X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=cd6ec36b48bc77078dffe8723c58d6c785a33137;hb=327dfe7647e3720b0f3125f9b19397cb9afc0ed3;hp=18e2d7d07d68ff56b23200cf9e0b0766850d0728;hpb=7eb058ef98b0003b379bf0db33e5c4c673b7f1e6;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 18e2d7d0..cd6ec36b 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/09/20 18:14:23 $ - Version: $Revision: 1.126 $ + Date: $Date: 2005/01/06 20:03:27 $ + Version: $Revision: 1.183 $ 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 @@ -17,17 +17,46 @@ =========================================================================*/ #include "gdcmFile.h" +#include "gdcmDocument.h" #include "gdcmDebug.h" -#include "jpeg/ljpg/jpegless.h" +#include "gdcmUtil.h" +#include "gdcmBinEntry.h" +#include "gdcmHeader.h" +#include "gdcmPixelReadConvert.h" +#include "gdcmPixelWriteConvert.h" +#include "gdcmDocEntryArchive.h" +#include + +namespace gdcm +{ typedef std::pair IterHT; //------------------------------------------------------------------------- // Constructor / Destructor /** - * \ingroup gdcmFile * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (gdcmHeader only deals with the ... header) + * 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). + */ +File::File( ) +{ + HeaderInternal = new Header( ); + SelfHeader = true; + Initialise(); +} + +/** + * \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 @@ -37,19 +66,18 @@ typedef std::pair IterHT; * This avoid a double parsing of public part of the header when * user sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). - * @param header already built gdcmHeader + * @param header already built Header */ -gdcmFile::gdcmFile(gdcmHeader *header) +File::File(Header *header) { - Header = header; + HeaderInternal = header; SelfHeader = false; - SaveInitialValues(); + Initialise(); } /** - * \ingroup gdcmFile * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (gdcmHeader only deals with the ... header) + * 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 @@ -61,288 +89,88 @@ gdcmFile::gdcmFile(gdcmHeader *header) * seen as a side effect). * @param filename file to be opened for parsing */ -gdcmFile::gdcmFile(std::string const & filename ) +File::File(std::string const & filename ) { - Header = new gdcmHeader( filename ); + HeaderInternal = new Header( filename ); SelfHeader = true; - SaveInitialValues(); + Initialise(); } /** - * \ingroup gdcmFile * \brief canonical destructor - * \note If the gdcmHeader was created by the gdcmFile constructor, - * it is destroyed by the gdcmFile + * \note If the Header was created by the File constructor, + * it is destroyed by the File */ -gdcmFile::~gdcmFile() +File::~File() { - if( SelfHeader ) + if( PixelReadConverter ) { - delete Header; + delete PixelReadConverter; } - Header = 0; - - DeleteInitialValues(); -} - -/** - * \ingroup gdcmFile - * \brief Sets some initial values for the Constructor - * \warning not end user intended - */ -void gdcmFile::SaveInitialValues() -{ - - PixelRead = -1; // no ImageData read yet. - LastAllocatedPixelDataLength = 0; - Pixel_Data = 0; - - InitialSpp = ""; - InitialPhotInt = ""; - InitialPlanConfig = ""; - InitialBitsAllocated = ""; - InitialHighBit = ""; - - InitialRedLUTDescr = 0; - InitialGreenLUTDescr = 0; - InitialBlueLUTDescr = 0; - InitialRedLUTData = 0; - InitialGreenLUTData = 0; - InitialBlueLUTData = 0; - - if ( Header->IsReadable() ) + if( PixelWriteConverter ) { - SetPixelDataSizeFromHeader(); - - // the following values *may* be modified - // by gdcmFile::GetImageDataIntoVectorRaw - // we save their initial value. - InitialSpp = Header->GetEntryByNumber(0x0028,0x0002); - InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004); - InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006); - - InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); - InitialHighBit = Header->GetEntryByNumber(0x0028,0x0102); - - // the following entries *may* be removed from the H table - // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw - // we keep a pointer on them. - InitialRedLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1101); - InitialGreenLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1102); - InitialBlueLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1103); - - InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201); - InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202); - InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203); + delete PixelWriteConverter; } -} - -/** - * \ingroup gdcmFile - * \brief restores some initial values - * \warning not end user intended - */ -void gdcmFile::RestoreInitialValues() -{ - if ( Header->IsReadable() ) - { - // the following values *may* have been modified - // by gdcmFile::GetImageDataIntoVectorRaw - // we restore their initial value. - if ( InitialSpp != "") - Header->SetEntryByNumber(InitialSpp,0x0028,0x0002); - if ( InitialPhotInt != "") - Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); - if ( InitialPlanConfig != "") - - Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); - if ( InitialBitsAllocated != "") - Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); - if ( InitialHighBit != "") - Header->SetEntryByNumber(InitialHighBit,0x0028,0x0102); - - // the following entries *may* be have been removed from the H table - // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw - // we restore them. - - if (InitialRedLUTDescr) - Header->AddEntry(InitialRedLUTDescr); - if (InitialGreenLUTDescr) - Header->AddEntry(InitialGreenLUTDescr); - if (InitialBlueLUTDescr) - Header->AddEntry(InitialBlueLUTDescr); - - if (InitialRedLUTData) - Header->AddEntry(InitialBlueLUTDescr); - if (InitialGreenLUTData) - Header->AddEntry(InitialGreenLUTData); - if (InitialBlueLUTData) - Header->AddEntry(InitialBlueLUTData); + if( Archive ) + { + delete Archive; } -} - -/** - * \ingroup gdcmFile - * \brief delete initial values (il they were saved) - * of InitialLutDescriptors and InitialLutData - */ -void gdcmFile::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; -} - -/** - * \ingroup gdcmFile - * \brief drop palette related initial values -if any- - * (InitialLutDescriptors and InitialLutData) - * out of header, to make it consistent with the Pixel_Data - * as it's loaded in memory - */ - -//FIXME : Should be nice, if we could let it here. -// will be moved to PixelData class -// Now, the job is done in gdcmHeader.cxx - - /* -void gdcmFile::DropInitialValues() -{ - gdcmHeader* h=GetHeader(); - if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' ) + if( SelfHeader ) { - // if SamplesPerPixel = 3, sure we don't need any LUT ! - // Drop 0028|1101, 0028|1102, 0028|1103 - // Drop 0028|1201, 0028|1202, 0028|1203 - - gdcmDocEntry* e = h->GetDocEntryByNumber(0x0028,0x01101); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1102); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1103); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x01201); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1202); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1203); - if (e) - { - h->RemoveEntryNoDestroy(e); - } + delete HeaderInternal; } + HeaderInternal = 0; } -*/ //----------------------------------------------------------------------------- // Print +void File::Print(std::ostream &os) +{ + HeaderInternal->SetPrintLevel(PrintLevel); + HeaderInternal->Print(os); + + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); +} //----------------------------------------------------------------------------- // Public - /** - * \ingroup gdcmFile - * \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). - * \warning : not end user intended ? + * \brief Get the size of the image data + * + * If the image can be RGB (with a lut or by default), the size + * corresponds to the RGB image + * @return The image size */ -void gdcmFile::SetPixelDataSizeFromHeader() +size_t File::GetImageDataSize() { - // see PS 3.3-2003 : C.7.6.3.2.1 - // - // MONOCHROME1 - // MONOCHROME2 - // PALETTE COLOR - // RGB - // HSV (Retired) - // ARGB (Retired) - // CMYK (Retired) - // YBR_FULL - // YBR_FULL_422 (no LUT, no Palette) - // YBR_PARTIAL_422 - // YBR_ICT - // YBR_RCT - - // LUT's - // ex : gdcm-US-ALOKA-16.dcm - // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data] - // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data] - // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data] - - // ex : OT-PAL-8-face.dcm - // 0028|1201 [US] [Red Palette Color Lookup Table Data] - // 0028|1202 [US] [Green Palette Color Lookup Table Data] - // 0028|1203 [US] [Blue Palette Color Lookup Table Data] - - // Number of "Bits Allocated" - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - - if ( str_nb == GDCM_UNFOUND ) + if ( PixelWriteConverter->GetUserData() ) { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - if (nb == 12) - { - nb =16; - } + return PixelWriteConverter->GetUserDataSize(); } - ImageDataSize = - ImageDataSizeRaw = 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() ) + + return PixelReadConverter->GetRGBSize(); +} + +/** + * \brief Get the size of the image data + * + * If the image can be RGB by transformation in a LUT, this + * transformation isn't considered + * @return The raw image size + */ +size_t File::GetImageDataRawSize() +{ + if ( PixelWriteConverter->GetUserData() ) { - ImageDataSize *= 3; + return PixelWriteConverter->GetUserDataSize(); } + + return PixelReadConverter->GetRawSize(); } /** - * \ingroup gdcmFile * \brief - Allocates necessary memory, * - Reads the pixels from disk (uncompress if necessary), * - Transforms YBR pixels, if any, into RGB pixels @@ -352,123 +180,31 @@ void gdcmFile::SetPixelDataSizeFromHeader() * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ -void *gdcmFile::GetImageData() +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 ) + if ( PixelWriteConverter->GetUserData() ) { - 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()->SetEntryVoidAreaByNumber( Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } - PixelRead = 0; // no PixelRaw - - return Pixel_Data; -} + return PixelWriteConverter->GetUserData(); + } -/** - * \ingroup gdcmFile - * \brief - * Read the pixels from disk (uncompress if necessary), - * Transforms YBR pixels, if any, into RGB pixels - * Transforms 3 planes R, G, B, if