X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=b91e7be504d581c816919563df8914326bffa773;hb=45c601b1fe996ebe3bf221541448f693a399173b;hp=ddde9fe44edd128eaf2c2157508876e15d136801;hpb=eb941e8785d3742b8a6a1aac964d43dcb4cf49f0;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index ddde9fe4..b91e7be5 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,871 +1,786 @@ -// 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: 2004/10/13 14:56:07 $ + Version: $Revision: 1.143 $ + + 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 -using namespace std; +#include "gdcmDebug.h" -#define str2num(str, typeNum) *((typeNum *)(str)) +namespace gdcm +{ +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 (Header 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 - * one sets an a posteriori shadow dictionary (efficiency can be + * user sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). - * - * @param filename file to be opened for parsing - * - * @return + * @param header already built Header */ - -gdcmFile::gdcmFile(string & filename) - :gdcmHeader(filename.c_str()) +File::File(Header *header) { - SetPixelDataSizeFromHeader(); + HeaderInternal = header; + SelfHeader = false; + Initialise(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) +/** + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (Header 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 + */ +File::File(std::string const & filename ) { - SetPixelDataSizeFromHeader(); + HeaderInternal = new Header( filename ); + SelfHeader = true; + Initialise(); } /** - * \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 Factorization for various forms of constructors. */ -void gdcmFile::SetPixelDataSizeFromHeader(void) { - int nb; - 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(); - - string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - if ( str_PhotometricInterpretation == "PALETTE COLOR " - || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !! - lgrTotale*=3; +void File::Initialise() +{ + if ( HeaderInternal->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( HeaderInternal->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } + + + + + // Just in case some access to a Header element requires disk access. + // Note: gdcmDocument::Fp is leaved open after OpenFile. + (void)HeaderInternal->OpenFile(); + // Number of Bits Allocated for storing a Pixel is defaulted to 16 + // when absent from the header. + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + if ( numberBitsAllocated == 0 ) + { + numberBitsAllocated = 16; + } + PixelConverter.SetBitsAllocated( numberBitsAllocated ); + + // Number of "Bits Stored" defaulted to number of "Bits Allocated" + // when absent from the header. + int numberBitsStored = HeaderInternal->GetBitsStored(); + if ( numberBitsStored == 0 ) + { + numberBitsStored = numberBitsAllocated; + } + PixelConverter.SetBitsStored( numberBitsStored ); + + // High Bit Position + int highBitPosition = HeaderInternal->GetHighBitPosition(); + if ( highBitPosition == 0 ) + { + highBitPosition = numberBitsAllocated - 1; + } + PixelConverter.SetHighBitPosition( highBitPosition ); + + + PixelConverter.SetXSize( HeaderInternal->GetXSize() ); + PixelConverter.SetYSize( HeaderInternal->GetYSize() ); + PixelConverter.SetZSize( HeaderInternal->GetZSize() ); + PixelConverter.SetSamplesPerPixel( HeaderInternal->GetSamplesPerPixel() ); + PixelConverter.SetPixelSize( HeaderInternal->GetPixelSize() ); + PixelConverter.SetPixelSign( HeaderInternal->IsSignedPixelData() ); + PixelConverter.SetSwapCode( HeaderInternal->GetSwapCode() ); + PixelConverter.SetIsUncompressed( + ! HeaderInternal->IsDicomV3() + || HeaderInternal->IsImplicitVRLittleEndianTransferSyntax() + || HeaderInternal->IsExplicitVRLittleEndianTransferSyntax() + || HeaderInternal->IsExplicitVRBigEndianTransferSyntax() + || HeaderInternal->IsDeflatedExplicitVRLittleEndianTransferSyntax() ); + PixelConverter.SetIsJPEG2000( HeaderInternal->IsJPEG2000() ); + PixelConverter.SetIsJPEGLossless( HeaderInternal->IsJPEGLossless() ); + PixelConverter.SetIsRLELossless( + HeaderInternal->IsRLELossLessTransferSyntax() ); + PixelConverter.SetPixelOffset( HeaderInternal->GetPixelOffset() ); + PixelConverter.SetPixelDataLength( HeaderInternal->GetPixelAreaLength() ); + PixelConverter.SetRLEInfo( &(HeaderInternal->RLEInfo) ); + PixelConverter.SetJPEGInfo( &(HeaderInternal->JPEGInfo) ); + PixelConverter.SetDecompressedSize( ImageDataSize ); + + PixelConverter.SetPlanarConfiguration( + HeaderInternal->GetPlanarConfiguration() ); + PixelConverter.SetIsMonochrome( HeaderInternal->IsMonochrome() ); + PixelConverter.SetIsPaletteColor( HeaderInternal->IsPaletteColor() ); + PixelConverter.SetIsYBRFull( HeaderInternal->IsYBRFull() ); + + HeaderInternal->CloseFile(); + } - - // remaining to check : - // str_PhotometricInterpretation == "YBR_FULL" - // str_PhotometricInterpretation == "YBR_FULL_422" (no LUT, no Palette) - // -->and some more !! + SaveInitialValues(); } -///////////////////////////////////////////////////////////////// /** - * \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 canonical destructor + * \note If the Header was created by the File constructor, + * it is destroyed by the File */ -size_t gdcmFile::GetImageDataSize(void) { - return (lgrTotale); -} +File::~File() +{ + if( SelfHeader ) + { + delete HeaderInternal; + } + HeaderInternal = 0; + DeleteInitialValues(); +} -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Parse pixel data from disk and *prints* the result - * \ For multi-fragment Jpeg 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) - * + * \brief Sets some initial values for the Constructor + * \warning not end user intended */ -bool gdcmFile::ParsePixelData(void) { - if ( !OpenFile()) - return false; - - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - return false; - } - - if ( !IsDicomV3() || - IsImplicitVRLittleEndianTransferSyntax() || - IsExplicitVRLittleEndianTransferSyntax() || - IsExplicitVRBigEndianTransferSyntax() || - IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - printf ("gdcmFile::ParsePixelData : non JPEG File\n"); - return 0; - } - - int nb; - string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; - } - int nBytes= nb/8; - - //int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel(); - int taille = GetXSize() * GetYSize() * GetSamplesPerPixel(); - - printf ("Checking the Dicom-Jpeg/RLE Pixels\n"); - - // ------------------------------- for Parsing : Position on begining of Jpeg Pixels - guint16 ItemTagGr,ItemTagEl; - int ln; - long ftellRes; - char * destination = NULL; - 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;iIsReadable() ) + { + // the following values *may* be modified + // by File::GetImageDataIntoVectorRaw + // we save their initial value. + InitialSpp = HeaderInternal->GetEntryByNumber(0x0028,0x0002); + InitialPhotInt = HeaderInternal->GetEntryByNumber(0x0028,0x0004); + InitialPlanConfig = HeaderInternal->GetEntryByNumber(0x0028,0x0006); - 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 ); + InitialBitsAllocated = HeaderInternal->GetEntryByNumber(0x0028,0x0100); + InitialHighBit = HeaderInternal->GetEntryByNumber(0x0028,0x0102); + + // the following entries *may* be removed from the H table + // (NOT deleted ...) by File::GetImageDataIntoVectorRaw + // we keep a pointer on them. + InitialRedLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1101); + InitialGreenLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1102); + InitialBlueLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1103); + + InitialRedLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1201); + InitialGreenLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1202); + InitialBlueLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1203); + } +} + +/** + * \brief restores some initial values + * \warning not end user intended + */ +void File::RestoreInitialValues() +{ + if ( HeaderInternal->IsReadable() ) + { + // the following values *may* have been modified + // by File::GetImageDataIntoVectorRaw + // we restore their initial value. + if ( InitialSpp != "") + HeaderInternal->SetEntryByNumber(InitialSpp,0x0028,0x0002); + if ( InitialPhotInt != "") + HeaderInternal->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); + if ( InitialPlanConfig != "") + + HeaderInternal->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); + if ( InitialBitsAllocated != "") + HeaderInternal->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); + if ( InitialHighBit != "") + HeaderInternal->SetEntryByNumber(InitialHighBit,0x0028,0x0102); - - } - return 1; + // the following entries *may* be have been removed from the H table + // (NOT deleted ...) by File::GetImageDataIntoVectorRaw + // we restore them. + + if (InitialRedLUTDescr) + HeaderInternal->AddEntry(InitialRedLUTDescr); + if (InitialGreenLUTDescr) + HeaderInternal->AddEntry(InitialGreenLUTDescr); + if (InitialBlueLUTDescr) + HeaderInternal->AddEntry(InitialBlueLUTDescr); + + if (InitialRedLUTData) + HeaderInternal->AddEntry(InitialBlueLUTDescr); + if (InitialGreenLUTData) + HeaderInternal->AddEntry(InitialGreenLUTData); + if (InitialBlueLUTData) + HeaderInternal->AddEntry(InitialBlueLUTData); + } } -///////////////////////////////////////////////////////////////// /** - * \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 delete initial values (il they were saved) + * of InitialLutDescriptors and InitialLutData */ -bool gdcmFile::ReadPixelData(void* destination) { +void File::DeleteInitialValues() +{ - if ( !OpenFile()) - return false; - - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - 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... -// ------------------------------- 