X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=9e6788e6dc945d4df6e31f1448831cd955cd3e1d;hb=be54aab0103af7dee1a3bb5b8b3ee93b59ca9073;hp=3de485f7c2057e172f551cbfa691f022e85f109f;hpb=6a800bd81da33ac35002fe93583d2bf319ee69f4;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 3de485f7..9e6788e6 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,10 +1,10 @@ - /*========================================================================= +/*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/12/07 09:32:24 $ - Version: $Revision: 1.172 $ + Date: $Date: 2005/01/24 16:44:54 $ + Version: $Revision: 1.199 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -17,759 +17,1385 @@ =========================================================================*/ #include "gdcmFile.h" -#include "gdcmDocument.h" -#include "gdcmDebug.h" +#include "gdcmGlobal.h" #include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmValEntry.h" #include "gdcmBinEntry.h" -#include "gdcmHeader.h" -#include "gdcmPixelReadConvert.h" -#include "gdcmPixelWriteConvert.h" -#include "gdcmDocEntryArchive.h" +#include //sscanf -#include +#include namespace gdcm { -typedef std::pair IterHT; - -//------------------------------------------------------------------------- +//----------------------------------------------------------------------------- // Constructor / Destructor /** - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (Header only deals with the ... header) - * Opens (in read only and when possible) an existing file and checks - * for DICOM compliance. Returns NULL on failure. - * It will be up to the user to load the pixels into memory - * (see GetImageData, GetImageDataRaw) - * \note the in-memory representation of all available tags found in - * the DICOM header is post-poned to first header information access. - * This avoid a double parsing of public part of the header when - * user sets an a posteriori shadow dictionary (efficiency can be - * seen as a side effect). - * @param header already built Header + * \brief Constructor + * @param filename name of the file whose header we want to analyze */ -File::File(Header *header) -{ - HeaderInternal = header; - SelfHeader = false; - Initialise(); +File::File( std::string const &filename ): + Document( filename ) +{ + // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 + // We may encounter the 'RETired' (0x0028, 0x0200) tag + // (Image Location") . This entry contains the number of + // the group that contains the pixel data (hence the "Pixel Data" + // is found by indirection through the "Image Location"). + // Inside the group pointed by "Image Location" the searched element + // is conventionally the element 0x0010 (when the norm is respected). + // When the "Image Location" is missing we default to group 0x7fe0. + // Note: this IS the right place for the code + + // Image Location + const std::string &imgLocation = GetEntryValue(0x0028, 0x0200); + if ( imgLocation == GDCM_UNFOUND ) + { + // default value + GrPixel = 0x7fe0; + } + else + { + GrPixel = (uint16_t) atoi( imgLocation.c_str() ); + } + + // sometimes Image Location value doesn't follow + // the supposed processor endianness. + // see gdcmData/cr172241.dcm + if ( GrPixel == 0xe07f ) + { + GrPixel = 0x7fe0; + } + + if ( GrPixel != 0x7fe0 ) + { + // This is a kludge for old dirty Philips imager. + NumPixel = 0x1010; + } + else + { + NumPixel = 0x0010; + } + + // Now, we know GrPixel and NumPixel. + // Let's create a VirtualDictEntry to allow a further VR modification + // and force VR to match with BitsAllocated. + DocEntry *entry = GetDocEntry(GrPixel, NumPixel); + if ( entry != 0 ) + { + + std::string PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + + DictEntry* newEntry = NewVirtualDictEntry( + GrPixel, NumPixel, + PixelVR, "PXL", "Pixel Data"); + + // friend class hunting : should we *create* a new entry, + // instead of modifying its DictEntry,in order not to use 'friend' ? + entry->SetDictEntry( newEntry ); + } } /** - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (Header only deals with the ... header) - * Opens (in read only and when possible) an existing file and checks - * for DICOM compliance. Returns NULL on failure. - * It will be up to the user to load the pixels into memory - * (see GetImageData, GetImageDataRaw) - * \note the in-memory representation of all available tags found in - * the DICOM header is post-poned to first header information access. - * This avoid a double parsing of public part of the header when - * one sets an a posteriori shadow dictionary (efficiency can be - * seen as a side effect). - * @param filename file to be opened for parsing + * \brief Constructor used when we want to generate dicom files from scratch */ -File::File(std::string const & filename ) +File::File() + :Document() { - HeaderInternal = new Header( filename ); - SelfHeader = true; - Initialise(); + InitializeDefaultFile(); } /** - * \brief Factorization for various forms of constructors. + * \brief Canonical destructor. */ -void File::Initialise() +File::~File () { - WriteMode = WMODE_DECOMPRESSED; - WriteType = ImplicitVR; +} - PixelReadConverter = new PixelReadConvert; - PixelWriteConverter = new PixelWriteConvert; - Archive = new DocEntryArchive( HeaderInternal ); +/** + * \brief Performs some consistency checking on various 'File related' + * (as opposed to 'DicomDir related') entries + * then writes in a file all the (Dicom Elements) included the Pixels + * @param fileName file name to write to + * @param filetype Type of the File to be written + * (ACR, ExplicitVR, ImplicitVR) + */ +bool File::Write(std::string fileName, FileType filetype) +{ + std::ofstream *fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (*fp == NULL) + { + gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str()); + return false; + } - if ( HeaderInternal->IsReadable() ) + // Bits Allocated + if ( GetEntryValue(0x0028,0x0100) == "12") { - PixelReadConverter->GrabInformationsFromHeader( HeaderInternal ); + SetEntryValue("16", 0x0028,0x0100); } -} -/** - * \brief canonical destructor - * \note If the Header was created by the File constructor, - * it is destroyed by the File - */ -File::~File() -{ - if( PixelReadConverter ) + /// \todo correct 'Pixel group' Length if necessary + + int i_lgPix = GetEntryLength(GrPixel, NumPixel); + if (i_lgPix != -2) { - delete PixelReadConverter; + // no (GrPixel, NumPixel) element + std::string s_lgPix = Util::Format("%d", i_lgPix+12); + s_lgPix = Util::DicomString( s_lgPix.c_str() ); + Insert(s_lgPix,GrPixel, 0x0000); } - if( PixelWriteConverter ) + + // FIXME : should be nice if we could move it to File + // (or in future gdcmPixelData class) + + // Drop Palette Color, if necessary + + if ( GetEntryValue(0x0028,0x0002).c_str()[0] == '3' ) { - delete PixelWriteConverter; + // if SamplesPerPixel = 3, sure we don't need any LUT ! + // Drop 0028|1101, 0028|1102, 0028|1103 + // Drop 0028|1201, 0028|1202, 0028|1203 + + DocEntry *e = GetDocEntry(0x0028,0x01101); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1102); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1103); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x01201); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1202); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1203); + if (e) + { + RemoveEntryNoDestroy(e); + } } - if( Archive ) + +/* +#ifdef GDCM_WORDS_BIGENDIAN + // Super Super hack that will make gdcm a BOMB ! but should + // Fix temporarily the dashboard + BinEntry *b = GetBinEntry(GrPixel,NumPixel); + if ( GetPixelSize() == 16 ) { - delete Archive; + uint16_t *im16 = (uint16_t*)b->GetBinArea(); + int lgr = b->GetLength(); + for( int i = 0; i < lgr / 2; i++ ) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } } +#endif //GDCM_WORDS_BIGENDIAN +*/ - if( SelfHeader ) + Document::WriteContent(fp,filetype); + +/* +#ifdef GDCM_WORDS_BIGENDIAN + // Flip back the pixel ... I told you this is a hack + if ( GetPixelSize() == 16 ) { - delete HeaderInternal; + uint16_t *im16 = (uint16_t*)b->GetBinArea(); + int lgr = b->GetLength(); + for( int i = 0; i < lgr / 2; i++ ) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } } - HeaderInternal = 0; +#endif //GDCM_WORDS_BIGENDIAN +*/ + + fp->close(); + delete fp; + + return true; } //----------------------------------------------------------------------------- // Print + //----------------------------------------------------------------------------- // Public + /** - * \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 + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current File was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable Dicom/Acr File. + * @return true when File is the one of a reasonable Dicom/Acr file, + * false otherwise. */ -size_t File::GetImageDataSize() +bool File::IsReadable() { - return PixelReadConverter->GetRGBSize(); + if( !Document::IsReadable() ) + { + return false; + } + + const std::string &res = GetEntryValue(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { + return false; // Image Dimensions + } + if ( !GetDocEntry(0x0028, 0x0100) ) + { + return false; // "Bits Allocated" + } + if ( !GetDocEntry(0x0028, 0x0101) ) + { + return false; // "Bits Stored" + } + if ( !GetDocEntry(0x0028, 0x0102) ) + { + return false; // "High Bit" + } + if ( !GetDocEntry(0x0028, 0x0103) ) + { + return false; // "Pixel Representation" i.e. 'Sign' + } + + return true; } /** - * \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 + * \brief Retrieve the number of columns of image. + * @return The encountered size when found, 0 by default. + * 0 means the file is NOT USABLE. The caller will have to check */ -size_t File::GetImageDataRawSize() +int File::GetXSize() { - return PixelReadConverter->GetDecompressedSize(); + const std::string &strSize = GetEntryValue(0x0028,0x0011); + if ( strSize == GDCM_UNFOUND ) + { + return 0; + } + + return atoi( strSize.c_str() ); } /** - * \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 + * \brief Retrieve the number of lines of image. + * \warning The defaulted value is 1 as opposed to File::GetXSize() + * @return The encountered size when found, 1 by default + * (The ACR-NEMA file contains a Signal, not an Image). */ -uint8_t* File::GetImageData() +int File::GetYSize() { - if ( ! GetDecompressed() ) + const std::string &strSize = GetEntryValue(0x0028,0x0010); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } + if ( IsDicomV3() ) { - // If the decompression failed nothing can be done. return 0; } - if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) + // The Rows (0028,0010) entry was optional for ACR/NEMA. It might + // hence be a signal (1D image). So we default to 1: + return 1; +} + +/** + * \brief Retrieve the number of planes of volume or the number + * of frames of a multiframe. + * \warning When present we consider the "Number of Frames" as the third + * dimension. When Missing we consider the third dimension as + * being the ACR-NEMA "Planes" tag content. + * @return The encountered size when found, 1 by default (single image). + */ +int File::GetZSize() +{ + // Both DicomV3 and ACR/Nema consider the "Number of Frames" + // as the third dimension. + const std::string &strSize = GetEntryValue(0x0028,0x0008); + if ( strSize != GDCM_UNFOUND ) { - return PixelReadConverter->GetRGB(); + return atoi( strSize.c_str() ); } - else + + // We then consider the "Planes" entry as the third dimension + const std::string &strSize2 = GetEntryValue(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) { - // When no LUT or LUT conversion fails, return the decompressed - return PixelReadConverter->GetDecompressed(); - } -} - -/** - * \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 File::GetImageDataIntoVector (void* destination, size_t maxSize) -{ - if ( ! GetDecompressed() ) - { - // If the decompression failed nothing can be done. - return 0; + return