X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=d21e7f25f638ecaff830e4f6d5641aff67d4be82;hb=e62d57cbd05c8e864fd2ba197a271cdcac9a2128;hp=ed51d6984503b8d15e0ef21f7e77c3abd586d808;hpb=fc41bb9afa4edfc95108e8fe9ab8c2554835dd0f;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index ed51d698..d21e7f25 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,70 +1,289 @@ -// gdcmFile.cxx + /*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/09/24 11:39:21 $ + Version: $Revision: 1.129 $ + + 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. + + 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 "gdcmDebug.h" #include "jpeg/ljpg/jpegless.h" -///////////////////////////////////////////////////////////////// +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) + * 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 + * user sets an a posteriori shadow dictionary (efficiency can be + * seen as a side effect). + * @param header already built gdcmHeader + */ +gdcmFile::gdcmFile(gdcmHeader *header) +{ + Header = header; + SelfHeader = false; + SaveInitialValues(); +} + /** * \ingroup gdcmFile - * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant - * file (see SetFileName, SetDcmTag and Write) + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (gdcmHeader only deals with the ... header) * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. - * \Note the in-memory representation of all available tags found in + * It will be up to the user to load the pixels into memory + * (see GetImageData, GetImageDataRaw) + * \note the in-memory representation of all available tags found in * the DICOM header is post-poned to first header information access. * This avoid a double parsing of public part of the header when * one sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). - * * @param filename file to be opened for parsing - * - * @return */ - -gdcmFile::gdcmFile(std::string & filename) - :gdcmHeader(filename.c_str()) +gdcmFile::gdcmFile(std::string const & filename ) { - if (IsReadable()) - SetPixelDataSizeFromHeader(); + Header = new gdcmHeader( filename ); + SelfHeader = true; + SaveInitialValues(); } -gdcmFile::gdcmFile(const char * filename) - :gdcmHeader(filename) -{ - if (IsReadable()) - SetPixelDataSizeFromHeader(); +/** + * \ingroup gdcmFile + * \brief canonical destructor + * \note If the gdcmHeader was created by the gdcmFile constructor, + * it is destroyed by the gdcmFile + */ +gdcmFile::~gdcmFile() +{ + if( SelfHeader ) + { + delete Header; + } + Header = 0; + + DeleteInitialValues(); } /** * \ingroup gdcmFile - * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les - * pixels de l'image ou DES images dans le cas d'un multiframe - * - * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels - * (dans le cas d'images compressees, elle n'a pas de sens). - * - * @return longueur a allouer + * \brief Sets some initial values for the Constructor + * \warning not end user intended */ -void gdcmFile::SetPixelDataSizeFromHeader(void) { - int nb; - std::string str_nb; +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() ) + { + 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); + } +} - str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; +/** + * \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); } - lgrTotale = GetXSize() * GetYSize() * GetZSize() - * (nb/8)* GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = - gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - if ( str_PhotometricInterpretation == "PALETTE COLOR " ) { - lgrTotale*=3; +} + +/** + * \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 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); + } } } +*/ + +//----------------------------------------------------------------------------- +// Print + +//----------------------------------------------------------------------------- +// 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 ? + */ +void gdcmFile::SetPixelDataSizeFromHeader() +{ // see PS 3.3-2003 : C.7.6.3.2.1 // // MONOCHROME1 @@ -80,329 +299,392 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { // 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] + // 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 : US-PAL-8-10x-echo.dcm, 8BitsRunLengthColor.dcm - // 0028|1201 [OW] [Red Palette Color Lookup Table Data] - // 0028|1202 [OW] [Green Palette Color Lookup Table Data] - // 0028|1203 [OW] [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] - // 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 ) + { + nb = 16; + } + else + { + nb = atoi( str_nb.c_str() ); + if (nb == 12) + { + nb =16; + } + } + 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() ) + { + ImageDataSize *= 3; + } +} -///////////////////////////////////////////////////////////////// /** - * \ingroup gdcmFile - * \brief Returns the size (in bytes) of required memory to hold - * the pixel data represented in this file. - * @return The size of pixel data in bytes. + * \ingroup gdcmFile + * \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 */ +uint8_t* gdcmFile::GetImageData() +{ + // FIXME (Mathieu) + // I need to deallocate Pixel_Data before doing any allocation: + + if ( Pixel_Data ) + if ( LastAllocatedPixelDataLength != ImageDataSize ) + free(Pixel_Data); + if ( !Pixel_Data ) + Pixel_Data = new uint8_t[ImageDataSize]; + + if ( Pixel_Data ) + { + LastAllocatedPixelDataLength = ImageDataSize; -size_t gdcmFile::GetImageDataSize(void) { - return (lgrTotale); -} + // we load the pixels (and transform grey level + LUT into RGB) + GetImageDataIntoVector(Pixel_Data, ImageDataSize); + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // Will be 7fe0, 0010 in standard case + GetHeader()->SetEntryBinAreaByNumber( Pixel_Data, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 0; // no PixelRaw + + return Pixel_Data; +} -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief Read pixel data from disk (optionaly decompressing) into the - * caller specified memory location. - * @param destination where the pixel data should be stored. - * + * \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. */ -bool gdcmFile::ReadPixelData(void* destination) { - - if ( !OpenFile()) - return false; - - if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) { - CloseFile(); - return false; +size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) +{ + GetImageDataIntoVectorRaw (destination, maxSize); + PixelRead = 0 ; // =0 : no ImageDataRaw + if ( !Header->HasLUT() ) + { + return ImageDataSize; } + + // from Lut R + Lut G + Lut B + uint8_t *newDest = new uint8_t[ImageDataSize]; + uint8_t *a = (uint8_t *)destination; + uint8_t *lutRGBA = Header->GetLUTRGBA(); + + if ( lutRGBA ) + { + int j; + // move Gray pixels to temp area + memmove(newDest, destination, ImageDataSizeRaw); + for (size_t i=0; 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); - if (GetBitsAllocated()==12) { - int nbPixels = GetXSize()*GetYSize(); - unsigned char b0, b1, b2; - - for(int p=0;p> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - /* A */ /* B */ /* D */ - *((unsigned short int*)destination)++ = - ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - /* F */ /* C */ /* E */ - - // Troubles expected on Big-Endian processors ? - } - return(true); } + 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 :-( - -// ------------------------- Uncompressed File - - if ( !IsDicomV3() || - IsImplicitVRLittleEndianTransferSyntax() || - IsExplicitVRLittleEndianTransferSyntax() || - IsExplicitVRBigEndianTransferSyntax() || - IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - - size_t ItemRead = fread(destination, lgrTotale, 1, fp); - if ( ItemRead != 1 ) { - CloseFile(); - return false; - } else { - CloseFile(); - return true; - } + std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation + Header->SetEntryByNumber(photomInterp,0x0028,0x0004); } - -// ------------------------- Run Length Encoding - - if (gdcmHeader::IsRLELossLessTransferSyntax()) { - int res = (bool)gdcm_read_RLE_file (destination); - return res; - } - - - -// ----------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - - int nb; - std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ? - } - int nBytes= nb/8; - - int taille = GetXSize() * GetYSize() * GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek - - bool jpg2000 = IsJPEG2000(); - bool jpgLossless = 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(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=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(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - - // parsing fragments until Sequence Delim. Tag found - - while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { - - // --- for each Fragment - - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Fragment Item length - - fragmentBegining=ftell(fp); - - if (jpg2000) { // JPEG 2000 : call to ??? - - res = (bool)gdcm_read_JPEG2000_file (destination); // Not Yet written - - } // ------------------------------------- endif (JPEG2000) - - else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG - - JPEGLosslessDecodeImage (fp, // Reading Fragment pixels - (unsigned short *)destination, - GetPixelSize()*8* GetSamplesPerPixel(), - ln); - res=1; // in order not to break the loop - - } // ------------------------------------- endif (JPEGLossless) - - else { // JPEG Lossy : call to IJG 6b - - if (GetBitsStored() == 8) { - res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels - } else { - res = (bool)gdcm_read_JPEG_file12 (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(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - - } // endWhile parsing fragments until Sequence Delim. Tag found - - return res; -} + /// \todo Drop Palette Color out of the Header? + return ImageDataSize; +} /** * \ingroup gdcmFile - * \brief Allocates necessary memory, copies the pixel data - * (image[s]/volume[s]) to newly allocated zone. + * \brief Allocates necessary memory, + * Transforms YBR pixels (if any) into RGB pixels + * Transforms 3 planes R, G, B (if any) into a single RGB Plane + * Copies the pixel data (image[s]/volume[s]) to newly allocated zone. + * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -void * gdcmFile::GetImageData (void) { - PixelData = (void *) malloc(lgrTotale); - if (PixelData) - GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); +uint8_t* gdcmFile::GetImageDataRaw () +{ + size_t imgDataSize; + if ( Header->HasLUT() ) + /// \todo Let gdcmHeader user a chance to get the right value + imgDataSize = ImageDataSizeRaw; + else + imgDataSize = ImageDataSize; + + // FIXME (Mathieu) + // I need to deallocate Pixel_Data before doing any allocation: + + if ( Pixel_Data ) + if ( LastAllocatedPixelDataLength != imgDataSize ) + free(Pixel_Data); + if ( !Pixel_Data ) + Pixel_Data = new uint8_t[imgDataSize]; + + if ( Pixel_Data ) + { + LastAllocatedPixelDataLength = imgDataSize; + + // we load the pixels ( grey level or RGB, but NO transformation) + GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize); + + // We say the value *is* loaded. + GetHeader()->SetEntryByNumber( GDCM_BINLOADED, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + + // will be 7fe0, 0010 in standard cases + GetHeader()->SetEntryBinAreaByNumber(Pixel_Data, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 1; // PixelRaw + + return Pixel_Data; } /** * \ingroup gdcmFile * \brief Copies at most MaxSize bytes of pixel data to caller's * memory space. + * \warning This function was designed to avoid people that want to build + * a volume from an image stack to need first to get the image pixels + * and then move them to the volume area. + * It's absolutely useless for any VTK user since vtk chooses + * to invert the lines of an image, that is the last line comes first + * (for some axis related reasons?). Hence he will have + * to load the image line by line, starting from the end. + * VTK users hace to call GetImageData + * \warning DOES NOT transform the Grey Plane + Palette Color (if any) + * into a single RGB Pixels Plane + * the (VTK) user will manage the palettes + * * @param destination Address (in caller's memory space) at which the * pixel data should be copied - * @param MaxSize Maximum number of bytes to be copied. When MaxSize + * @param maxSize Maximum number of bytes to be copied. When MaxSize * is not sufficient to hold the pixel data the copy is not * executed (i.e. no partial copy). * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ +size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) +{ + int nb, nbu, highBit, sign; -size_t gdcmFile::GetImageDataIntoVector (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) - int nb, nbu, highBit, signe; - std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; - - if ( lgrTotale > MaxSize ) { + if ( PixelRead != -1 ) // File was "read" before + { + RestoreInitialValues(); + } + + PixelRead = 1 ; // PixelRaw + + if ( ImageDataSize > maxSize ) + { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" "than caller's expected MaxSize"); - return (size_t)0; - } - - (void)ReadPixelData(destination); - - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { + return (size_t)0; + } + + ReadPixelData( destination ); + + // Number of Bits Allocated for storing a Pixel + std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); + if ( str_nb == GDCM_UNFOUND ) + { nb = 16; - } else { - nb = atoi(str_nb.c_str() ); } - - // Nombre de Bits Utilises - str_nbu=GetPubElValByNumber(0x0028,0x0101); - if (str_nbu == GDCM_UNFOUND ) { + 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() ); - } - - // Position du Bit de Poids Fort - str_highBit=GetPubElValByNumber(0x0028,0x0102); - if (str_highBit == GDCM_UNFOUND ) { + } + 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() ); } - - // Signe des Pixels - str_signe=GetPubElValByNumber(0x0028,0x0103); - if (str_signe == GDCM_UNFOUND ) { - signe = 1; - } else { - signe = atoi(str_signe.c_str() ); + 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; i> (nb-nbu); - guint16 *deb = (guint16 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; + uint16_t *deb = (uint16_t *)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 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: wierd image"); - return (size_t)0; } - } + else + { + dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); + return 0; + } + } +// DO NOT remove this code commented out. +// Nobody knows what's expecting you ... +// Just to 'see' what was actually read on disk :-( -// Just to 'see' was was actually read on disk :-( -// Some troubles expected +// FILE* f2; +// f2 = fopen("SpuriousFile.RAW","wb"); +// fwrite(destination,ImageDataSize,1,f2); +// fclose(f2); - // *Try* to deal with the color - // ---------------------------- + // Deal with the color + // ------------------- - std::string str_PhotometricInterpretation = - gdcmHeader::GetPubElValByNumber(0x0028,0x0004); - - if ( (str_PhotometricInterpretation == "MONOCHROME1 ") - || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { - return lgrTotale; - } + std::string str_PhotometricInterpretation = + Header->GetEntryByNumber(0x0028,0x0004); + + if ( str_PhotometricInterpretation == "MONOCHROME1 " + || str_PhotometricInterpretation == "MONOCHROME2 " ) + { + return ImageDataSize; + } // Planar configuration = 0 : Pixels are already RGB // Planar configuration = 1 : 3 planes : R, G, B @@ -413,416 +695,250 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( - int planConf=GetPlanarConfiguration(); // 0028,0006 + 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; + // 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 + switch ( planConf ) + { + case 0: + // Pixels are already RGB break; - case 1: - + if (str_PhotometricInterpretation == "YBR_FULL") { - if (str_PhotometricInterpretation == "YBR_FULL") { // Warning : YBR_FULL_422 acts as RGB (?!) - - // need to make RGB Pixels from Planes Y,cB,cR - // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - // for code optimisation - - int l = GetXSize()*GetYSize(); - int nbFrames = 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; - + // 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 - 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; + /// \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,lgrTotale); - free(newDest); - - } else { - - // need to make RGB Pixels from Planes R,G,B - - int l = GetXSize()*GetYSize(); - int nbFrames = GetZSize(); - - char * newDest = (char*) malloc(lgrTotale); - char *x = newDest; - char * a = (char *)destination; - char * b = a + l; - char * c = b + l; - - // TODO : - // any trick not to have to allocate temporary buffer is welcome ... - - for (int i=0;iGetXSize() * 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++); } - - free(newDest); - - } else { - // need to make RGB Pixels (?) - // from grey Pixels (?!) - // and Gray Lut (!?!) - //unsigned char *lutGray =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1200); - - // Well . I'll wait till I find such an image - - // or Segmented Green Palette Color Lookup Table Data and so on - - // Oops! I get one (gdcm-US-ALOKA-16.dcm) - // No idea how to manage it :-( - // Segmented xxx Palette Color are *more* than 65535 long ?!? - - // WARNING : quick and dirty trick to produce a single plane Grey image - // See also gdcmHeaderHelper::GetNumberOfScalarComponents() - lgrTotale /=3; - return lgrTotale; - // end of dirty trick + memmove(destination, newDest, ImageDataSize); + delete[] newDest; } break; - } - } - - // now, it's an RGB image - // Lets's write it in the Header - - // CreateOrReplaceIfExist ? - - std::string spp = "3"; // Samples Per Pixel - gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002); - std::string rgb="RGB "; // Photometric Interpretation - gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004); - std::string planConfig = "0"; // Planar Configuration - gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006); - - // + Drop Palette Color ? - - return lgrTotale; -} - -// -// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs -// - -/** - * \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("valeur de SWAP (16 bits) not allowed : %d\n", swap); - } + 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 -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; + // Droping Palette Color out of the Header + // has been moved to the Write process. - 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; -} + // 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 ?! -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * \brief TODO JPR - * \warning doit-etre etre publique ? - * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions - * - * @param inData - * @param ExpectedSize - * - * @return integer acts as a boolean - */ -int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(1); + 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; } - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief Sets the Pixel Area size in the Header - * --> not-for-rats function - * - * \warning WARNING doit-etre etre publique ? - * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions + * \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 * - * @param ImageDataSize new Pixel Area Size - * warning : nothing else is checked + * @return boolean */ - -void gdcmFile::SetImageDataSize(size_t ImageDataSize) { - std::string content1; - char car[20]; - // Assumes ElValue (0x7fe0, 0x0010) exists ... - sprintf(car,"%d",ImageDataSize); - - gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010); - a->SetLength(ImageDataSize); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetPubElValByNumber(content1, 0x7fe0, 0x0000); +bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize) +{ + Header->SetImageDataSize( expectedSize ); +// FIXME : if already allocated, memory leak ! + Pixel_Data = inData; + ImageDataSize = ImageDataSizeRaw = expectedSize; + PixelRead = 1; +// FIXME : 7fe0, 0010 IS NOT set ... + return true; } - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief Ecrit sur disque 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) - * - * @param fileName - * @return + * \brief Writes on disk A SINGLE Dicom file + * NO test is performed on processor "Endiannity". + * It's up to the user to call his Reader properly + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails */ -int gdcmFile::WriteRawData (std::string fileName) { - FILE * fp1; - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); - return (0); - } - fwrite (PixelData,lgrTotale, 1, fp1); +bool gdcmFile::WriteRawData(std::string const & fileName) +{ + FILE* fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Fail to open (write) file [%s] \n", fileName.c_str()); + return false; + } + fwrite (Pixel_Data, ImageDataSize, 1, fp1); fclose (fp1); - return(1); + + return true; } -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief Ecrit sur disque UNE image Dicom - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * - * @param fileName - * @return int acts as a boolean + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention + * NO test is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmImplVR (std::string fileName) { - return WriteBase(fileName, ImplicitVR); +bool gdcmFile::WriteDcmImplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmImplicitVR); } -///////////////////////////////////////////////////////////////// -/** - * \ingroup gdcmFile - * \brief - * @param fileName - * @return int acts as a boolean - */ - -int gdcmFile::WriteDcmImplVR (const char* fileName) { - return WriteDcmImplVR (std::string (fileName)); -} - -///////////////////////////////////////////////////////////////// /** * \ingroup gdcmFile - * \brief - * @param fileName - * @return int acts as a boolean +* \brief Writes on disk A SINGLE Dicom file, + * using the Explicit Value Representation convention + * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteDcmExplVR (std::string fileName) { - return WriteBase(fileName, ExplicitVR); +bool gdcmFile::WriteDcmExplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmExplicitVR); } - -///////////////////////////////////////////////////////////////// + /** * \ingroup gdcmFile - * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels + * \brief Writes on disk A SINGLE Dicom file, + * using the ACR-NEMA convention + * NO test is performed on processor "Endiannity". * (a l'attention des logiciels cliniques * qui ne prennent en entrée QUE des images ACR ... - * \warning si un header DICOM est fourni en entree, - * les groupes < 