any, into a single RGB Plane - * Transforms single Grey plane + 3 Palettes into a RGB Plane - * Copies at most MaxSize bytes of pixel data to caller allocated - * memory space. - * \warning This function allows people that want to build a volume - * from an image stack *not to* have, first to get the image pixels, - * and then move them to the volume area. - * It's absolutely useless for any VTK user since vtk chooses - * to invert the lines of an image, that is the last line comes first - * (for some axis related reasons?). Hence he will have - * to load the image line by line, starting from the end. - * VTK users have to call GetImageData - * - * @param destination Address (in caller's memory space) at which the - * pixel data should be copied - * @param maxSize Maximum number of bytes to be copied. When MaxSize - * is not sufficient to hold the pixel data the copy is not - * executed (i.e. no partial copy). - * @return On success, the number of bytes actually copied. Zero on - * failure e.g. MaxSize is lower than necessary. - */ -size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) -{ - GetImageDataIntoVectorRaw (destination, maxSize); - PixelRead = 0 ; // =0 : no ImageDataRaw - if ( !Header->HasLUT() ) + if ( ! GetRaw() ) { - return ImageDataSize; + // If the decompression failed nothing can be done. + return 0; } - - // from Lut R + Lut G + Lut B - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *a = (uint8_t *)destination; - uint8_t *lutRGBA = Header->GetLUTRGBA(); - if ( lutRGBA ) + if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) { - int j; - // move Gray pixels to temp area - memmove(newDest, destination, ImageDataSizeRaw); - for (size_t i=0; iSetEntryByNumber(spp,0x0028,0x0002); - std::string rgb = "RGB "; // Photometric Interpretation - Header->SetEntryByNumber(rgb,0x0028,0x0004); - std::string planConfig = "0"; // Planar Configuration - Header->SetEntryByNumber(planConfig,0x0028,0x0006); - + return PixelReadConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the Raw + return PixelReadConverter->GetRaw(); } - else // GetLUTRGBA() failed - { - // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color - // that are *more* than 65535 long ?!? - // No idea how to manage such an image ! - // Need to make RGB Pixels (?) from grey Pixels (?!) and Gray Lut (!?!) - // It seems that *no Dicom Viewer* has any idea :-( - - std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation - Header->SetEntryByNumber(photomInterp,0x0028,0x0004); - } - - /// \todo Drop Palette Color out of the Header? - return ImageDataSize; } /** - * \ingroup gdcmFile * \brief Allocates necessary memory, * Transforms YBR pixels (if any) into RGB pixels * Transforms 3 planes R, G, B (if any) into a single RGB Plane @@ -477,59 +213,27 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -void * gdcmFile::GetImageDataRaw () +uint8_t *File::GetImageDataRaw () { - size_t imgDataSize; - if ( Header->HasLUT() ) - /// \todo Let gdcmHeader user a chance to get the right value - imgDataSize = ImageDataSizeRaw; - else - imgDataSize = ImageDataSize; - - // FIXME (Mathieu) - // I need to deallocate Pixel_Data before doing any allocation: - - if ( Pixel_Data ) - if ( LastAllocatedPixelDataLength != imgDataSize ) - free(Pixel_Data); - if ( !Pixel_Data ) - Pixel_Data = new uint8_t[imgDataSize]; - - if ( Pixel_Data ) - { - LastAllocatedPixelDataLength = imgDataSize; - - // we load the pixels ( grey level or RGB, but NO transformation) - GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize); - - // We say the value *is* loaded. - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - - // will be 7fe0, 0010 in standard cases - GetHeader()->SetEntryVoidAreaByNumber(Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } - PixelRead = 1; // PixelRaw - - return Pixel_Data; + return GetRaw(); } /** - * \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 * (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 + * VTK users have to call GetImageData * * @param destination Address (in caller's memory space) at which the * pixel data should be copied @@ -539,301 +243,123 @@ void * gdcmFile::GetImageDataRaw () * @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) +size_t File::GetImageDataIntoVector (void *destination, size_t maxSize) { - int nb, nbu, highBit, sign; - - // 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 ) + if ( ! GetRaw() ) { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return (size_t)0; + // If the decompression failed nothing can be done. + return 0; } - ReadPixelData( destination ); - - // Number of Bits Allocated for storing a Pixel - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) + if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - // FIXME - // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated - // separately, correct ? - } - - // Number of Bits actually used - std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101); - if ( str_nbu == GDCM_UNFOUND ) - { - nbu = nb; - } - else - { - nbu = atoi( str_nbu.c_str() ); - } - - // High Bit Position - std::string 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 - std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103); - if ( str_sign == GDCM_UNFOUND ) - { - sign = 0; // default is unsigned - } - else - { - sign = atoi( str_sign.c_str() ); - } - - // re arange bytes inside the integer (processor endianity) - if ( nb != 8 ) - { - SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); - } - - // to avoid pb with some xmedcon breakers images - if ( nb == 16 && nbu < nb && sign == 0) - { - int l = (int)(ImageDataSize / (nb/8)); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; iGetRGBSize() > maxSize ) { - if( *deb == 0xffff ) - { - *deb = 0; - } - deb++; + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; } + memcpy( destination, + (void*)PixelReadConverter->GetRGB(), + PixelReadConverter->GetRGBSize() ); + return PixelReadConverter->GetRGBSize(); } - // re arange bits inside the bytes - if ( nbu != nb ) + // Either no LUT conversion necessary or LUT conversion failed + if ( PixelReadConverter->GetRawSize() > maxSize ) { - int l = (int)(ImageDataSize / (nb/8)); - if ( nb == 16 ) - { - uint16_t mask = 0xffff; - mask = mask >> (nb-nbu); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } - } - else if ( nb == 32 ) - { - uint32_t mask = 0xffffffff; - mask = mask >> (nb - nbu); - uint32_t *deb = (uint32_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } - } - else - { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); - return 0; - } + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; } -// DO NOT remove this code commented out. -// Nobody knows what's expecting you ... -// Just to 'see' what was actually read on disk :-( + memcpy( destination, + (void*)PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize() ); + return PixelReadConverter->GetRawSize(); +} -// FILE * f2; -// f2 = fopen("SpuriousFile.RAW","wb"); -// fwrite(destination,ImageDataSize,1,f2); -// fclose(f2); +/** + * \brief Points the internal 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 + * + * @return boolean + */ +void File::SetImageData(uint8_t *inData, size_t expectedSize) +{ + SetUserData(inData,expectedSize); +} - // Deal with the color - // ------------------- - - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); +/** + * \brief Set the image datas defined by the user + * \warning When writting the file, this datas are get as default datas to write + */ +void File::SetUserData(uint8_t *data, size_t expectedSize) +{ + PixelWriteConverter->SetUserData(data,expectedSize); +} - if ( str_PhotometricInterpretation == "MONOCHROME1 " - || str_PhotometricInterpretation == "MONOCHROME2 " ) - { - return ImageDataSize; - } - - // Planar configuration = 0 : Pixels are already RGB - // Planar configuration = 1 : 3 planes : R, G, B - // Planar configuration = 2 : 1 gray Plane + 3 LUT +/** + * \brief Get the image datas defined by the user + * \warning When writting the file, this datas are get as default data to write + */ +uint8_t *File::GetUserData() +{ + return PixelWriteConverter->GetUserData(); +} - // Well ... supposed to be ! - // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0, - // PhotometricInterpretation=PALETTE COLOR - // and heuristic has to be found :-( +/** + * \brief Get the image data size defined by the user + * \warning When writting the file, this datas are get as default data to write + */ +size_t File::GetUserDataSize() +{ + return PixelWriteConverter->GetUserDataSize(); +} - int planConf = Header->GetPlanarConfiguration(); // 0028,0006 +/** + * \brief Get the image datas from the file. + * If a LUT is found, the data are expanded to be RGB + */ +uint8_t *File::GetRGBData() +{ + return PixelReadConverter->GetRGB(); +} - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if ( str_PhotometricInterpretation == "PALETTE COLOR ") - { - planConf = 2; - } +/** + * \brief Get the image data size from the file. + * If a LUT is found, the data are expanded to be RGB + */ +size_t File::GetRGBDataSize() +{ + return PixelReadConverter->GetRGBSize(); +} - 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(); - - uint8_t* newDest = new uint8_t[ImageDataSize]; - uint8_t* x = newDest; - uint8_t* a = (uint8_t*)destination; - uint8_t* b = a + l; - uint8_t* 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; i < nbFrames; i++) - { - for (int j = 0; j < l; j++) - { - R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; - G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; - B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; - - if (R < 0.0) R = 0.0; - if (G < 0.0) G = 0.0; - if (B < 0.0) B = 0.0; - if (R > 255.0) R = 255.0; - if (G > 255.0) G = 255.0; - if (B > 255.0) B = 255.0; - - *(x++) = (uint8_t)R; - *(x++) = (uint8_t)G; - *(x++) = (uint8_t)B; - a++; b++; c++; - } - } - memmove(destination, newDest, ImageDataSize); - 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(); - - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *x = newDest; - uint8_t *a = (uint8_t *)destination; - uint8_t *b = a + l; - uint8_t *c = b + l; - - for (int j = 0; j < l; j++) - { - *(x++) = *(a++); - *(x++) = *(b++); - *(x++) = *(c++); - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - break; - case 2: - // Palettes were found - // Let