atoi( strSize2.c_str() ); + } + + return 1; +} + +/** + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return X dimension of a pixel + */ +float File::GetXSpacing() +{ + float xspacing, yspacing; + const std::string &strSpacing = GetEntryValue(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" ); + return 1.; } - if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) + int nbValues; + if( ( nbValues = sscanf( strSpacing.c_str(), + "%f\\%f", &yspacing, &xspacing)) != 2 ) { - if ( PixelReadConverter->GetRGBSize() > maxSize ) + // if single value is found, xspacing is defaulted to yspacing + if ( nbValues == 1 ) { - dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return 0; + xspacing = yspacing; } - memcpy( destination, - (void*)PixelReadConverter->GetRGB(), - PixelReadConverter->GetRGBSize() ); - return PixelReadConverter->GetRGBSize(); + + if ( xspacing == 0.0 ) + xspacing = 1.0; + + return xspacing; + } - // Either no LUT conversion necessary or LUT conversion failed - if ( PixelReadConverter->GetDecompressedSize() > maxSize ) + // to avoid troubles with David Clunie's-like images + if ( xspacing == 0. && yspacing == 0.) + return 1.; + + if ( xspacing == 0.) { - dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return 0; + gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem"); + // seems to be a bug in the header ... + nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + gdcmAssertMacro( nbValues == 2 ); } - memcpy( destination, - (void*)PixelReadConverter->GetDecompressed(), - PixelReadConverter->GetDecompressedSize() ); - return PixelReadConverter->GetDecompressedSize(); + + return xspacing; } /** - * \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 - */ -uint8_t* File::GetImageDataRaw () + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float File::GetYSpacing() { - return GetDecompressed(); -} + float yspacing = 1.; + std::string strSpacing = GetEntryValue(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)"); + return 1.; + } + + // if sscanf cannot read any float value, it won't affect yspacing + sscanf( strSpacing.c_str(), "%f", &yspacing); + + if ( yspacing == 0.0 ) + yspacing = 1.0; -uint8_t* File::GetDecompressed() + return yspacing; +} + +/** + * \brief gets the info from 0018,0088 : Space Between Slices + * else from 0018,0050 : Slice Thickness + * else 1.0 + * @return Z dimension of a voxel-to be + */ +float File::GetZSpacing() { - uint8_t* decompressed = PixelReadConverter->GetDecompressed(); - if ( ! decompressed ) - { - // The decompressed image migth not be loaded yet: - std::ifstream* fp = HeaderInternal->OpenFile(); - PixelReadConverter->ReadAndDecompressPixelData( fp ); - if(fp) - HeaderInternal->CloseFile(); + // Spacing Between Slices : distance entre le milieu de chaque coupe + // Les coupes peuvent etre : + // jointives (Spacing between Slices = Slice Thickness) + // chevauchantes (Spacing between Slices < Slice Thickness) + // disjointes (Spacing between Slices > Slice Thickness) + // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal + // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... + // Si le Spacing Between Slices est Missing, + // on suppose que les coupes sont jointives + + const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); - decompressed = PixelReadConverter->GetDecompressed(); - if ( ! decompressed ) + if ( strSpacingBSlices == GDCM_UNFOUND ) + { + gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)"); + const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050); + if ( strSliceThickness == GDCM_UNFOUND ) { - dbg.Verbose(0, "File::GetDecompressed: read/decompress of " - "pixel data apparently went wrong."); - return 0; + gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)"); + return 1.; + } + else + { + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + // if they don't, we're fucked up + return (float)atof( strSliceThickness.c_str() ); } } - - return decompressed; + //else + return (float)atof( strSpacingBSlices.c_str() ); } /** - * \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 + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept */ -bool File::SetImageData(uint8_t* inData, size_t expectedSize) +float File::GetRescaleIntercept() { - PixelWriteConverter->SetUserData(inData,expectedSize); + float resInter = 0.; + /// 0028 1052 DS IMG Rescale Intercept + const std::string &strRescInter = GetEntryValue(0x0028,0x1052); + if ( strRescInter != GDCM_UNFOUND ) + { + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + { + // bug in the element 0x0028,0x1052 + gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." ); + } + } - return true; + return resInter; } /** - * \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 + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope */ - -bool File::WriteRawData(std::string const & fileName) +float File::GetRescaleSlope() { - std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); - if (!fp1) + float resSlope = 1.; + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryValue(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) { - dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); - return false; + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + { + // bug in the element 0x0028,0x1053 + gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty."); + } } - if(PixelWriteConverter->GetUserData()) - fp1.write((char*)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize()); - else if(PixelReadConverter->GetRGB()) - fp1.write((char*)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); - else if(PixelReadConverter->GetDecompressed()) - fp1.write((char*)PixelReadConverter->GetDecompressed(), PixelReadConverter->GetDecompressedSize()); - - fp1.close(); - - return true; + return resSlope; } /** - * \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 + * \brief This function is intended to user who doesn't want + * to have to manage a LUT and expects to get an RBG Pixel image + * (or a