/*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ Date: $Date: 2004/06/28 14:12:03 $ Version: $Revision: 1.112 $ 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 "gdcmDebug.h" #include "jpeg/ljpg/jpegless.h" typedef std::pair IterHT; //----------------------------------------------------------------------------- // Constructor / Destructor /** * \ingroup gdcmFile * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant * file (see SetFileName, SetDcmTag and Write) * 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 * 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 header file to be opened for reading datas * @return */ gdcmFile::gdcmFile(gdcmHeader *header) { Header = header; SelfHeader = false; PixelRead = -1; // no ImageData read yet. if (Header->IsReadable()) { SetPixelDataSizeFromHeader(); } } /** * \ingroup gdcmFile * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant * file (see SetFileName, SetDcmTag and Write) * 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 * the DICOM header is post-poned to first header information access. * This avoid a double parsing of public part of the header when * one sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). * @param filename file to be opened for parsing * @param exception_on_error whether we throw an exception or not * @param enable_sequences = true to allow the header * to be parsed *inside* the SeQuences, * when they have an actual length * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files * @param ignore_shadow to allow skipping the shadow elements, * to save memory space. * \warning The TRUE value for this param has to be used * with a FALSE value for the 'enable_sequence' param. * ('public elements' may be embedded in 'shadow Sequences') */ gdcmFile::gdcmFile(std::string const & filename, bool exception_on_error, bool enable_sequences, bool ignore_shadow) { Header = new gdcmHeader( filename, exception_on_error, enable_sequences, ignore_shadow ); SelfHeader = true; PixelRead = -1; // no ImageData read yet. if ( Header->IsReadable() ) { SetPixelDataSizeFromHeader(); } } /** * \ingroup gdcmFile * \brief canonical destructor * \note If the gdcmHeader is created by the gdcmFile, it is destroyed * by the gdcmFile */ gdcmFile::~gdcmFile() { if( SelfHeader ) { delete Header; } Header = 0; } //----------------------------------------------------------------------------- // Print //----------------------------------------------------------------------------- // Public /** * \ingroup gdcmFile * \brief computes the length (in bytes) to ALLOCATE to receive the * image(s) pixels (multiframes taken into account) * \warning : it is NOT the group 7FE0 length * (no interest for compressed images). * @return length to allocate */ void gdcmFile::SetPixelDataSizeFromHeader() { // 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 ) { 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. */ size_t gdcmFile::GetImageDataSize() { return ImageDataSize; } /** * \ingroup gdcmFile * \brief Returns the size (in bytes) of required memory to hold * the pixel data represented in this file, when user DOESN'T want * to get RGB pixels image when it's stored as a PALETTE COLOR image * -the (vtk) user is supposed to know how deal with LUTs- * \warning to be used with GetImagePixelsRaw() * @return The size of pixel data in bytes. */ size_t gdcmFile::GetImageDataSizeRaw() { return ImageDataSizeRaw; } /** * \ingroup gdcmFile * \brief Allocates necessary memory, copies the pixel data * (image[s]/volume[s]) to newly allocated zone. * Transforms YBR pixels into RGB pixels if any * Transforms 3 planes R, G, B into a single RGB Plane * Transforms single Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ void *gdcmFile::GetImageData() { // FIXME // I need to deallocate PixelData before doing any allocation: PixelData = new uint8_t[ImageDataSize]; if ( PixelData ) { GetImageDataIntoVector(PixelData, ImageDataSize); GetHeader()->SetEntryVoidAreaByNumber( PixelData, GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } PixelRead = 0; // no PixelRaw return PixelData; } /** * \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 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) { //size_t l = GetImageDataIntoVectorRaw (destination, maxSize); GetImageDataIntoVectorRaw (destination, maxSize); PixelRead = 0 ; // no PixelRaw 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; //int l = ImageDataSizeRaw; //loss of precision // 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); } else //why is there a 'else' when an allocation failed ? { // need to make RGB Pixels (?) // from grey Pixels (?!) // and Gray Lut (!?!) // or Segmented xxx Palette Color Lookup Table Data and so on // Oops! I get one (gdcm-US-ALOKA-16.dcm) // No idea how to manage such an image // It seems that *no Dicom Viewer* has any idea :-( // Segmented xxx Palette Color are *more* than 65535 long ?!? std::string rgb = "MONOCHROME1 "; // Photometric Interpretation Header->SetEntryByNumber(rgb,0x0028,0x0004); } /// \todo