the user deal with them ! - return ImageDataSize; - } - // 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 - - Header->SetEntryByNumber(spp,0x0028,0x0002); - Header->SetEntryByNumber(photInt,0x0028,0x0004); - Header->SetEntryByNumber(planConfig,0x0028,0x0006); - - return ImageDataSize; +/** + * \brief Get the image datas from the file. + * If a LUT is found, the datas are not expanded ! + */ +uint8_t *File::GetRawData() +{ + return PixelReadConverter->GetRaw(); } /** - * \ingroup gdcmFile - * \brief performs a shalow 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 : plane per plane - * \warning user is kindly requested NOT TO 'free' the Pixel area - * @param inData user supplied pixel area - * @param expectedSize total image size, in Bytes - * - * @return boolean + * \brief Get the image data size from the file. + * If a LUT is found, the data are not expanded ! */ -bool gdcmFile::SetImageData(void *inData, size_t expectedSize) +size_t File::GetRawDataSize() { - Header->SetImageDataSize( expectedSize ); -// FIXME : if already allocated, memory leak ! - Pixel_Data = inData; - ImageDataSize = ImageDataSizeRaw = expectedSize; - PixelRead = 1; -// FIXME : 7fe0, 0010 IS NOT set ... - return true; + return PixelReadConverter->GetRawSize(); } /** - * \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 @@ -842,22 +368,28 @@ bool gdcmFile::SetImageData(void *inData, size_t expectedSize) * @return false if write fails */ -bool gdcmFile::WriteRawData(std::string const & fileName) +bool File::WriteRawData(std::string const &fileName) { - FILE *fp1 = fopen(fileName.c_str(), "wb"); - if (fp1 == NULL) + std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); + if (!fp1) { - printf("Fail to open (write) file [%s] \n", fileName.c_str()); + dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); return false; } - fwrite (Pixel_Data, ImageDataSize, 1, fp1); - fclose (fp1); + + if(PixelWriteConverter->GetUserData()) + fp1.write((char*)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize()); + else if(PixelReadConverter->GetRGB()) + fp1.write((char*)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); + else if(PixelReadConverter->GetRaw()) + fp1.write((char*)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); + + 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". @@ -866,27 +398,28 @@ bool gdcmFile::WriteRawData(std::string const & fileName) * @return false if write fails */ -bool gdcmFile::WriteDcmImplVR (std::string const & fileName) +bool File::WriteDcmImplVR (std::string const &fileName) { - return WriteBase(fileName, gdcmImplicitVR); + 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 + * 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::WriteDcmExplVR (std::string const & fileName) +bool File::WriteDcmExplVR (std::string const &fileName) { - return WriteBase(fileName, gdcmExplicitVR); + 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". @@ -900,45 +433,34 @@ bool gdcmFile::WriteDcmExplVR (std::string const & fileName) * @return false if write fails */ -bool gdcmFile::WriteAcr (std::string const & fileName) +bool File::WriteAcr (std::string const &fileName) { - return WriteBase(fileName, gdcmACR); + SetWriteTypeToAcr(); + return Write(fileName); } -//----------------------------------------------------------------------------- -// Protected /** - * \ingroup gdcmFile - * \brief NOT a end user inteded function - * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) + * \brief Writes on disk A SINGLE Dicom file, * @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 */ -bool gdcmFile::WriteBase (std::string const & fileName, FileType type) +bool File::Write(std::string const &fileName) { - if ( PixelRead == -1 && type != gdcmExplicitVR) - { - 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 == gdcmImplicitVR || type == gdcmExplicitVR ) + switch(WriteType) { - // writing Dicom File Preamble - uint8_t* filePreamble = new uint8_t[128]; - memset(filePreamble, 0, 128); - fwrite(filePreamble, 128, 1, fp1); - fwrite("DICM", 4, 1, fp1); - - delete[] filePreamble; + case ImplicitVR: + SetWriteFileTypeToImplicitVR(); + break; + case ExplicitVR: + SetWriteFileTypeToExplicitVR(); + break; + case ACR: + case ACR_LIBIDO: + SetWriteFileTypeToACR(); + break; + default: + SetWriteFileTypeToExplicitVR(); } // -------------------------------------------------------------- @@ -947,350 +469,459 @@ bool gdcmFile::WriteBase (std::string const & 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() == gdcmACR_LIBIDO) + if( WriteType == ACR_LIBIDO ) { - rows = Header->GetEntryByNumber(0x0028, 0x0010); - columns = Header->GetEntryByNumber(0x0028, 0x0011); - - Header->SetEntryByNumber(columns, 0x0028, 0x0010); - Header->SetEntryByNumber(rows , 0x0028, 0x0011); + SetWriteToLibido(); + } + else + { + SetWriteToNoLibido(); } // ----------------- End of Special Patch ---------------- - - uint16_t grPixel = Header->GetGrPixel(); - uint16_t numPixel = Header->GetNumPixel();; - - gdcmDocEntry* PixelElement = - GetHeader()->GetDocEntryByNumber(grPixel, numPixel); - - if ( PixelRead == 1 ) + + switch(WriteMode) { - // we read pixel 'as is' (no tranformation LUT -> RGB) - PixelElement->SetLength( ImageDataSizeRaw ); + case WMODE_RAW : + SetWriteToRaw(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; } - else if ( PixelRead == 0 ) + + bool check = CheckWriteIntegrity(); + if(check) { - // we tranformed GrayLevel pixels + LUT into RGB Pixel - PixelElement->SetLength( ImageDataSize ); + check = HeaderInternal->Write(fileName,WriteType); } - - Header->Write(fp1, type); + + RestoreWrite(); + RestoreWriteFileType(); // -------------------------------------------------------------- // 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 ( Header->GetFileType() == gdcmACR_LIBIDO ) - { - Header->SetEntryByNumber(rows , 0x0028, 0x0010); - Header->SetEntryByNumber(columns, 0x0028, 0x0011); - } + RestoreWriteOfLibido(); // ----------------- End of Special Patch ---------------- - - // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now - fclose (fp1); - return true; + return check; } -//----------------------------------------------------------------------------- -// 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 Accesses an existing DocEntry (i.e. a Dicom Element) + * through it's (group, element) and modifies it's content with + * the given value. + * @param content new value (string) to substitute with + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify + */ +bool File::SetEntryByNumber(std::string const &content, + uint16_t group, uint16_t element) +{ + return HeaderInternal->SetEntryByNumber(content,group,element); +} + + +/** + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) + * through it's (group, element) and modifies it's content with + * the given value. + * @param content new value (void* -> uint8_t*) to substitute with + * @param lgth new value length + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify */ -void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) +bool File::SetEntryByNumber(uint8_t *content, int lgth, + uint16_t group, uint16_t element) { - int i; + return HeaderInternal->SetEntryByNumber(content,lgth,group,element); +} + +/** + * \brief Modifies the value of a given Doc Entry (Dicom Element) + * when it exists. Create it with the given value when unexistant. + * @param content (string) Value to be set + * @param group Group number of the Entry + * @param element Element number of the Entry + * \return pointer to the modified/created Header Entry (NULL when creation + * failed). + */ +bool File::ReplaceOrCreateByNumber(std::string const &content, + uint16_t group, uint16_t element) +{ + return HeaderInternal->ReplaceOrCreateByNumber(content,group,element) != NULL; +} - if( nb == 16 ) +/* + * \brief Modifies the value of a given Header Entry (Dicom Element) + * when it exists. Create it with the given value when unexistant. + * A copy of the binArea is made to be kept in the Document. + * @param binArea (binary) value to be set + * @param group Group number of the Entry + * @param element Element number of the Entry + * \return pointer to the modified/created Header Entry (NULL when creation + * failed). + */ +bool File::ReplaceOrCreateByNumber(uint8_t *binArea, int lgth, + uint16_t group, uint16_t element) +{ + return HeaderInternal->ReplaceOrCreateByNumber(binArea,lgth,group,element) != NULL; +} + +/** + * \brief Access to the underlying \ref PixelReadConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelReadConverter->GetLutRGBA(); +} + +//----------------------------------------------------------------------------- +// Protected + +/** + * \brief Check the write integrity + * + * The tests made are : + * - verify the size of the image to write with the possible write + * when the user set an image data + * @return true if the check successfulls + */ +bool File::CheckWriteIntegrity() +{ + if(PixelWriteConverter->GetUserData()) { - uint16_t* im16 = (uint16_t*)im; - switch( swap ) + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) { - case 0: - case 12: - case 1234: - break; - case 21: - case 3412: - case 2143: - case 4321: - for(i=0; i < lgr/2; i++) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - break; - default: - std::cout << "SWAP value (16 bits) not allowed :i" << swap << - std::endl; + numberBitsAllocated = 16; } - } - else if( nb == 32 ) - { - uint32_t s32; - uint16_t fort, faible; - uint32_t* im32 = (uint32_t*)im; - switch ( swap ) + + size_t decSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + size_t rgbSize = decSize; + if( HeaderInternal->HasLUT() ) + rgbSize = decSize * 3; + + switch(WriteMode) { - case 0: - case 1234: - break; - case 4321: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 4321 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8 ) | ( faible << 8); - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; - } - break; - case 2143: - for(i = 0; i < lgr/4; i++) + case WMODE_RAW : + if( decSize!