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; - } - } - - // ----------------------------- JPEG Compressed File . - - int nb; - string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; - } - int nBytes= nb/8; - - //int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel(); - int taille = GetXSize() * GetYSize() * GetSamplesPerPixel(); - - - // ------------------------------- JPEG LossLess : call to Jpeg Libido - - if (IsJPEGLossless() && GetZSize() == 1) { - - int ln; // Position on begining of Jpeg Pixels - fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : Basic Offset Table Item - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Item length - fseek(fp,ln,SEEK_CUR); // skipping Basic Offset Table ('ln' bytes) - fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : First fragment Item Tag - fread(&ln,4,1,fp); // First fragment length (just to know) - if(GetSwapCode()) - ln=SwapLong(ln); - - ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one. - // (We use the LibIDO one :-( - if(jpg == NULL) { - CloseFile(); - return false; - } - int * dataJpg = jpg->DataImg; - - 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; iGetBitsAllocated(); + // Number of "Bits Allocated" is fixed to 16 when: + // - it is not defined (i.e. it's value is 0) + // - it's 12, since we will expand the image to 16 bits (see + // PixelConvert::ConvertDecompress12BitsTo16Bits() ) + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) + { + numberBitsAllocated = 16; + } + + int DecompressedSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + + return DecompressedSize; +} + +/** + * \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 + * NULL if alloc fails */ -void * gdcmFile::GetImageData (void) { - PixelData = (void *) malloc(lgrTotale); - if (PixelData) - GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); +uint8_t* File::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; + + // we load the pixels (and transform grey level + LUT into RGB) + GetImageDataIntoVector(Pixel_Data, ImageDataSize); + + // 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; } /** - * \ingroup gdcmFile - * \brief Copies at most MaxSize bytes of pixel data to caller's + * \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 + * @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 File::GetImageDataIntoVector (void* destination, size_t maxSize) +{ + GetImageDataIntoVectorRaw (destination, maxSize); + PixelRead = 0 ; // =0 : no ImageDataRaw + if ( !HeaderInternal->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 = HeaderInternal->GetLUTRGBA(); + + if ( lutRGBA ) + { + int j; + // move Gray pixels to temp area + memmove(newDest, destination, ImageDataSizeRaw); + for (size_t i=0; i 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() ); - } + std::string spp = "3"; // Samples Per Pixel + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + std::string rgb = "RGB "; // Photometric Interpretation + HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004); + std::string planConfig = "0"; // Planar Configuration + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); - // 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 - // -------------------------- - - string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - - if ( (str_PhotometricInterpretation == "MONOCHROME1 ") - || (str_PhotometricInterpretation == "MONOCHROME2 ") - || (str_PhotometricInterpretation == "RGB")) { - return lgrTotale; } - - switch ( GetPlanarConfiguration() ) { - case 0: - // Pixels are already RGB - break; - - case 1: - // need to make RGB Pixels from Planes R,G,B - { - 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;jSetEntryByNumber(photomInterp,0x0028,0x0004); } - - return lgrTotale; -} -// -// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs -// + /// \todo Drop Palette Color out of the Header? + return ImageDataSize; +} /** - * \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 + * \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 */ +uint8_t* File::GetImageDataRaw () +{ + size_t imgDataSize; + if ( HeaderInternal->HasLUT() ) + /// \todo Let Header 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); -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); - } + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); -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); + // will be 7fe0, 0010 in standard cases + GetHeader()->SetEntryBinAreaByNumber(Pixel_Data, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } -return; + PixelRead = 1; // PixelRaw + + return Pixel_Data; } -///////////////////////////////////////////////////////////////// /** - * \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 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 + * 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. */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(1); -} +void