Drop Palette Color out of the Header? return ImageDataSize; } /** * \ingroup gdcmFile * \brief Allocates necessary memory, copies the pixel data * (image[s]/volume[s]) to newly allocated zone. * Transforms YBR pixels into RGB pixels if any * Transforms 3 planes R, G, B into a single RGB Plane * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ void * gdcmFile::GetImageDataRaw () { size_t imgDataSize = ImageDataSize; if ( Header->HasLUT() ) { /// \todo Let gdcmHeader user a chance to get the right value // ImageDataSize /= 3; //dangerous imgDataSize = ImageDataSizeRaw; } // FIXME // I need to deallocate PixelData before doing any allocation: PixelData = new uint8_t[imgDataSize]; if ( PixelData ) { GetImageDataIntoVectorRaw(PixelData, ImageDataSize); GetHeader()->SetEntryVoidAreaByNumber(PixelData, GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } PixelRead = 1; // PixelRaw return PixelData; } /** * \ingroup gdcmFile * \brief Copies at most MaxSize bytes of pixel data to caller's * memory space. * \warning This function was designed to avoid people that want to build * a volume from an image stack to need first to get the image pixels * and then move them to the volume area. * It's absolutely useless for any VTK user since vtk chooses * to invert the lines of an image, that is the last line comes first * (for some axis related reasons?). Hence he will have * to load the image line by line, starting from the end. * VTK users hace to call GetImageData * \warning DOES NOT transform the Grey Plane + Palette Color (if any) * into a single RGB Pixels Plane * the (VTK) user will manage the palettes * * @param destination Address (in caller's memory space) at which the * pixel data should be copied * @param MaxSize Maximum number of bytes to be copied. When MaxSize * is not sufficient to hold the pixel data the copy is not * executed (i.e. no partial copy). * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize) { int nb, nbu, highBit, sign; PixelRead = 1 ; // PixelRaw if ( ImageDataSize > maxSize ) { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" "than caller's expected MaxSize"); return (size_t)0; } ReadPixelData( destination ); // Number of Bits Allocated for storing a Pixel std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); if ( str_nb == GDCM_UNFOUND ) { 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; i> (nb-nbu); 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 { 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 :-( // FILE * f2; // f2 = fopen("SpuriousFile.RAW","wb"); // fwrite(destination,ImageDataSize,1,f2); // fclose(f2); // Deal with the color // ------------------- 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 // Planar configuration = 2 : 1 gray Plane + 3 LUT // Well ... supposed to be ! // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0, // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( int planConf = Header->GetPlanarConfiguration(); // 0028,0006 // Whatever Planar Configuration is, // "PALETTE COLOR " implies that we deal with the palette. if ( str_PhotometricInterpretation == "PALETTE COLOR ") { planConf = 2; } switch ( planConf ) { case 0: // Pixels are already RGB break; case 1: if (str_PhotometricInterpretation == "YBR_FULL") { // Warning : YBR_FULL_422 acts as RGB // : we need to make RGB Pixels from Planes Y,cB,cR // to see the tricks about YBR_FULL, YBR_FULL_422, // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf // and be *very* affraid // int l = Header->GetXSize() * Header->GetYSize(); int nbFrames = Header->GetZSize(); 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 // CreateOrReplaceIfExist ? std::string spp = "3"; // Samples Per Pixel std::string rgb = "RGB "; // Photometric Interpretation std::string planConfig = "0"; // Planar Configuration Header->SetEntryByNumber(spp,0x0028,0x0002); Header->SetEntryByNumber(rgb,0x0028,0x0004); Header->SetEntryByNumber(planConfig,0x0028,0x0006); /// \todo Drop Palette Color out of the Header? return ImageDataSize; } /** * \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 : lane 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 */ bool gdcmFile::SetImageData(void *inData, size_t expectedSize) { Header->SetImageDataSize( expectedSize ); PixelData = inData; ImageDataSize = expectedSize; PixelRead = 1; return true; } /** * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file * NO test is performed on processor "Endiannity". * It's up to the user to call his Reader properly * @param fileName name of the file to be created * (any already existing file is over written) * @return false if write fails */ bool gdcmFile::WriteRawData(std::string const & fileName) { FILE *fp1; fp1 = fopen(fileName.c_str(), "wb"); if (fp1 == NULL) { printf("Fail to open (write) file [%s] \n", fileName.c_str()); return false; } fwrite (PixelData,ImageDataSize, 1, fp1); fclose (fp1); return true; } /** * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the Implicit Value Representation convention * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created * (any already existing file is overwritten) * @return false if write fails */ bool gdcmFile::WriteDcmImplVR (std::string const & fileName) { return WriteBase(fileName, gdcmImplicitVR); } /** * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the Explicit Value Representation convention * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created * (any already existing file is overwritten) * @return false if write fails */ bool gdcmFile::WriteDcmExplVR (std::string const & fileName) { return WriteBase(fileName, gdcmExplicitVR); } /** * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the ACR-NEMA convention * NO test is performed on processor "Endiannity". * (a l'attention des logiciels cliniques * qui ne prennent en entrée QUE des images ACR ... * \warning if a DICOM_V3 header is supplied, * groups < 0x0008 and shadow groups are ignored * \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 */ bool gdcmFile::WriteAcr (std::string const & fileName) { return WriteBase(fileName, gdcmACR); } //----------------------------------------------------------------------------- // Protected /** * \ingroup gdcmFile * \brief NOT a end user inteded function * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) * @param fileName name of the file to be created * (any already existing file is overwritten) * @param type file type (ExplicitVR, ImplicitVR, ...) * @return false if write fails */ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { FILE *fp1; if ( PixelRead == -1 && type != gdcmExplicitVR) { return false; } fp1 = fopen(fileName.c_str(), "wb"); if (fp1 == NULL) { printf("Failed to open (write) File [%s] \n", fileName.c_str()); return false; } if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) { // 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; } // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images // // if recognition code tells us we dealt with a LibIDO image // we reproduce on disk the switch between lineNumber and columnNumber // just before writting ... /// \todo the best trick would be *change* the recognition code /// but pb expected if user deals with, e.g. COMPLEX images std::string rows, columns; if ( Header->GetFileType() == gdcmACR_LIBIDO) { rows = Header->GetEntryByNumber(0x0028, 0x0010); columns = Header->GetEntryByNumber(0x0028, 0x0011); Header->SetEntryByNumber(columns, 0x0028, 0x0010); Header->SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only) uint16_t grPixel = Header->GetGrPixel(); uint16_t numPixel = Header->GetNumPixel();; // Update Pixel Data Length // the *last* of the (GrPixel, NumPixel), if many. TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel); TagDocEntryHT::iterator p2; gdcmDocEntry* PixelElement; IterHT it = Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym if ( Header->GetEntry().count(key) == 1 ) // only the first is significant { p2 = it.first; // iterator on the first (unique) synonym } else { p2 = it.second;// iterator on the last synonym } PixelElement = p2->second; // H Table target column (2-nd col) // PixelElement->SetPrintLevel(2); // PixelElement->Print(); if ( PixelRead == 1 ) { PixelElement->SetLength( ImageDataSizeRaw ); } else if ( PixelRead == 0 ) { PixelElement->SetLength( ImageDataSize ); } //PixelElement->SetPrintLevel(2); //PixelElement->Print(); Header->Write(fp1, type); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images // // ...and we restore the Header to be Dicom Compliant again // just after writting if ( Header->GetFileType() == gdcmACR_LIBIDO ) { Header->SetEntryByNumber(rows , 0x0028, 0x0010); Header->SetEntryByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); return true; } //----------------------------------------------------------------------------- // Private /** * \ingroup gdcmFile * \brief Swap the bytes, according to swap code. * \warning not end user intended * @param im area to deal with * @param swap swap code * @param lgr Area Length * @param nb Pixels Bit number */ void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) { 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 = (bool)gdcm_read_RLE_file (fp,destination); Header->CloseFile(); return res; } // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 int nb; std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); if ( str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi( str_nb.c_str() ); if ( nb == 12 ) { nb = 16; // ?? 12 should be ACR-NEMA only } } int nBytes= nb/8; int taille = Header->GetXSize() * Header->GetYSize() * Header->GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek bool jpg2000 = Header->IsJPEG2000(); bool jpgLossless = Header->IsJPEGLossless(); bool res = true; 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 = (bool)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 = (bool)gdcm_read_JPEG_file (fp,destination); } else { // Reading Fragment pixels res = (bool)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; } //-----------------------------------------------------------------------------