monochrome one ...) + * \warning to be used with GetImagePixels() + * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) */ - -bool File::WriteDcmImplVR (std::string const & fileName) +int File::GetNumberOfScalarComponents() { - SetWriteTypeToDcmImplVR(); - return Write(fileName); -} + if ( GetSamplesPerPixel() == 3 ) + { + return 3; + } + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryValue(0x0028,0x0100) == "24" ) + { + return 3; + } + + std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); -/** -* \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 - */ + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) + { + if ( HasLUT() )// PALETTE COLOR is NOT enough + { + return 3; + } + else + { + return 1; + } + } -bool File::WriteDcmExplVR (std::string const & fileName) -{ - SetWriteTypeToDcmExplVR(); - return Write(fileName); + // beware of trailing space at end of string + // DICOM tags are never of odd length + if ( strPhotometricInterpretation == GDCM_UNFOUND || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") ) + { + return 1; + } + else + { + // we assume that *all* kinds of YBR are dealt with + return 3; + } } /** - * \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 + * \brief This function is intended to user that 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 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) */ - -bool File::WriteAcr (std::string const & fileName) +int File::GetNumberOfScalarComponentsRaw() { - SetWriteTypeToAcr(); - return Write(fileName); -} + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( File::GetEntryValue(0x0028,0x0100) == "24" ) + { + return 3; + } -bool File::Write(std::string const& fileName) -{ - return WriteBase(fileName); + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); } -bool File::SetEntryByNumber(std::string const& content, - uint16_t group, uint16_t element) -{ - HeaderInternal->SetEntryByNumber(content,group,element); - return true; -} +// +// -------------- Remember ! ---------------------------------- +// +// Image Position Patient (0020,0032): +// If not found (ACR_NEMA) we try Image Position (0020,0030) +// If not found (ACR-NEMA), we consider Slice Location (0020,1041) +// or Location (0020,0050) +// as the Z coordinate, +// 0. for all the coordinates if nothing is found + +// \todo find a way to inform the caller nothing was found +// \todo How to tell the caller a wrong number of values was found? +// +// --------------------------------------------------------------- +// /** - * \brief Access to the underlying \ref PixelReadConverter RGBA LUT + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner X position */ -uint8_t* File::GetLutRGBA() +float File::GetXOrigin() { - return PixelReadConverter->GetLutRGBA(); -} + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); -//----------------------------------------------------------------------------- -// Protected -/** - * \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 File::WriteBase (std::string const & fileName) -{ - switch(WriteType) - { - case ImplicitVR: - SetWriteFileTypeToImplicitVR(); - break; - case ExplicitVR: - SetWriteFileTypeToExplicitVR(); - break; - case ACR: - case ACR_LIBIDO: - SetWriteFileTypeToACR(); - break; - default: - SetWriteFileTypeToExplicitVR(); - } - - // -------------------------------------------------------------- - // 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 - if( WriteType == ACR_LIBIDO ) - { - SetWriteToLibido(); - } - else + if ( strImPos == GDCM_UNFOUND ) { - SetWriteToNoLibido(); + gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? + return 0.; + } } - // ----------------- End of Special Patch ---------------- - - switch(WriteMode) + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) { - case WMODE_DECOMPRESSED : - SetWriteToDecompressed(); - break; - case WMODE_RGB : - SetWriteToRGB(); - break; + return 0.; } - bool check = CheckWriteIntegrity(); - if(check) + return xImPos; +} + +/** + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner Y position + */ +float File::GetYOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) { - check = HeaderInternal->Write(fileName,WriteType); + gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? + return 0.; + } } - 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 - RestoreWriteOfLibido(); - // ----------------- End of Special Patch ---------------- + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } - return check; + return yImPos; } /** - * \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 + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else from 0020,1041 : Slice Location + * else from 0020,0050 : Location + * else 0. + * @return up-left image corner Z position */ -bool File::CheckWriteIntegrity() +float File::GetZOrigin() { - if(PixelWriteConverter->GetUserData()) + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos != GDCM_UNFOUND ) { - int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); - if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - numberBitsAllocated = 16; + gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)"); + return 0.; // bug in the element 0x0020,0x0032 } - - 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) + else { - case WMODE_DECOMPRESSED : - if( decSize!