0x0008 et les groupes impairs sont ignores) - * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * - * @param fileName - * @return int acts as a boolean + * \warning if a DICOM_V3 header is supplied, + * groups < 0x0008 and shadow groups are ignored + * \warning NO TEST is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ -int gdcmFile::WriteAcr (std::string fileName) { - return WriteBase(fileName, ACR); +bool gdcmFile::WriteAcr (std::string const & fileName) +{ + return WriteBase(fileName, gdcmACR); } -///////////////////////////////////////////////////////////////// +//----------------------------------------------------------------------------- +// Protected /** * \ingroup gdcmFile - * - * @param FileName - * @param type - * - * @return int acts as a boolean + * \brief NOT a end user inteded function + * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @param type file type (ExplicitVR, ImplicitVR, ...) + * @return false if write fails */ -int gdcmFile::WriteBase (std::string FileName, FileType type) { +bool gdcmFile::WriteBase (std::string const & fileName, FileType type) +{ + if ( PixelRead == -1 && type != gdcmExplicitVR) + { + return false; + } - FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); - return (0); + FILE* fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Failed to open (write) File [%s] \n", fileName.c_str()); + return false; } - if ( (type == ImplicitVR) || (type == ExplicitVR) ) { - char * filePreamble; + if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + { // writing Dicom File Preamble - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble, 128, 1, fp1); + fwrite("DICM", 4, 1, fp1); + + delete[] filePreamble; } // -------------------------------------------------------------- @@ -831,17 +947,39 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // if recognition code tells us we dealt with a LibIDO image // we reproduce on disk the switch between lineNumber and columnNumber // just before writting ... + + /// \todo the best trick would be *change* the recognition code + /// but pb expected if user deals with, e.g. COMPLEX images std::string rows, columns; - if ( filetype == ACR_LIBIDO){ - rows = GetPubElValByNumber(0x0028, 0x0010); - columns = GetPubElValByNumber(0x0028, 0x0011); - SetPubElValByNumber(columns, 0x0028, 0x0010); - SetPubElValByNumber(rows , 0x0028, 0x0011); - } - // ----------------- End of Special Patch ---------------- + if ( Header->GetFileType() == gdcmACR_LIBIDO) + { + rows = Header->GetEntryByNumber(0x0028, 0x0010); + columns = Header->GetEntryByNumber(0x0028, 0x0011); - gdcmHeader::Write(fp1, type); + Header->SetEntryByNumber(columns, 0x0028, 0x0010); + Header->SetEntryByNumber(rows , 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- + + uint16_t grPixel = Header->GetGrPixel(); + uint16_t numPixel = Header->GetNumPixel();; + + gdcmDocEntry* PixelElement = + GetHeader()->GetDocEntryByNumber(grPixel, numPixel); + + if ( PixelRead == 1 ) + { + // we read pixel 'as is' (no tranformation LUT -> RGB) + PixelElement->SetLength( ImageDataSizeRaw ); + } + else if ( PixelRead == 0 ) + { + // we tranformed GrayLevel pixels + LUT into RGB Pixel + PixelElement->SetLength( ImageDataSize ); + } + + Header->Write(fp1, type); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -849,13 +987,310 @@ int gdcmFile::WriteBase (std::string FileName, FileType type) { // ...and we restore the Header to be Dicom Compliant again // just after writting - if (filetype == ACR_LIBIDO){ - SetPubElValByNumber(rows , 0x0028, 0x0010); - SetPubElValByNumber(columns, 0x0028, 0x0011); - } + if ( Header->GetFileType() == gdcmACR_LIBIDO ) + { + Header->SetEntryByNumber(rows , 0x0028, 0x0010); + Header->SetEntryByNumber(columns, 0x0028, 0x0011); + } // ----------------- End of Special Patch ---------------- - - fwrite(PixelData, lgrTotale, 1, fp1); + + // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); - return(1); + + return true; +} + +//----------------------------------------------------------------------------- +// Private +/** + * \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) +{ + int i; + + if( nb == 16 ) + { + uint16_t* im16 = (uint16_t*)im; + switch( swap ) + { + 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; + } + } + else if( nb == 32 ) + { + uint32_t s32; + uint16_t fort, faible; + uint32_t* im32 = (uint32_t*)im; + switch ( swap ) + { + 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++) + { + 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; + } + break; + case 