X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=b565a3a498604de9b834ae91a247ae9f15d7ed4f;hb=5bf7c51796867388334836847a6874640bc83f89;hp=888c5758d966586acdb905fd8bcb99f52fd48b53;hpb=d1cf86f331e421ff841ac1bb7323369751a648b9;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 888c5758..b565a3a4 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,76 +1,231 @@ -// gdcmFile.cxx -//----------------------------------------------------------------------------- + /*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/10/20 14:30:40 $ + Version: $Revision: 1.146 $ + + 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 "jpeg/ljpg/jpegless.h" +#include "gdcmDebug.h" -//----------------------------------------------------------------------------- +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 header file to be opened for reading datas - * - * @return + * @param header already built Header */ - -gdcmFile::gdcmFile(gdcmHeader *header) { - Header=header; - SelfHeader=false; - - 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. - * \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 * seen as a side effect). * @param filename file to be opened for parsing - * @return */ -gdcmFile::gdcmFile(std::string & filename) { - Header=new gdcmHeader(filename.c_str()); - SelfHeader=true; - - if (Header->IsReadable()) - SetPixelDataSizeFromHeader(); +File::File(std::string const & filename ) +{ + HeaderInternal = new Header( filename ); + SelfHeader = true; + Initialise(); } -gdcmFile::gdcmFile(const char * filename) { - Header=new gdcmHeader(filename); - SelfHeader=true; +/** + * \brief Factorization for various forms of constructors. + */ +void File::Initialise() +{ + if ( HeaderInternal->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( HeaderInternal->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } - if (Header->IsReadable()) - SetPixelDataSizeFromHeader(); + PixelConverter = new PixelConvert; + 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 + */ +File::~File() +{ + if( SelfHeader ) + { + delete HeaderInternal; + } + HeaderInternal = 0; + + DeleteInitialValues(); +} + +/** + * \brief Sets some initial values for the Constructor + * \warning not end user intended + */ +void File::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 ( HeaderInternal->IsReadable() ) + { + // 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); + + 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 */ -gdcmFile::~gdcmFile(void) { - if(SelfHeader) - delete Header; - Header=NULL; +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); + + // 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); + } +} + +/** + * \brief delete initial values (il they were saved) + * of InitialLutDescriptors and InitialLutData + */ +void File::DeleteInitialValues() +{ + +// 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 ( InitialBlueLUTDescr ) + delete InitialBlueLUTDescr; + + if ( InitialRedLUTData ) + delete InitialRedLUTData; + + if ( InitialGreenLUTData != NULL) + delete InitialGreenLUTData; + + if ( InitialBlueLUTData != NULL) + delete InitialBlueLUTData; } //----------------------------------------------------------------------------- @@ -78,24 +233,15 @@ gdcmFile::~gdcmFile(void) { //----------------------------------------------------------------------------- // Public -/** - * \ingroup gdcmFile - * \brief - * @return - */ -gdcmHeader *gdcmFile::GetHeader(void) { - return(Header); -} /** - * \ingroup gdcmFile - * \brief computes the length (in bytes) to ALLOCATE to receive the - * image(s) pixels (multiframes taken into account) + * \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(void) { +int File::ComputeDecompressedPixelDataSizeFromHeader() +{ // see PS 3.3-2003 : C.7.6.3.2.1 // // MONOCHROME1 @@ -122,74 +268,76 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { // 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->GetPubEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; - } - lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize() - * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = - Header->GetPubEntryByNumber(0x0028,0x0004); - - /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ - // pb when undealt Segmented Palette Color + 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; + } + + int DecompressedSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); - if (Header->HasLUT()) { - lgrTotale*=3; - } + return DecompressedSize; } /** - * \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 - 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 */ -size_t gdcmFile::GetImageDataSize(void) { - return (lgrTotale); -} +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; -/** - * \ingroup gdcmFile - * \brief Returns the size (in bytes) of required memory to hold - * \ the pixel data represented in this file, when user DOESN'T want - * \ to get RGB pixels image when it's stored as a PALETTE COLOR image - * \ - the (vtk) user is supposed to know how deal with LUTs - - * \warning to be used with GetImagePixelsRaw() - * @return The size of pixel data in bytes. - */ -size_t gdcmFile::GetImageDataSizeRaw(void) { - return (lgrTotaleRaw); -} + // we load the pixels (and transform grey level + LUT into RGB) + GetImageDataIntoVector(Pixel_Data, ImageDataSize); -/** - * \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 - * @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); + // 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 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 @@ -199,87 +347,108 @@ void * gdcmFile::GetImageData (void) { * * @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); - - if (!Header->HasLUT()) - return lgrTotale; +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 - unsigned char * newDest = (unsigned char *)malloc(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;iOpenFile(); + if ( PixelConverter->BuildRGBImage( fp ) ) + { + memmove( destination, + (void*)PixelConverter->GetRGB(), + PixelConverter->GetRGBSize() ); - // now, it's an RGB image - // Lets's write it in the Header + // now, it's an RGB image + // Lets's write it in the Header + + // FIXME : Better use CreateOrReplaceIfExist ? + + 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); + + } + else + { + // PixelConverter->BuildRGBImage() failed probably because + // PixelConverter->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 + HeaderInternal->SetEntryByNumber(photomInterp,0x0028,0x0004); + } + HeaderInternal->CloseFile(); - // CreateOrReplaceIfExist ? - - std::string spp = "3"; // Samples Per Pixel - Header->SetPubEntryByNumber(spp,0x0028,0x0002); - std::string rgb= "RGB "; // Photometric Interpretation - Header->SetPubEntryByNumber(rgb,0x0028,0x0004); - std::string planConfig = "0"; // Planar Configuration - Header->SetPubEntryByNumber(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->SetPubEntryByNumber(rgb,0x0028,0x0004); - } - // TODO : Drop Palette Color out of the Header? - return lgrTotale; + /// \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. - * 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 (void) { - if (Header->HasLUT()) - lgrTotale /= 3; // TODO Let gdcmHeadar user a chance - // to get the right value - // Create a member lgrTotaleRaw ??? - PixelData = (void *) malloc(lgrTotale); - if (PixelData) - GetImageDataIntoVectorRaw(PixelData, lgrTotale); - return(PixelData); +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); + + // 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 @@ -296,357 +465,193 @@ void * gdcmFile::GetImageDataRaw (void) { * * @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) { - - int nb, nbu, highBit, signe; - std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; - - if ( lgrTotale > MaxSize ) { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" +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 (size_t)0; + return; } - - (void)ReadPixelData(destination); - - // Number of Bits Allocated for storing a Pixel - str_nb = Header->GetPubEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - } - // Number of Bits actually used - str_nbu=Header->GetPubEntryByNumber(0x0028,0x0101); - if (str_nbu == GDCM_UNFOUND ) { - nbu = nb; - } else { - nbu = atoi(str_nbu.c_str() ); - } - // High Bit Position - str_highBit=Header->GetPubEntryByNumber(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->GetPubEntryByNumber(0x0028,0x0103); - if (str_signe == GDCM_UNFOUND ) { - signe = 0; // default is unsigned - } else { - signe = atoi(str_signe.c_str() ); + + FILE* fp = HeaderInternal->OpenFile(); + PixelConverter->ReadAndDecompressPixelData( fp ); + HeaderInternal->CloseFile(); + memmove( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + + if ( ! PixelConverter->IsDecompressedRGB() ) + { + return; } - // 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: wierd image"); - return (size_t)0; - } - } -// DO NOT remove this code commented out. -// Nobody knows what's expecting you ... -// Just to 'see' what was actually read on disk :-( -// FILE * f2; -// f2 = fopen("SpuriousFile.raw","wb"); -// fwrite(destination,lgrTotale,1,f2); -// fclose(f2); - - // Deal with the color - // ------------------- - - std::string str_PhotometricInterpretation = - Header->GetPubEntryByNumber(0x0028,0x0004); - - if ( (str_PhotometricInterpretation == "MONOCHROME1 ") - || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { - return lgrTotale; - } - - // 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 = (unsigned char*) malloc(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); - free(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 = (char*) malloc(lgrTotale); - char * x = newDest; - char * a = (char *)destination; - char * b = a + l; - char * c = b + l; - - for (int j=0;jSetPubEntryByNumber(spp,0x0028,0x0002); - std::string rgb="RGB "; // Photometric Interpretation - Header->SetPubEntryByNumber(rgb,0x0028,0x0004); + // 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 planConfig = "0"; // Planar Configuration - Header->SetPubEntryByNumber(planConfig,0x0028,0x0006); - - // TODO : Drop Palette Color out of the Header? - return lgrTotale; + 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 TODO JPR - * \warning doit-etre etre publique ? - * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions + * \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 inData - * @param ExpectedSize - * - * @return boolean + * @return boolean */ -bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - Header->SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(true); +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 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 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 fileName) { - FILE * fp1; - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); - return (false); - } - fwrite (PixelData,lgrTotale, 1, fp1); +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); + + 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) - * + * \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 fileName) { +bool File::WriteDcmImplVR (std::string const & fileName) +{ return WriteBase(fileName, ImplicitVR); } /** - * \ingroup gdcmFile - * \brief - * @param fileName name of the file to be created +* \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 - */ - -bool gdcmFile::WriteDcmImplVR (const char* fileName) { - return WriteDcmImplVR (std::string (fileName)); -} - -/** - * \ingroup gdcmFile - * \brief - * @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 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 if a DICOM_V3 header is supplied, - * groups < 0x0008 and shadow groups are ignored) + * groups < 0x0008 and shadow groups are ignored * \warning NO TEST is performed on processor "Endiannity". - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * * @param fileName 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 fileName) { +bool File::WriteAcr (std::string const & fileName) +{ return WriteBase(fileName, ACR); } //----------------------------------------------------------------------------- // Protected /** - * \ingroup gdcmFile - * -* @param fileName name of the file to be created + * \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 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 (false); + 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; } // -------------------------------------------------------------- @@ -655,17 +660,39 @@ bool 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 ( Header->GetFileType() == ACR_LIBIDO){ - rows = Header->GetPubEntryByNumber(0x0028, 0x0010); - columns = Header->GetPubEntryByNumber(0x0028, 0x0011); - Header->SetPubEntryByNumber(columns, 0x0028, 0x0010); - Header->SetPubEntryByNumber(rows , 0x0028, 0x0011); - } - // ----------------- End of Special Patch ---------------- + if ( HeaderInternal->GetFileType() == ACR_LIBIDO) + { + rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010); + columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011); - Header->Write(fp1, type); + 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 @@ -673,268 +700,26 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { // ...and we restore the Header to be Dicom Compliant again // just after writting - if (Header->GetFileType() == ACR_LIBIDO){ - Header->SetPubEntryByNumber(rows , 0x0028, 0x0010); - Header->SetPubEntryByNumber(columns, 0x0028, 0x0011); - } + if ( HeaderInternal->GetFileType() == ACR_LIBIDO ) + { + HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010); + HeaderInternal->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(true); -} -//----------------------------------------------------------------------------- -// Private -/** - * \ingroup gdcmFile - * \brief Swap the bytes, according to swap code. - * \warning not end user intended - * @param im area to deal with - * @param swap swap code - * @param lgr Area Length - * @param nb Pixels Bit number - */ -void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { -guint32 s32; -guint16 fort,faible; -int i; - -if(nb == 16) - switch(swap) { - case 0: - case 12: - case 1234: - break; - - case 21: - case 3412: - case 2143: - case 4321: - - for(i=0;i>8) - | ((((unsigned short int*)im)[i])<<8); - break; - - default: - printf("SWAP value (16 bits) not allowed : %d\n", swap); - } - -if( nb == 32 ) - switch (swap) { - case 0: - case 1234: - break; - - case 4321: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - case 2143: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=fort; - ((unsigned long int*)im)[i]=(s32<<16)|faible; - } - break; - - case 3412: - for(i=0;i>16; - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - default: - printf("SWAP value (32 bits) not allowed : %d\n", swap); - } -return; + return true; } /** - * \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 Access to the underlying \ref PixelConverter RGBA LUT */ -bool gdcmFile::ReadPixelData(void* destination) { - - FILE *fp; - - if ( !(fp=Header->OpenFile())) - return false; - - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) { - Header->CloseFile(); - return false; - } - - - // ---------------------- Compacted File (12 Bits Per Pixel) - /* unpack 12 Bits pixels into 16 Bits pixels */ - /* 2 pixels 12bit = [0xABCDEF] */ - /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */ - if (Header->GetBitsAllocated()==12) { - int nbPixels = Header->GetXSize() * Header->GetYSize(); - unsigned char b0, b1, b2; - - unsigned short int* pdestination = (unsigned short int*)destination; - for(int p=0;p> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - /* A */ /* B */ /* D */ - *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - /* F */ /* C */ /* E */ - - // Troubles expected on Big-Endian processors ? - } - return(true); - } - - // ---------------------- Uncompressed File - if ( !Header->IsDicomV3() || - Header->IsImplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - - if ( ItemRead != 1 ) { - Header->CloseFile(); - return false; - } else { - Header->CloseFile(); - return true; - } - } - - // ---------------------- Run Length Encoding - if (Header->IsRLELossLessTransferSyntax()) { - bool res = (bool)gdcm_read_RLE_file (fp,destination); - return res; - } - - // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int nb; - std::string str_nb=Header->GetPubEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ? - } +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); +} - int nBytes= nb/8; - - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek - - bool jpg2000 = Header->IsJPEG2000(); - bool jpgLossless = Header->IsJPEGLossless(); - - bool res = true; - guint16 ItemTagGr,ItemTagEl; - int ln; - - // Position on begining of Jpeg Pixels - - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); - } - fread(&ln,4,1,fp); - if(Header->GetSwapCode()) - ln=Header->SwapLong(ln); // Basic Offset Table Item length - - if (ln != 0) { - // What is it used for ?!? - char *BasicOffsetTableItemValue = (char *)malloc(ln+1); - fread(BasicOffsetTableItemValue,ln,1,fp); - } - - // first Fragment initialisation - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); - } - - // parsing fragments until Sequence Delim. Tag found - while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { - // --- for each Fragment - - fread(&ln,4,1,fp); - if(Header->GetSwapCode()) - ln=Header->SwapLong(ln); // Fragment Item length - - fragmentBegining=ftell(fp); +} // end namespace gdcm - 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; -} -//-----------------------------------------------------------------------------