - - fwrite(PixelData, lgrTotale, 1, fp1); + + // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); - return(1); + + return true; } + +//----------------------------------------------------------------------------- +// Private +/** + * \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 = Header->OpenFile(); + + if ( !fp ) + { + return false; + } + if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) + { + Header->CloseFile(); + return false; + } + + if ( Header->GetBitsAllocated() == 12 ) + { + gdcmPixelConvert::ConvertDecompress12BitsTo16Bits( + (uint8_t*)destination, + Header->GetXSize(), + Header->GetYSize(), + fp); + Header->CloseFile(); + return true; + } + + // ---------------------- 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 = gdcmPixelConvert::gdcm_read_RLE_file ( destination, + Header->GetXSize(), + Header->GetYSize(), + Header->GetZSize(), + Header->GetBitsAllocated(), + &(Header->RLEInfo), + fp ); + Header->CloseFile(); + return res; + } + + // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) + { + numberBitsAllocated = 16; + } + + int nBytes= numberBitsAllocated/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 if ( Header->GetBitsStored() == 12) + { + // Reading Fragment pixels + res = gdcm_read_JPEG_file12 (fp,destination); + } + else + { + // other JPEG lossy not supported + dbg.Error(" gdcmFile::ReadPixelData : unknown jpeg lossy compression"); + return 0; + } + // ------------------------------------- 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; +} +