3412: + for(i = 0; i < lgr/4; i++) + { + faible = im32[i] & 0x0000ffff; // 3412 + fort = im32[i] >> 16; + s32 = faible; + im32[i] = ( s32 << 16 ) | fort; + } + break; + default: + std::cout << "SWAP value (32 bits) not allowed : " << swap << + std::endl; + } + } +} + +/** + * \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) +{ + FILE* fp = Header->OpenFile(); + + if ( !fp ) + { + 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(); + uint8_t b0, b1, b2; + + uint16_t* pdestination = (uint16_t*)destination; + for(int p = 0; p < nbPixels; p += 2 ) + { + 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 ? + } + + Header->CloseFile(); + return true; + } + + // ---------------------- Uncompressed File + if ( !Header->IsDicomV3() || + Header->IsImplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRLittleEndianTransferSyntax() || + Header->IsExplicitVRBigEndianTransferSyntax() || + Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) + { + size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); + Header->CloseFile(); + if ( ItemRead != 1 ) + { + return false; + } + else + { + return true; + } + } + + // ---------------------- Run Length Encoding + if ( Header->IsRLELossLessTransferSyntax() ) + { + bool res = gdcm_read_RLE_file (fp,destination); + Header->CloseFile(); + return res; + } + + // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 + int nb; + std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); + if ( str_nb == GDCM_UNFOUND ) + { + nb = 16; + } + else + { + nb = atoi( str_nb.c_str() ); + if ( nb == 12 ) + { + nb = 16; // ?? 12 should be ACR-NEMA only + } + } + + int nBytes= nb/8; + int taille = Header->GetXSize() * Header->GetYSize() + * Header->GetSamplesPerPixel(); + long fragmentBegining; // for ftell, fseek + + bool jpg2000 = Header->IsJPEG2000(); + bool jpgLossless = Header->IsJPEGLossless(); + + bool res = true; + uint16_t ItemTagGr, ItemTagEl; + int ln; + + // Position on begining of Jpeg Pixels + + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if(Header->GetSwapCode()) + { + ItemTagGr = Header->SwapShort(ItemTagGr); + ItemTagEl = Header->SwapShort(ItemTagEl); + } + + fread(&ln,4,1,fp); + if( Header->GetSwapCode() ) + { + ln = Header->SwapLong( ln ); // Basic Offset Table Item length + } + + if ( ln != 0 ) + { + // What is it used for ?!? + uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1]; + fread(BasicOffsetTableItemValue,ln,1,fp); + //delete[] BasicOffsetTableItemValue; + } + + // first Fragment initialisation + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if( Header->GetSwapCode() ) + { + ItemTagGr = Header->SwapShort( ItemTagGr ); + ItemTagEl = Header->SwapShort( ItemTagEl ); + } + + // parsing fragments until Sequence Delim. Tag found + while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd ) + { + // --- for each Fragment + fread(&ln,4,1,fp); + if( Header->GetSwapCode() ) + { + ln = Header->SwapLong(ln); // Fragment Item length + } + fragmentBegining = ftell( fp ); + + if ( jpg2000 ) + { + // JPEG 2000 : call to ??? + res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written + // ------------------------------------- endif (JPEG2000) + } + else if (jpgLossless) + { + // JPEG LossLess : call to xmedcom Lossless JPEG + // Reading Fragment pixels + JPEGLosslessDecodeImage (fp, (uint16_t*)destination, + Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln); + res = 1; // in order not to break the loop + + } // ------------------------------------- endif (JPEGLossless) + else + { + // JPEG Lossy : call to IJG 6b + if ( Header->GetBitsStored() == 8) + { + // Reading Fragment pixels + res = gdcm_read_JPEG_file (fp,destination); + } + else + { + // Reading Fragment pixels + res = gdcm_read_JPEG_file12 (fp,destination); + } + // ------------------------------------- endif (JPEGLossy) + } + + if ( !res ) + { + break; + } + + // location in user's memory + // for next fragment (if any) + destination = (uint8_t*)destination + taille * nBytes; + + fseek(fp,fragmentBegining, SEEK_SET); // To be sure we start + fseek(fp,ln,SEEK_CUR); // at the begining of next fragment + + ItemTagGr = ItemTagEl = 0; + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if( Header->GetSwapCode() ) + { + ItemTagGr = Header->SwapShort( ItemTagGr ); + ItemTagEl = Header->SwapShort( ItemTagEl ); + } + } + // endWhile parsing fragments until Sequence Delim. Tag found + + Header->CloseFile(); + return res; } +//-----------------------------------------------------------------------------