=PixelWriteConverter->GetUserDataSize() ) - { - dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); - return false; - } - break; - case WMODE_RGB : - if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) - { - dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); - return false; - } - break; + return zImPos; } } - - return true; -} -void File::SetWriteToDecompressed() -{ - if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos != GDCM_UNFOUND ) { - SetWriteToRGB(); - } - else + if( sscanf( strImPos.c_str(), + "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) + { + gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)"); + return 0.; // bug in the element 0x0020,0x0032 + } + else + { + return zImPos; + } + } + + std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images + if ( strSliceLocation != GDCM_UNFOUND ) { - ValEntry* photInt = CopyValEntry(0x0028,0x0004); - if(HeaderInternal->HasLUT()) + if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) { - photInt->SetValue("PALETTE COLOR "); - photInt->SetLength(14); + gdcmVerboseMacro( "Wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 } else { - photInt->SetValue("MONOCHROME1 "); - photInt->SetLength(12); + return zImPos; } + } + gdcmVerboseMacro( "Unfound Slice Location (0020,1041)"); - PixelWriteConverter->SetReadData(PixelReadConverter->GetDecompressed(), - PixelReadConverter->GetDecompressedSize()); + std::string strLocation = GetEntryValue(0x0020,0x0050); + if ( strLocation != GDCM_UNFOUND ) + { + if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) + { + gdcmVerboseMacro( "Wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 + } + else + { + return zImPos; + } + } + gdcmVerboseMacro( "Unfound Location (0020,0050)"); - BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); - pixel->SetBinArea(PixelWriteConverter->GetData(),false); - pixel->SetLength(PixelWriteConverter->GetDataSize()); + return 0.; // Hopeless +} - Archive->Push(photInt); - Archive->Push(pixel); +/** + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +int File::GetImageNumber() +{ + // The function i atoi() takes the address of an area of memory as + // parameter and converts the string stored at that location to an integer + // using the external decimal to internal binary conversion rules. This may + // be preferable to sscanf() since atoi() is a much smaller, simpler and + // faster function. sscanf() can do all possible conversions whereas + // atoi() can only do single decimal integer conversions. + //0020 0013 IS REL Image Number + std::string strImNumber = GetEntryValue(0x0020,0x0013); + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); } + return 0; //Hopeless } -void File::SetWriteToRGB() +/** + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type + */ +ModalityType File::GetModality() { - if(HeaderInternal->GetNumberOfScalarComponents()==3) + // 0008 0060 CS ID Modality + std::string strModality = GetEntryValue(0x0008,0x0060); + if ( strModality != GDCM_UNFOUND ) { - PixelReadConverter->BuildRGBImage(); - - ValEntry* spp = CopyValEntry(0x0028,0x0002); - spp->SetValue("3 "); - spp->SetLength(2); - - ValEntry* planConfig = CopyValEntry(0x0028,0x0006); - planConfig->SetValue("0 "); - planConfig->SetLength(2); + if ( strModality.find("AU") < strModality.length()) return AU; + else if ( strModality.find("AS") < strModality.length()) return AS; + else if ( strModality.find("BI") < strModality.length()) return BI; + else if ( strModality.find("CF") < strModality.length()) return CF; + else if ( strModality.find("CP") < strModality.length()) return CP; + else if ( strModality.find("CR") < strModality.length()) return CR; + else if ( strModality.find("CT") < strModality.length()) return CT; + else if ( strModality.find("CS") < strModality.length()) return CS; + else if ( strModality.find("DD") < strModality.length()) return DD; + else if ( strModality.find("DF") < strModality.length()) return DF; + else if ( strModality.find("DG") < strModality.length()) return DG; + else if ( strModality.find("DM") < strModality.length()) return DM; + else if ( strModality.find("DS") < strModality.length()) return DS; + else if ( strModality.find("DX") < strModality.length()) return DX; + else if ( strModality.find("ECG") < strModality.length()) return ECG; + else if ( strModality.find("EPS") < strModality.length()) return EPS; + else if ( strModality.find("FA") < strModality.length()) return FA; + else if ( strModality.find("FS") < strModality.length()) return FS; + else if ( strModality.find("HC") < strModality.length()) return HC; + else if ( strModality.find("HD") < strModality.length()) return HD; + else if ( strModality.find("LP") < strModality.length()) return LP; + else if ( strModality.find("LS") < strModality.length()) return LS; + else if ( strModality.find("MA") < strModality.length()) return MA; + else if ( strModality.find("MR") < strModality.length()) return MR; + else if ( strModality.find("NM") < strModality.length()) return NM; + else if ( strModality.find("OT") < strModality.length()) return OT; + else if ( strModality.find("PT") < strModality.length()) return PT; + else if ( strModality.find("RF") < strModality.length()) return RF; + else if ( strModality.find("RG") < strModality.length()) return RG; + else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; + else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; + else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; + else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; + else if ( strModality.find("SM") < strModality.length()) return SM; + else if ( strModality.find("ST") < strModality.length()) return ST; + else if ( strModality.find("TG") < strModality.length()) return TG; + else if ( strModality.find("US") < strModality.length()) return US; + else if ( strModality.find("VF") < strModality.length()) return VF; + else if ( strModality.find("XA") < strModality.length()) return XA; + else if ( strModality.find("XC") < strModality.length()) return XC; - ValEntry* photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("RGB "); - photInt->SetLength(4); - - if(PixelReadConverter->GetRGB()) - { - PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), - PixelReadConverter->GetRGBSize()); - } - else // Decompressed data + else { - PixelWriteConverter->SetReadData(PixelReadConverter->GetDecompressed(), - PixelReadConverter->GetDecompressedSize()); + /// \todo throw error return value ??? + /// specified <> unknown in our database + return Unknow; } + } - 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 "); - bitsAlloc->SetLength(2); + return Unknow; +} - ValEntry* bitsStored = CopyValEntry(0x0028,0x0101); - bitsStored->SetValue("8 "); - bitsStored->SetLength(2); +/** + * \brief Retrieve the number of Bits Stored (actually used) + * (as opposite to number of Bits Allocated) + * @return The encountered number of Bits Stored, 0 by default. + * 0 means the file is NOT USABLE. The caller has to check it ! + */ +int File::GetBitsStored() +{ + std::string strSize = GetEntryValue( 0x0028, 0x0101 ); + if ( strSize == GDCM_UNFOUND ) + { + gdcmVerboseMacro("(0028,0101) is supposed to be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); +} - ValEntry* highBit = CopyValEntry(0x0028,0x0102); - highBit->SetValue("7 "); - highBit->SetLength(2); +/** + * \brief Retrieve the high bit position. + * \warning The method defaults to 0 when information is Missing. + * The responsability of checking this value is left to the caller. + * @return The high bit positin when present. 0 when Missing. + */ +int File::GetHighBitPosition() +{ + std::string strSize = GetEntryValue( 0x0028, 0x0102 ); + if ( strSize == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory"); + return 0; + } + return atoi( strSize.c_str() ); +} - Archive->Push(bitsAlloc); - Archive->Push(bitsStored); - Archive->Push(highBit); - } +/** + * \brief Check whether the pixels are signed or UNsigned data. + * \warning The method defaults to false (UNsigned) when information is Missing. + * The responsability of checking this value is left to the caller. + * @return True when signed, false when UNsigned + */ +bool File::IsSignedPixelData() +{ + std::string strSize = GetEntryValue( 0x0028, 0x0103 ); + if ( strSize == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory"); + return false; } - else + int sign = atoi( strSize.c_str() ); + if ( sign == 0 ) { - SetWriteToDecompressed(); + return false; } + return true; } -void File::RestoreWrite() +/** + * \brief Retrieve the number of Bits Allocated + * (8, 12 -compacted ACR-NEMA files, 16, ...) + * @return The encountered number of Bits Allocated, 0 by default. + * 0 means the file is NOT USABLE. The caller has to check it ! + */ +int File::GetBitsAllocated() { - 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); + std::string strSize = GetEntryValue(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); } -void File::SetWriteFileTypeToACR() +/** + * \brief Retrieve the number of Samples Per Pixel + * (1 : gray level, 3 : RGB -1 or 3 Planes-) + * @return The encountered number of Samples Per Pixel, 1 by default. + * (Gray level Pixels) + */ +int File::GetSamplesPerPixel() { - Archive->Push(0x0002,0x0010); + const std::string& strSize = GetEntryValue(0x0028,0x0002); + if ( strSize == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "(0028,0002) is supposed to be mandatory"); + return 1; // Well, it's supposed to be mandatory ... + // but sometimes it's missing : *we* assume Gray pixels + } + return atoi( strSize.c_str() ); } -void File::SetWriteFileTypeToExplicitVR() +/** + * \brief Check whether this a monochrome picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. + */ +bool File::IsMonochrome() { - std::string ts = Util::DicomString( - Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() ); - - ValEntry* tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); - tss->SetLength(ts.length()); - - Archive->Push(tss); + const std::string& PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)"); + } + return false; } -void File::SetWriteFileTypeToImplicitVR() +/** + * \brief Check whether this a "PALETTE COLOR" picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "PALETTE COLOR". False otherwise. + */ +bool File::IsPaletteColor() { - std::string ts = Util::DicomString( - Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() ); - - ValEntry* tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); - tss->SetLength(ts.length()); + std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( PhotometricInterp == "PALETTE COLOR " ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Not found : Palette color (0028,0004)"); + } + return false; } -void File::RestoreWriteFileType() +/** + * \brief Check whether this a "YBR_FULL" color picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "YBR_FULL". False otherwise. + */ +bool File::IsYBRFull() { - Archive->Restore(0x0002,0x0010); + std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( PhotometricInterp == "YBR_FULL" ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Not found : YBR Full (0028,0004)"); + } + return false; } -void File::SetWriteToLibido() +/** + * \brief Retrieve the Planar Configuration for RGB images + * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) + * @return The encountered Planar Configuration, 0 by default. + */ +int File::GetPlanarConfiguration() { - ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); - ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); - - if( oldRow && oldCol ) + std::string strSize = GetEntryValue(0x0028,0x0006); + if ( strSize == GDCM_UNFOUND ) { - std::string rows, columns; + gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)"); + return 0; + } + return atoi( strSize.c_str() ); +} - ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); - ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); +/** + * \brief Return the size (in bytes) of a single pixel of data. + * @return The size in bytes of a single pixel of data; 0 by default + * 0 means the file is NOT USABLE; the caller will have to check + */ +int File::GetPixelSize() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + // if (File::GetEntryValue(0x0028,0x0100) == "24") + // return 3; - newRow->Copy(oldCol); - newCol->Copy(oldRow); + std::string pixelType = GetPixelType(); + if ( pixelType == "8U" || pixelType == "8S" ) + { + return 1; + } + if ( pixelType == "16U" || pixelType == "16S") + { + return 2; + } + if ( pixelType == "32U" || pixelType == "32S") + { + return 4; + } + if ( pixelType == "FD" ) + { + return 