X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=666a8e96f5fdd0245ddfb14ec1d15cb82937732e;hb=0b01703cc07d46a6ae718e01c6beee14599a9da1;hp=bd35f100dc44b0df4eb8eb4874f0fdf6bdc0c559;hpb=934741ba56fd719a775e93cc93616c25b3d10901;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index bd35f100..666a8e96 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,14 +1,14 @@ -/*========================================================================= + /*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/06/23 09:30:22 $ - Version: $Revision: 1.108 $ + Date: $Date: 2004/11/24 11:17:47 $ + Version: $Revision: 1.161 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + 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 @@ -18,83 +18,118 @@ #include "gdcmFile.h" #include "gdcmDebug.h" -#include "jpeg/ljpg/jpegless.h" +#include "gdcmUtil.h" +#include "gdcmBinEntry.h" +#include +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. + * 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 header file to be opened for reading datas - * @return + * @param header already built Header */ -gdcmFile::gdcmFile(gdcmHeader *header) { - Header=header; - SelfHeader=false; - PixelRead=-1; // no ImageData read yet. - - if (Header->IsReadable()) - SetPixelDataSizeFromHeader(); +File::File(Header *header) +{ + HeaderInternal = header; + SelfHeader = false; + Initialise(); } /** - * \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. + * 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 - * @param exception_on_error whether we throw an exception or not - * @param enable_sequences = true to allow the header - * to be parsed *inside* the SeQuences, - * when they have an actual length - * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files - * @param ignore_shadow to allow skipping the shadow elements, - * to save memory space. - * \warning The TRUE value for this param has to be used - * with a FALSE value for the 'enable_sequence' param. - * ('public elements' may be embedded in 'shadow Sequences') */ -gdcmFile::gdcmFile(std::string const & filename, - bool exception_on_error, - bool enable_sequences, - bool ignore_shadow) { - Header=new gdcmHeader(filename.c_str(), - exception_on_error, - enable_sequences, - ignore_shadow); - SelfHeader=true; - PixelRead=-1; // no ImageData read yet. - - if (Header->IsReadable()) - SetPixelDataSizeFromHeader(); +File::File(std::string const & filename ) +{ + HeaderInternal = new Header( filename ); + SelfHeader = true; + Initialise(); +} + +/** + * \brief Factorization for various forms of constructors. + */ +void File::Initialise() +{ + WriteMode = WMODE_RGB; + WriteType = WTYPE_IMPL_VR; + + PixelConverter = new PixelConvert; + Archive = new DocEntryArchive( HeaderInternal ); + + if ( HeaderInternal->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( HeaderInternal->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } + + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + } + + SaveInitialValues(); } /** - * \ingroup gdcmFile * \brief canonical destructor - * \note If the gdcmHeader is created by the gdcmFile, it is destroyed - * by the gdcmFile + * \note If the Header was created by the File constructor, + * it is destroyed by the File */ -gdcmFile::~gdcmFile() { - if(SelfHeader) - delete Header; - Header=NULL; +File::~File() +{ + if( PixelConverter ) + { + delete PixelConverter; + } + if( Archive ) + { + delete Archive; + } + + if( SelfHeader ) + { + delete HeaderInternal; + } + HeaderInternal = 0; +} + +/** + * \brief Sets some initial values for the Constructor + * \warning not end user intended + */ +void File::SaveInitialValues() +{ + PixelRead = -1; // no ImageData read yet. + Pixel_Data = 0; } //----------------------------------------------------------------------------- @@ -104,14 +139,13 @@ gdcmFile::~gdcmFile() { // Public /** - * \ingroup gdcmFile - * \brief computes the length (in bytes) to ALLOCATE to receive the + * \brief computes the length (in bytes) we must ALLOCATE to receive the * image(s) pixels (multiframes taken into account) * \warning : it is NOT the group 7FE0 length * (no interest for compressed images). - * @return length to allocate */ -void gdcmFile::SetPixelDataSizeFromHeader() { +int File::ComputeDecompressedPixelDataSizeFromHeader() +{ // see PS 3.3-2003 : C.7.6.3.2.1 // // MONOCHROME1 @@ -138,80 +172,140 @@ void gdcmFile::SetPixelDataSizeFromHeader() { // 0028|1202 [US] [Green Palette Color Lookup Table Data] // 0028|1203 [US] [Blue Palette Color Lookup Table Data] - int nb; - std::string str_nb; - str_nb=Header->GetEntryByNumber(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->GetEntryByNumber(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() { - return lgrTotale; -} + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + // 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; + } -/** - * \ingroup gdcmFile - * \brief Returns the size (in bytes) of required memory to hold - * the pixel data represented in this file, when user DOESN'T want - * to get RGB pixels image when it's stored as a PALETTE COLOR image - * -the (vtk) user is supposed to know how deal with LUTs- - * \warning to be used with GetImagePixelsRaw() - * @return The size of pixel data in bytes. - */ -size_t gdcmFile::GetImageDataSizeRaw() { - return lgrTotaleRaw; + int DecompressedSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + + return DecompressedSize; } /** - * \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 - * Transforms single Grey plane + 3 Palettes into a RGB Plane + * \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 */ -void * gdcmFile::GetImageData () { - PixelData = new unsigned char[lgrTotale]; //consistant with GetImageDataIntoVector - if (PixelData) { - GetImageDataIntoVector(PixelData, lgrTotale); - GetHeader()->SetEntryVoidAreaByNumber(PixelData, - GetHeader()->GetGrPixel(), - GetHeader()->GetNumPixel()); - } - PixelRead=0; // no PixelRaw - - return PixelData; +uint8_t* File::GetImageData() +{ + if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + return PixelConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the decompressed + return PixelConverter->GetDecompressed(); + } + +/* if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + uint8_t* pixelData; + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + pixelData = PixelConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the decompressed + pixelData = PixelConverter->GetDecompressed(); + } + +// PIXELCONVERT CLEANME + // 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(); + } + if ( PixelConverter->GetRGB() ) + { + // now, it's an RGB image + // Lets's write it in the Header + 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); + PixelRead = 0; // no PixelRaw + } + else + { + if ( HeaderInternal->HasLUT() ) + { + // The LUT interpretation failed + std::string photometricInterpretation = Util::DicomString("MONOCHROME1"); + HeaderInternal->SetEntryByNumber( photometricInterpretation, + 0x0028, 0x0004 ); + PixelRead = 0; // no PixelRaw + } + else + { + if ( PixelConverter->IsDecompressedRGB() ) + { + /////////////////////////////////////////////////// + // now, it's an RGB image + // Lets's write it in the Header + // 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); + } + PixelRead = 1; // PixelRaw + } + } + + // We say the value *is* loaded. + SetPixelData(pixelData); +// END PIXELCONVERT CLEANME + + return pixelData;*/ } /** - * \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 was designed to avoid people that want to build - * a volume from an image stack to need first to get the image pixels + * \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 @@ -221,410 +315,198 @@ void * gdcmFile::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 gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { - //size_t l = GetImageDataIntoVectorRaw (destination, MaxSize); - GetImageDataIntoVectorRaw (destination, MaxSize); - PixelRead=0 ; // no PixelRaw - if (!Header->HasLUT()) - return lgrTotale; - - // from Lut R + Lut G + Lut B - unsigned char *newDest = new unsigned char[lgrTotale]; - unsigned char *a = (unsigned char *)destination; - unsigned char *lutRGBA = Header->GetLUTRGBA(); - - if (lutRGBA) { - int l = lgrTotaleRaw; - memmove(newDest, destination, l);// move Gray pixels to temp area - int j; - for (int i=0;iHasLUT() && PixelConverter->BuildRGBImage() ) + { + if ( PixelConverter->GetRGBSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; } - delete[] newDest; - - // now, it's an RGB image - // Lets's write it in the Header - - // CreateOrReplaceIfExist ? - - std::string spp = "3"; // Samples Per Pixel - Header->SetEntryByNumber(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 { - // need to make RGB Pixels (?) - // from grey Pixels (?!) - // and Gray Lut (!?!) - // or Segmented xxx Palette