=PixelWriteConverter->GetUserDataSize() ) { - faible = im32[i] & 0x0000ffff; // 2143 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8) | ( faible << 8); - s32 = fort; - im32[i] = ( s32 << 16 ) | faible; + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (Raw)"); + //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (Raw)\n" + // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n"; + return false; } break; - case 3412: - for(i = 0; i < lgr/4; i++) + case WMODE_RGB : + if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) { - faible = im32[i] & 0x0000ffff; // 3412 - fort = im32[i] >> 16; - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (RGB)"); + //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (RGB)\n" + // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n"; + return false; } break; - default: - std::cout << "SWAP value (32 bits) not allowed : " << swap << - std::endl; } } + + 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. - * - */ -bool gdcmFile::ReadPixelData(void *destination) +void File::SetWriteToRaw() { - FILE *fp = Header->OpenFile(); - - if ( !fp ) - { - return false; - } - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) + if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) { - 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 ) + SetWriteToRGB(); + } + else { - int nbPixels = Header->GetXSize() * Header->GetYSize(); - uint8_t b0, b1, b2; - - uint16_t* pdestination = (uint16_t*)destination; - for(int p = 0; p < nbPixels; p += 2 ) + ValEntry *photInt = CopyValEntry(0x0028,0x0004); + if(HeaderInternal->HasLUT()) { - fread(&b0,1,1,fp); - fread(&b1,1,1,fp); - fread(&b2,1,1,fp); - - //Two steps is necessary to please VC++ - *pdestination++ = ((b0 >> 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 ? + photInt->SetValue("PALETTE COLOR "); + } + else + { + photInt->SetValue("MONOCHROME1 "); } - Header->CloseFile(); - return true; + PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize()); + + BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelWriteConverter->GetData(),false); + pixel->SetLength(PixelWriteConverter->GetDataSize()); + + Archive->Push(photInt); + Archive->Push(pixel); } +} - // ---------------------- Uncompressed File - if ( !Header->IsDicomV3() || - Header->IsImplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) +void File::SetWriteToRGB() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3) { - size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - Header->CloseFile(); - if ( ItemRead != 1 ) + PixelReadConverter->BuildRGBImage(); + + ValEntry *spp = CopyValEntry(0x0028,0x0002); + spp->SetValue("3 "); + + ValEntry *planConfig = CopyValEntry(0x0028,0x0006); + planConfig->SetValue("0 "); + + ValEntry *photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("RGB "); + + if(PixelReadConverter->GetRGB()) { - return false; + PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), + PixelReadConverter->GetRGBSize()); } - else + else // Raw data { - return true; + PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize()); } - } - // ---------------------- Run Length Encoding - if ( Header->IsRLELossLessTransferSyntax() ) - { - bool res = 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; + BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelWriteConverter->GetData(),false); + pixel->SetLength(PixelWriteConverter->GetDataSize()); + + Archive->Push(spp); + Archive->Push(planConfig); + Archive->Push(photInt); + Archive->Push(pixel); + + // Remove any LUT + Archive->Push(0x0028,0x1101); + Archive->Push(0x0028,0x1102); + Archive->Push(0x0028,0x1103); + Archive->Push(0x0028,0x1201); + Archive->Push(0x0028,0x1202); + Archive->Push(0x0028,0x1203); + + // For old ACR-NEMA + // Thus, we have a RGB image and the bits allocated = 24 and + // samples per pixels = 1 (in the read file) + if(HeaderInternal->GetBitsAllocated()==24) + { + ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100); + bitsAlloc->SetValue("8 "); + + ValEntry *bitsStored = CopyValEntry(0x0028,0x0101); + bitsStored->SetValue("8 "); + + ValEntry *highBit = CopyValEntry(0x0028,0x0102); + highBit->SetValue("7 "); + + Archive->Push(bitsAlloc); + Archive->Push(bitsStored); + Archive->Push(highBit); + } } else { - nb = atoi( str_nb.c_str() ); - if ( nb == 12 ) - { - nb = 16; // ?? 12 should be ACR-NEMA only - } + SetWriteToRaw(); } +} - int nBytes= nb/8; - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek +void File::RestoreWrite() +{ + Archive->Restore(0x0028,0x0002); + Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); + Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + + // For old ACR-NEMA (24 bits problem) + Archive->Restore(0x0028,0x0100); + Archive->Restore(0x0028,0x0101); + Archive->Restore(0x0028,0x0102); + + // For the LUT + Archive->Restore(0x0028,0x1101); + Archive->Restore(0x0028,0x1102); + Archive->Restore(0x0028,0x1103); + Archive->Restore(0x0028,0x1201); + Archive->Restore(0x0028,0x1202); + Archive->Restore(0x0028,0x1203); +} - bool jpg2000 = Header->IsJPEG2000(); - bool jpgLossless = Header->IsJPEGLossless(); +void File::SetWriteFileTypeToACR() +{ + Archive->Push(0x0002,0x0010); +} - bool res = true; - uint16_t ItemTagGr, ItemTagEl; - int ln; - - // Position on begining of Jpeg Pixels +void File::SetWriteFileTypeToExplicitVR() +{ + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() ); + + ValEntry *tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + + Archive->Push(tss); +} + +void File::SetWriteFileTypeToImplicitVR() +{ + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() ); + + ValEntry *tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + + Archive->Push(tss); +} + +void File::RestoreWriteFileType() +{ + Archive->Restore(0x0002,0x0010); +} + +void File::SetWriteToLibido() +{ + ValEntry *oldRow = dynamic_cast + (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); + ValEntry *oldCol = dynamic_cast + (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) + if( oldRow && oldCol ) { - ItemTagGr = Header->SwapShort(ItemTagGr); - ItemTagEl = Header->SwapShort(ItemTagEl); + std::string rows, columns; + + ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); + ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + + newRow->Copy(oldCol); + newCol->Copy(oldRow); + + newRow->SetValue(oldCol->GetValue()); + newCol->SetValue(oldRow->GetValue()); + + Archive->Push(newRow); + Archive->Push(newCol); } - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue("ACRNEMA_LIBIDO_1.1"); + Archive->Push(libidoCode); +} + +void File::SetWriteToNoLibido() +{ + ValEntry *recCode = dynamic_cast + (HeaderInternal->GetDocEntryByNumber(0x0008,0x0010)); + if( recCode ) { - ln = Header->SwapLong( ln ); // Basic Offset Table Item length + if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + { + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue(""); + Archive->Push(libidoCode); + } } +} + +void File::RestoreWriteOfLibido() +{ + Archive->Restore(0x0028,0x0010); + Archive->Restore(0x0028,0x0011); + Archive->Restore(0x0008,0x0010); +} + +ValEntry *File::CopyValEntry(uint16_t group,uint16_t element) +{ + DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element); + ValEntry *newE; - if ( ln != 0 ) + if(oldE) { - // What is it used for ?!? - uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); - //delete[] BasicOffsetTableItemValue; + newE = new ValEntry(oldE->GetDictEntry()); + newE->Copy(oldE); } - - // 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() ) + else { - ItemTagGr = Header->SwapShort( ItemTagGr ); - ItemTagEl = Header->SwapShort( ItemTagEl ); + newE = GetHeader()->NewValEntryByNumber(group,element); } - // parsing fragments until Sequence Delim. Tag found - while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd ) + return(newE); +} + +BinEntry *File::CopyBinEntry(uint16_t group,uint16_t element) +{ + DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element); + BinEntry *newE; + + if(oldE) { - // --- for each Fragment - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) - { - ln = Header->SwapLong(ln); // Fragment Item length - } - fragmentBegining = ftell( fp ); + newE = new BinEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewBinEntryByNumber(group,element); + } - if ( jpg2000 ) - { - // JPEG 2000 : call to ??? - res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written - // ------------------------------------- endif (JPEG2000) - } - else if (jpgLossless) - { - // JPEG LossLess : call to xmedcom Lossless JPEG - // Reading Fragment pixels - JPEGLosslessDecodeImage (fp, (uint16_t*)destination, - Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln); - res = 1; // in order not to break the loop - - } // ------------------------------------- endif (JPEGLossless) - else - { - // JPEG Lossy : call to IJG 6b - if ( Header->GetBitsStored() == 8) - { - // Reading Fragment pixels - res = gdcm_read_JPEG_file (fp,destination); - } - else - { - // Reading Fragment pixels - res = gdcm_read_JPEG_file12 (fp,destination); - } - // ------------------------------------- endif (JPEGLossy) - } + return(newE); +} - if ( !res ) - { - break; - } - - // location in user's memory - // for next fragment (if any) - destination = (uint8_t*)destination + taille * nBytes; +//----------------------------------------------------------------------------- +// Protected +/** + * \brief Factorization for various forms of constructors. + */ +void File::Initialise() +{ + WriteMode = WMODE_RAW; + WriteType = ExplicitVR; - 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() ) + PixelReadConverter = new PixelReadConvert; + PixelWriteConverter = new PixelWriteConvert; + Archive = new DocEntryArchive( HeaderInternal ); + + if ( HeaderInternal->IsReadable() ) + { + PixelReadConverter->GrabInformationsFromHeader( HeaderInternal ); + } +} + +uint8_t *File::GetRaw() +{ + uint8_t *raw = PixelReadConverter->GetRaw(); + if ( ! raw ) + { + // The Raw image migth not be loaded yet: + std::ifstream *fp = HeaderInternal->OpenFile(); + PixelReadConverter->ReadAndDecompressPixelData( fp ); + if(fp) + HeaderInternal->CloseFile(); + + raw = PixelReadConverter->GetRaw(); + if ( ! raw ) { - ItemTagGr = Header->SwapShort( ItemTagGr ); - ItemTagEl = Header->SwapShort( ItemTagEl ); + dbg.Verbose(0, "File::GetRaw: read/decompress of " + "pixel data apparently went wrong."); + return 0; } } - // endWhile parsing fragments until Sequence Delim. Tag found - Header->CloseFile(); - return res; + return raw; } + +//----------------------------------------------------------------------------- +// Private + //----------------------------------------------------------------------------- +} // end namespace gdcm +