8; + } + gdcmVerboseMacro( "Unknown pixel type"); + return 0; +} - newRow->SetValue(oldCol->GetValue()); - newCol->SetValue(oldRow->GetValue()); +/** + * \brief Build the Pixel Type of the image. + * Possible values are: + * - 8U unsigned 8 bit, + * - 8S signed 8 bit, + * - 16U unsigned 16 bit, + * - 16S signed 16 bit, + * - 32U unsigned 32 bit, + * - 32S signed 32 bit, + * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) + * \warning 12 bit images appear as 16 bit. + * 24 bit images appear as 8 bit + * @return 0S if nothing found. NOT USABLE file. The caller has to check + */ +std::string File::GetPixelType() +{ + std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)"); + bitsAlloc = "16"; // default and arbitrary value, not to polute the output + } - Archive->Push(newRow); - Archive->Push(newCol); + if ( bitsAlloc == "64" ) + { + return "FD"; + } + else if ( bitsAlloc == "12" ) + { + // It will be unpacked + bitsAlloc = "16"; } + else if ( bitsAlloc == "24" ) + { + // (in order no to be messed up + bitsAlloc = "8"; // by old RGB images) + } + + std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation" - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue("ACRNEMA_LIBIDO_1.1"); - libidoCode->SetLength(10); - Archive->Push(libidoCode); + if (sign == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)"); + sign = "U"; // default and arbitrary value, not to polute the output + } + else if ( sign == "0" ) + { + sign = "U"; + } + else + { + sign = "S"; + } + return bitsAlloc + sign; } -void File::SetWriteToNoLibido() + +/** + * \brief Recover the offset (from the beginning of the file) + * of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset + */ +size_t File::GetPixelOffset() { - ValEntry *recCode = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0008,0x0010)); - if( recCode ) + DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + if ( pxlElement ) { - if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) - { - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue(""); - libidoCode->SetLength(0); - Archive->Push(libidoCode); - } + return pxlElement->GetOffset(); + } + else + { +#ifdef GDCM_DEBUG + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; +#endif //GDCM_DEBUG + return 0; } } -void File::RestoreWriteOfLibido() +/// \todo TODO : unify those two (previous one and next one) +/** + * \brief Recover the pixel area length (in Bytes) + * @return Pixel Element Length, as stored in the header + * (NOT the memory space necessary to hold the Pixels + * -in case of embeded compressed image-) + * 0 : NOT USABLE file. The caller has to check. + */ +size_t File::GetPixelAreaLength() { - Archive->Restore(0x0028,0x0010); - Archive->Restore(0x0028,0x0011); - Archive->Restore(0x0008,0x0010); + DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); + } + else + { +#ifdef GDCM_DEBUG + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; +#endif //GDCM_DEBUG + return 0; + } } -ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) +/** + * \brief tells us if LUT are used + * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' + * are NOT considered as LUT, since nobody knows + * how to deal with them + * Please warn me if you know sbdy that *does* know ... jprx + * @return true if LUT Descriptors and LUT Tables were found + */ +bool File::HasLUT() { - DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); - ValEntry* newE; + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntry(0x0028,0x1101) ) + { + return false; + } + // LutDescriptorGreen + if ( !GetDocEntry(0x0028,0x1102) ) + { + return false; + } + // LutDescriptorBlue + if ( !GetDocEntry(0x0028,0x1103) ) + { + return false; + } + // Red Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1201) ) + { + return false; + } + // Green Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1202) ) + { + return false; + } + // Blue Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1203) ) + { + return false; + } + + // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent) + // NOT taken into account, but we don't know how to use it ... + return true; +} - if(oldE) +/** + * \brief gets the info from 0028,1101 : Lookup Table Desc-Red + * else 0 + * @return Lookup Table number of Bits , 0 by default + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * @ return bit number of each LUT item + */ +int File::GetLUTNbits() +{ + std::vector tokens; + int lutNbits; + + //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red + // = Lookup Table Desc-Blue + // Consistency already checked in GetLUTLength + std::string lutDescription = GetEntryValue(0x0028,0x1101); + if ( lutDescription == GDCM_UNFOUND ) { - newE = new ValEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + return 0; } - else + + tokens.clear(); // clean any previous value + Util::Tokenize ( lutDescription, tokens, "\\" ); + //LutLength=atoi(tokens[0].c_str()); + //LutDepth=atoi(tokens[1].c_str()); + + lutNbits = atoi( tokens[2].c_str() ); + tokens.clear(); + + return lutNbits; +} + + +//----------------------------------------------------------------------------- +// Protected + +/** + * \brief anonymize a File (removes Patient's personal info) + * (read the code to see which ones ...) + */ +bool File::AnonymizeFile() +{ + // If exist, replace by spaces + SetEntryValue (" ",0x0010, 0x2154); // Telephone + SetEntryValue (" ",0x0010, 0x1040); // Adress + SetEntryValue (" ",0x0010, 0x0020); // Patient ID + + DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); + + if ( patientNameHE ) // we replace it by Study Instance UID (why not) { - newE = GetHeader()->NewValEntryByNumber(group,element); + std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + Insert(studyInstanceUID, 0x0010, 0x0010); + } + else + { + Insert("anonymised", 0x0010, 0x0010); + } } - return(newE); + // Just for fun :-( + // (if any) remove or replace all the stuff that contains a Date + +//0008 0012 DA ID Instance Creation Date +//0008 0020 DA ID Study