Color Lookup Table Data and so on - - // Oops! I get one (gdcm-US-ALOKA-16.dcm) - // No idea how to manage such an image - // It seems that *no Dicom Viewer* has any idea :-( - // Segmented xxx Palette Color are *more* than 65535 long ?!? - - std::string rgb= "MONOCHROME1 "; // Photometric Interpretation - Header->SetEntryByNumber(rgb,0x0028,0x0004); - } - /// \todo Drop Palette Color out of the Header? - return lgrTotale; + memcpy( destination, + (void*)PixelConverter->GetRGB(), + PixelConverter->GetRGBSize() ); + return PixelConverter->GetRGBSize(); + } + + // Either no LUT conversion necessary or LUT conversion failed + if ( PixelConverter->GetDecompressedSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memcpy( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + return PixelConverter->GetDecompressedSize(); } /** - * \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 + * \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::GetImageDataRaw () { - if (Header->HasLUT()) - /// \todo Let gdcmHeadar user a chance to get the right value - /// Create a member lgrTotaleRaw ??? - lgrTotale /= 3; - PixelData = new unsigned char[lgrTotale]; - - if (PixelData) { - GetImageDataIntoVectorRaw(PixelData, lgrTotale); - GetHeader()->SetEntryVoidAreaByNumber(PixelData, - GetHeader()->GetGrPixel(), - GetHeader()->GetNumPixel()); - } - PixelRead=1; // PixelRaw - - return PixelData; -} +uint8_t* File::GetImageDataRaw () +{ + return GetDecompressed(); +/* uint8_t* decompressed = GetDecompressed(); + if ( ! decompressed ) + { + return 0; + } -/** - * \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 - * 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) { +// PIXELCONVERT CLEANME + // 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(); + } + if ( PixelConverter->IsDecompressedRGB() ) + { + /////////////////////////////////////////////////// + // now, it's an RGB image + // Lets's write it in the Header + // 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); + } - int nb, nbu, highBit, signe; - std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; - PixelRead=1 ; // PixelRaw + // We say the value *is* loaded. + SetPixelData(decompressed); - if ( lgrTotale > MaxSize ) { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return (size_t)0; - } - - ReadPixelData(destination); - - // Number of Bits Allocated for storing a Pixel - str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - } - // Number of Bits actually used - str_nbu=Header->GetEntryByNumber(0x0028,0x0101); - if (str_nbu == GDCM_UNFOUND ) { - nbu = nb; - } else { - nbu = atoi(str_nbu.c_str() ); - } - // High Bit Position - str_highBit=Header->GetEntryByNumber(0x0028,0x0102); - if (str_highBit == GDCM_UNFOUND ) { - highBit = nb - 1; - } else { - highBit = atoi(str_highBit.c_str() ); - } - // Pixel sign - // 0 = Unsigned - // 1 = Signed - str_signe=Header->GetEntryByNumber(0x0028,0x0103); - if (str_signe == GDCM_UNFOUND ) { - signe = 0; // default is unsigned - } else { - signe = atoi(str_signe.c_str() ); - } - - // re arange bytes inside the integer (processor endianity) - if (nb != 8) - SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb); - - // to avoid pb with some xmedcon breakers images - if (nb==16 && nbu> (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: weird image"); - return 0; - } - } -// DO NOT remove this commented out code . -// Nobody knows what's expecting you ... -// Just to 'see' what was actually read on disk :-( + PixelRead = 1; // PixelRaw +// END PIXELCONVERT CLEANME -// FILE * f2; -// f2 = fopen("SpuriousFile.RAW","wb"); -// fwrite(destination,lgrTotale,1,f2); -// fclose(f2); + return decompressed;*/ +} - // Deal with the color - // ------------------- - - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); - - if ( (str_PhotometricInterpretation == "MONOCHROME1 ") - || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { - return lgrTotale; +uint8_t* File::GetDecompressed() +{ + uint8_t* decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + // The decompressed image migth not be loaded yet: + std::ifstream* fp = HeaderInternal->OpenFile(); + PixelConverter->ReadAndDecompressPixelData( fp ); + if(fp) HeaderInternal->CloseFile(); + decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + dbg.Verbose(0, "File::GetDecompressed: read/decompress of " + "pixel data apparently went wrong."); + return 0; } - - // 