File::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) + if ( PixelRead != -1 ) // File was "read" before + { + RestoreInitialValues(); + } + + PixelRead = 1 ; // PixelRaw + + if ( ImageDataSize > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return; + } -///////////////////////////////////////////////////////////////// -/** - * \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 - */ + FILE* fp = HeaderInternal->OpenFile(); + PixelConverter.ReadAndDecompressPixelData( destination, fp ); + HeaderInternal->CloseFile(); + + if ( ! PixelConverter.HandleColor( (uint8_t*)destination ) ) + { + return; + } -void gdcmFile::SetImageDataSize(size_t ImageDataSize) { - string content1; - char car[20]; - // Assumes ElValue (0x7fe0, 0x0010) exists ... - sprintf(car,"%d",ImageDataSize); +/////////////////////////////////////////////////// + // now, it's an RGB image + // Lets's write it in the Header - gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010); - a->SetLength(ImageDataSize); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetPubElValByNumber(content1, 0x7fe0, 0x0000); -} + // Droping Palette Color out of the Header + // has been moved to the Write process. + // TODO : move 'values' modification to the write process + // : save also (in order to be able to restore) + // : 'high bit' -when not equal to 'bits stored' + 1 + // : 'bits allocated', when it's equal to 12 ?! + + std::string spp = "3"; // Samples Per Pixel + std::string photInt = "RGB "; // Photometric Interpretation + std::string planConfig = "0"; // Planar Configuration + + HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); + HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); + HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); + + return; +} -///////////////////////////////////////////////////////////////// /** - * \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 (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 File::SetImageData(uint8_t* inData, size_t expectedSize) +{ + HeaderInternal->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 (string fileName) { - return WriteBase(fileName, ImplicitVR); +bool File::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 (string (fileName)); + +bool File::WriteDcmImplVR (std::string const & fileName) +{ + return WriteBase(fileName, ImplicitVR); } - -///////////////////////////////////////////////////////////////// + /** - * \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 (string fileName) { +bool File::WriteDcmExplVR (std::string const & fileName) +{ return WriteBase(fileName, ExplicitVR); } - -///////////////////////////////////////////////////////////////// + /** - * \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 (string fileName) { +bool File::WriteAcr (std::string const & fileName) +{ return WriteBase(fileName, ACR); } -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// 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 (string FileName, FileType type) { +bool File::WriteBase (std::string const & fileName, FileType type) +{ + if ( PixelRead == -1 && type != ExplicitVR) + { + 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 == ImplicitVR || type == ExplicitVR ) + { // 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; } - gdcmHeader::Write(fp1, type); - fwrite(PixelData, lgrTotale, 1, fp1); + // -------------------------------------------------------------- + // Special Patch to allow gdcm to re-write ACR-LibIDO formated images + // + // if recognition code tells us we dealt with a LibIDO image + // we reproduce on disk the switch between lineNumber and columnNumber + // just before writting ... + + /// \todo the best trick would be *change* the recognition code + /// but pb expected if user deals with, e.g. COMPLEX images + + std::string rows, columns; + if ( HeaderInternal->GetFileType() == ACR_LIBIDO) + { + rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010); + columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011); + + HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0010); + HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- + + uint16_t grPixel = HeaderInternal->GetGrPixel(); + uint16_t numPixel = HeaderInternal->GetNumPixel();; + + DocEntry* 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 ); + } + + HeaderInternal->Write(fp1, type); + + // -------------------------------------------------------------- + // Special Patch to allow gdcm to re-write ACR-LibIDO formated images + // + // ...and we restore the Header to be Dicom Compliant again + // just after writting + + if ( HeaderInternal->GetFileType() == ACR_LIBIDO ) + { + HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010); + HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- + + // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); - return(1); + + return true; } + +} // end namespace gdcm +