Date +//0008 0021 DA ID Series Date +//0008 0022 DA ID Acquisition Date +//0008 0023 DA ID Content Date +//0008 0024 DA ID Overlay Date +//0008 0025 DA ID Curve Date +//0008 002a DT ID Acquisition Datetime +//0018 9074 DT ACQ Frame Acquisition Datetime +//0018 9151 DT ACQ Frame Reference Datetime +//0018 a002 DT ACQ Contribution Date Time +//0020 3403 SH REL Modified Image Date (RET) +//0032 0032 DA SDY Study Verified Date +//0032 0034 DA SDY Study Read Date +//0032 1000 DA SDY Scheduled Study Start Date +//0032 1010 DA SDY Scheduled Study Stop Date +//0032 1040 DA SDY Study Arrival Date +//0032 1050 DA SDY Study Completion Date +//0038 001a DA VIS Scheduled Admission Date +//0038 001c DA VIS Scheduled Discharge Date +//0038 0020 DA VIS Admitting Date +//0038 0030 DA VIS Discharge Date +//0040 0002 DA PRC Scheduled Procedure Step Start Date +//0040 0004 DA PRC Scheduled Procedure Step End Date +//0040 0244 DA PRC Performed Procedure Step Start Date +//0040 0250 DA PRC Performed Procedure Step End Date +//0040 2004 DA PRC Issue Date of Imaging Service Request +//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time +//0040 4011 DT PRC Expected Completion Date and Time +//0040 a030 DT PRC Verification Date Time +//0040 a032 DT PRC Observation Date Time +//0040 a120 DT PRC DateTime +//0040 a121 DA PRC Date +//0040 a13a DT PRC Referenced Datetime +//0070 0082 DA ??? Presentation Creation Date +//0100 0420 DT ??? SOP Autorization Date and Time +//0400 0105 DT ??? Digital Signature DateTime +//2100 0040 DA PJ Creation Date +//3006 0008 DA SSET Structure Set Date +//3008 0024 DA ??? Treatment Control Point Date +//3008 0054 DA ??? First Treatment Date +//3008 0056 DA ??? Most Recent Treatment Date +//3008 0162 DA ??? Safe Position Exit Date +//3008 0166 DA ??? Safe Position Return Date +//3008 0250 DA ??? Treatment Date +//300a 0006 DA RT RT Plan Date +//300a 022c DA RT Air Kerma Rate Reference Date +//300e 0004 DA RT Review Date + + return true; } -BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +/** + * \brief gets the info from 0020,0037 : Image Orientation Patient + * (needed to organize DICOM files based on their x,y,z position) + * @param iop adress of the (6)float aray to receive values + * @return cosines of image orientation patient + */ +void File::GetImageOrientationPatient( float iop[6] ) { - DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); - BinEntry* newE; + std::string strImOriPat; + //iop is supposed to be float[6] + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; - if(oldE) + // 0020 0037 DS REL Image Orientation (Patient) + if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) { - newE = new BinEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); + } } - else + //For ACR-NEMA + // 0020 0035 DS REL Image Orientation (RET) + else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND ) { - newE = GetHeader()->NewBinEntryByNumber(group,element); + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); + } } +} - return(newE); +/** + * \brief Initialize a default DICOM File that should contain all the + * field require by other reader. DICOM standard does not + * explicitely defines those fields, heuristic has been choosen. + * This is not perfect as we are writting a CT image... + */ +void File::InitializeDefaultFile() +{ + typedef struct + { + const char *value; + uint16_t group; + uint16_t elem; + } DICOM_DEFAULT_VALUE; + + std::string date = Util::GetCurrentDate(); + std::string time = Util::GetCurrentTime(); + std::string uid = Util::CreateUniqueUID(); + std::string uidMedia = uid; + std::string uidClass = uid + ".1"; + std::string uidInst = uid + ".10"; + std::string uidStudy = uid + ".100"; + std::string uidSerie = uid + ".1000"; + + static DICOM_DEFAULT_VALUE defaultvalue[] = { + { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ? + { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage) + { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID + { "1.2.840.10008.1.2.1 ", 0x0002, 0x0010}, // Transfer Syntax UID (Explicit VR Little Endian) + { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID + { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title + + { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date + { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time + { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID + { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID + { "CT", 0x0008, 0x0060}, // Modality + { "GDCM", 0x0008, 0x0070}, // Manufacturer + { "GDCM", 0x0008, 0x0080}, // Institution Name + { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address + + { "GDCM", 0x0010, 0x0010}, // Patient's Name + { "GDCMID", 0x0010, 0x0020}, // Patient ID + + { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID + { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID + { "1", 0x0020, 0x0010}, // StudyID + { "1", 0x0020, 0x0011}, // SeriesNumber + + { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3 + { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation + { "0", 0x0028, 0x0010}, // nbRows + { "0", 0x0028, 0x0011}, // nbCols + { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16 + { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated + { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1 + { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed) + { 0, 0, 0 } + }; + + // default value + // Special case this is the image (not a string) + GrPixel = 0x7fe0; + NumPixel = 0x0010; + Insert(0, 0, GrPixel, NumPixel); + + // All remaining strings: + unsigned int i = 0; + DICOM_DEFAULT_VALUE current = defaultvalue[i]; + while( current.value ) + { + Insert(current.value, current.group, current.elem); + current = defaultvalue[++i]; + } } + //----------------------------------------------------------------------------- // Private //----------------------------------------------------------------------------- -} // end namespace gdcm +} // end namespace gdcm