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(); // 0028,0006 - - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if (str_PhotometricInterpretation == "PALETTE COLOR ") - planConf=2; - - switch (planConf) { - case 0: - // Pixels are already RGB - break; - - case 1: - - { - if (str_PhotometricInterpretation == "YBR_FULL") { - - // Warning : YBR_FULL_422 acts as RGB - // : we need to make RGB Pixels from Planes Y,cB,cR - - // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : - // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf - // and be *very* affraid - // - int l = Header->GetXSize()*Header->GetYSize(); - int nbFrames = Header->GetZSize(); - - unsigned char *newDest = new unsigned char[lgrTotale]; - unsigned char *x = newDest; - unsigned char *a = (unsigned char *)destination; - unsigned char *b = a + l; - unsigned char *c = b + l; - double R,G,B; - - /// \todo : Replace by the 'well known' integer computation - /// counterpart - /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - /// for code optimisation - - for (int i=0;i255.0) R=255.0; - if (G>255.0) G=255.0; - if (B>255.0) B=255.0; - - *(x++) = (unsigned char)R; - *(x++) = (unsigned char)G; - *(x++) = (unsigned char)B; - a++; b++; c++; - } - } - memmove(destination,newDest,lgrTotale); - delete[] newDest; - - } else { - - // need to make RGB Pixels from R,G,B Planes - // (all the Frames at a time) - - int l = Header->GetXSize()*Header->GetYSize()*Header->GetZSize(); - - char *newDest = new char[lgrTotale]; - char *x = newDest; - char *a = (char *)destination; - char *b = a + l; - char *c = b + l; - - for (int j=0;jSetEntryByNumber(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); - - /// \todo Drop Palette Color out of the Header? - return lgrTotale; + return decompressed; } /** - * \ingroup gdcmFile - * \brief performs a shadow copy (not a deep copy) of the user given - * pixel area. - * 'image' Pixels are presented as C-like 2D arrays : line per line. - * 'volume'Pixels are presented as C-like 3D arrays : lane per plane - * \warning user is kindly requested NOT TO 'free' the Pixel area + * \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 expectedSize total image size, in Bytes * - * @return boolean + * @return boolean */ -bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) { - Header->SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - PixelRead = 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 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 + * @return false if write fails */ -bool gdcmFile::WriteRawData (std::string const & fileName) { - FILE *fp1; - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Fail to open (write) file [%s] \n",fileName.c_str()); +bool File::WriteRawData(std::string const & fileName) +{ + std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); + if (!fp1) + { + dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); return false; - } - fwrite (PixelData,lgrTotale, 1, fp1); - fclose (fp1); + } + fp1.write((char*)Pixel_Data, ImageDataSize); + fp1.close(); return true; } /** - * \ingroup gdcmFile * \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 + * @return false if write fails */ -bool gdcmFile::WriteDcmImplVR (std::string const & fileName) { - return WriteBase(fileName, gdcmImplicitVR); +bool File::WriteDcmImplVR (std::string const & fileName) +{ + SetWriteTypeToDcmImplVR(); + return Write(fileName); } /** - * \ingroup gdcmFile * \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 + * @return false if write fails */ -bool gdcmFile::WriteDcmExplVR (std::string const & fileName) { - return WriteBase(fileName, gdcmExplicitVR); +bool File::WriteDcmExplVR (std::string const & fileName) +{ + SetWriteTypeToDcmExplVR(); + return Write(fileName); } - + /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the ACR-NEMA convention * NO test is performed on processor "Endiannity". @@ -635,46 +517,74 @@ bool gdcmFile::WriteDcmExplVR (std::string const & fileName) { * \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 + * @return false if write fails */ -bool gdcmFile::WriteAcr (std::string const & fileName) { - return WriteBase(fileName, gdcmACR); +bool File::WriteAcr (std::string const & fileName) +{ + SetWriteTypeToAcr(); + return Write(fileName); +} + +bool File::Write(std::string const& fileName) +{ + switch(WriteType) + { + case WTYPE_IMPL_VR: + return WriteBase(fileName,ImplicitVR); + case WTYPE_EXPL_VR: + return WriteBase(fileName,ExplicitVR); + case WTYPE_ACR: + return WriteBase(fileName,ACR); + } + return(false); } //----------------------------------------------------------------------------- // Protected /** - * \ingroup gdcmFile * \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 + * @return false if write fails */ -bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { +bool File::WriteBase (std::string const & fileName, FileType type) +{ +/* if ( PixelRead == -1 && type != ExplicitVR) + { + return false; + }*/ - FILE *fp1; - - if (PixelRead==-1 && type != gdcmExplicitVR) { - return false; + std::ofstream* fp1 = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (fp1 == NULL) + { + dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); + return false; } - 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 ) + { + // writing Dicom File Preamble + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp1->write(filePreamble, 128); + fp1->write("DICM", 4); } - if ( (type == gdcmImplicitVR) || (type == gdcmExplicitVR) ) { - char *filePreamble; - // writing Dicom File Preamble - filePreamble=new char[128]; - memset(filePreamble,0,128); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - delete[] filePreamble; + switch(WriteMode) + { + case WMODE_NATIVE : + SetWriteToNative(); + break; + case WMODE_DECOMPRESSED : + SetWriteToDecompressed(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; } // -------------------------------------------------------------- @@ -688,45 +598,30 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { /// but pb expected if user deals with, e.g. COMPLEX images std::string rows, columns; - if ( Header->GetFileType() == gdcmACR_LIBIDO){ - rows = Header->GetEntryByNumber(0x0028, 0x0010); - columns = Header->GetEntryByNumber(0x0028, 0x0011); - Header->SetEntryByNumber(columns, 0x0028, 0x0010); - Header->SetEntryByNumber(rows , 0x0028, 0x0011); - } + if ( HeaderInternal->GetFileType() == ACR_LIBIDO) + { + SetWriteToLibido(); + } // ----------------- End of Special Patch ---------------- - - /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only) - - guint16 grPixel =Header->GetGrPixel(); - guint16 numPixel=Header->GetNumPixel();; - - // Update Pixel Data Length - // the *last* of the (GrPixel, NumPixel), if many. + +/* uint16_t grPixel = HeaderInternal->GetGrPixel(); + uint16_t numPixel = HeaderInternal->GetNumPixel();; - TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel); - TagDocEntryHT::iterator p2; - gdcmDocEntry *PixelElement; - - IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym - - if (Header->GetEntry().count(key) == 1) // only the first is significant - p2=it.first; // iterator on the first (unique) synonym - else - p2=it.second;// iterator on the last synonym - - PixelElement=p2->second; // H Table target column (2-nd col) - // PixelElement->SetPrintLevel(2); - // PixelElement->Print(); + DocEntry* PixelElement = + GetHeader()->GetDocEntryByNumber(grPixel, numPixel); - if (PixelRead==1) - PixelElement->SetLength(lgrTotaleRaw); - else if (PixelRead==0) - PixelElement->SetLength(lgrTotale); - - //PixelElement->SetPrintLevel(2); - //PixelElement->Print(); - Header->Write(fp1, type); + 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 @@ -734,268 +629,187 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { // ...and we restore the Header to be Dicom Compliant again // just after writting - if (Header->GetFileType() == gdcmACR_LIBIDO){ - Header->SetEntryByNumber(rows , 0x0028, 0x0010); - Header->SetEntryByNumber(columns, 0x0028, 0x0011); - } + if ( HeaderInternal->GetFileType() == ACR_LIBIDO ) + { + RestoreWriteFromLibido(); + } // ----------------- End of Special Patch ---------------- - - // fwrite(PixelData, lgrTotale, 1, fp1); // should be useless, now - fclose (fp1); + + RestoreWrite(); + + + fp1->close (); + delete fp1; return true; } +/** + * \brief Access to the underlying \ref PixelConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); +} + //----------------------------------------------------------------------------- // 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 + * \brief Set the pixel datas in the good entry of the Header */ -void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) { - guint32 s32; - guint16 fort,faible; - int i; - - if(nb == 16) - switch(swap) { - case 0: - case 12: - case 1234: - break; - - case 21: - case 3412: - case 2143: - case 4321: - - for(i=0;i>8) - | ((((unsigned short int *)im)[i])<<8); - } - break; - - default: - printf("SWAP value (16 bits) not allowed : %d\n", swap); - } - - if( nb == 32 ) - switch (swap) { - case 0: - case 1234: - break; +void File::SetPixelData(uint8_t* data) +{ + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // Will be 7fe0, 0010 in standard case + DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + if ( currentEntry ) + { + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + // Flag is to false because datas are kept in the gdcmPixelConvert + binEntry->SetBinArea( data, false ); + } +} - 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; +void File::SetWriteToNative() +{ +// Nothing to do +} - 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: - std::cout << "SWAP value (32 bits) not allowed : " << swap << std::endl; +void File::SetWriteToDecompressed() +{ +// if (( !HeaderInternal->HasLUT() ) || (!PixelConverter->BuildRGBImage())) + if(HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage()) + { + SetWriteToRGB(); } + else + { + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("MONOCHROME1 "); + photInt->SetLength(12); + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); + + Archive->Push(photInt); + Archive->Push(pixel); + } +/* else + { + SetWriteToRGB(); + } */ } -/** - * \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) { +void File::SetWriteToRGB() +{ + if(PixelConverter->BuildRGBImage()) + { + ValEntry* spp = CopyValEntry(0x0028,0x0002); + spp->SetValue("3 "); + spp->SetLength(2); + + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("RGB "); + photInt->SetLength(4); + + ValEntry* planConfig = CopyValEntry(0x0028,0x0006); + planConfig->SetValue("0 "); + planConfig->SetLength(2); + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelConverter->GetRGB(),false); + pixel->SetLength(PixelConverter->GetRGBSize()); + + Archive->Push(spp); + Archive->Push(photInt); + Archive->Push(planConfig); + Archive->Push(pixel); + } + else + { + SetWriteToDecompressed(); + } +} - FILE *fp; +void File::RestoreWrite() +{ + Archive->Restore(0x0028,0x0002); + Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); + Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); +} - 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] */ +void File::SetWriteToLibido() +{ + ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); + ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); - 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 ? - } + if( oldRow && oldCol ) + { + std::string rows, columns; - 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); - if ( ItemRead != 1 ) { - Header->CloseFile(); - return false; - } else { - Header->CloseFile(); - return true; - } - } + ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); + ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); - // ---------------------- Run Length Encoding - if (Header->IsRLELossLessTransferSyntax()) { - bool res = (bool)gdcm_read_RLE_file (fp,destination); - Header->CloseFile(); - return res; - } - - // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int nb; - std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ? - } - - int nBytes= nb/8; - - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek - - bool jpg2000 = Header->IsJPEG2000(); - bool jpgLossless = Header->IsJPEGLossless(); - - bool res = true; - 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 = new char[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); + newRow->Copy(oldCol); + newCol->Copy(oldRow); + + newRow->SetValue(oldCol->GetValue()); + newCol->SetValue(oldRow->GetValue()); + + Archive->Push(newRow); + Archive->Push(newCol); } - - // 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; +void File::RestoreWriteFromLibido() +{ + Archive->Restore(0x0028,0x0010); + Archive->Restore(0x0028,0x0011); +} + +ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + ValEntry* newE; + + if(oldE) + { + newE = new ValEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewValEntryByNumber(group,element); + } + + return(newE); +} + +BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + BinEntry* newE; + + if(oldE) + { + newE = new BinEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewBinEntryByNumber(group,element); + } + + + return(newE); } + //----------------------------------------------------------------------------- +} // end namespace gdcm +