X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=04c501ac428fe735bb535efa7ed7a16803210d98;hb=be592d55a8d38139cea05c9b22292af14645133b;hp=79aa0139dc2654de387de3a8094183e96dd9b559;hpb=88af35455d7d4b056766880c5d3a3b5a7340bd8b;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 79aa0139..04c501ac 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,340 +1,868 @@ -#include "gdcmlib.h" +// gdcmHeader.cxx +//----------------------------------------------------------------------------- +#include "gdcmHeader.h" -/* ======================================================================= +#include +#include +#include // for isalpha - _IdDcmCheckSwap - La seule maniere sure que l'on aie pour determiner - si on est en LITTLE_ENDIAN, BIG-ENDIAN, - BAD-LITTLE-ENDIAN, BAD-BIG-ENDIAN - est de trouver l'element qui donne la longueur d'un 'GROUP' - (on sait que la longueur de cet element vaut 0x00000004) - et de regarder comment cette longueur est codee en memoire +#include "gdcmUtil.h" +#include "gdcmTS.h" - Le probleme vient de ce que parfois, il n'y en a pas ... - On fait alors le pari qu'on a a faire a du LITTLE_ENDIAN propre. - (Ce qui est la norme -pas respectee- depuis ACR-NEMA) - Si ce n'est pas le cas, on ne peut rien faire. +//----------------------------------------------------------------------------- +// Constructor / Destructor +/** + * \ingroup gdcmHeader + * \brief Constructor + * @param InFilename + * @param exception_on_error + * @param enable_sequences = true to allow the header + * to be parsed *inside* the SeQuences, + * when they have an actual length + * @param ignore_shadow = true if user wants to skip shadow groups + * during parsing, to save memory space + */ +gdcmHeader::gdcmHeader(const char *InFilename, + bool exception_on_error, + bool enable_sequences, + bool ignore_shadow): + gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow) +{ + + // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 + // We may encounter the 'RETired' (0x0028, 0x0200) tag + // (Image Location") . This Element 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 absent we default to group 0x7fe0. + + // This IS the right place for the code + + std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); + if ( ImageLocation == GDCM_UNFOUND ) { // Image Location + GrPixel = 0x7fe0; // default value + } else { + GrPixel = (guint16) atoi( ImageLocation.c_str() ); + } + if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow + GrPixel = 0x7fe0; // the supposed processor endianity. + // see gdcmData/cr172241.dcm + if (GrPixel != 0x7fe0) + // This is a kludge for old dirty Philips imager. + NumPixel = 0x1010; + else + NumPixel = 0x0010; + + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel); + countGrPixel = GetEntry().count(key); +} + +/** + * \ingroup gdcmHeader + * \brief Constructor + * @param exception_on_error + */ +gdcmHeader::gdcmHeader(bool exception_on_error) : + gdcmParser(exception_on_error) +{ +} + +/** + * \ingroup gdcmHeader + * \brief Canonical destructor. + */ +gdcmHeader::~gdcmHeader (void) { +} - (il faudrait avoir des fonctions auxquelles - on passe le code Swap en parametre, pour faire des essais 'manuels') +//----------------------------------------------------------------------------- +// Print - ======================================================================= */ +// see gdcmParser.cxx +//----------------------------------------------------------------------------- +// Public -EndianType gdcmHeader::gdcmHeader() -{ - //guint32 s; - guint32 x=4; // x : pour ntohs - bool net2host; // true when HostByteOrder is the same as NetworkByteOrder - - int sw; - int lgrLue; - char * entCur; - char deb[LGR_ENTETE_A_LIRE]; - - // On teste le processeur - if (x==ntohs(x)) { - net2host = true; - } else { - net2host = false; +/** + * \ingroup gdcmHeader + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current gdcmParser was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable Dicom/Acr File. + * @return true when gdcmParser is the one of a reasonable Dicom/Acr file, + * false otherwise. + */ +bool gdcmHeader::IsReadable(void) { + if(!gdcmParser::IsReadable()) { + return(false); } + std::string res = GetEntryByNumber(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + return false; // Image Dimensions + if ( !GetHeaderEntryByNumber(0x0028, 0x0100) ) + return false; // "Bits Allocated" + if ( !GetHeaderEntryByNumber(0x0028, 0x0101) ) + return false; // "Bits Stored" + if ( !GetHeaderEntryByNumber(0x0028, 0x0102) ) + return false; // "High Bit" + if ( !GetHeaderEntryByNumber(0x0028, 0x0103) ) + return false; // "Pixel Representation" i.e. 'Sign' + return true; +} + +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGBaseLineProcess1 one. + * @return True when JPEGBaseLineProcess1found. False in all other cases. + */ +bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.50" ) + return true; + return false; +} - // On commence par verifier si c'est du DICOM 'actuel' - // ------------- +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendedProcess2-4 one. + * @return True when JPEGExtendedProcess2-4 found. False in all other cases. + */ +bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" ); +} - lgrLue = fread(deb,1,LGR_ENTETE_A_LIRE,e->fp); +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendeProcess3-5 one. + * @return True when JPEGExtendedProcess3-5 found. False in all other cases. + */ +bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.52" ) + return true; + return false; +} - entCur = deb+128; - if(memcmp(entCur, "DICM", (size_t)4) == 0) { - filetype = TrueDicom; - if (DEBUG) printf ("_IdDcmCheckSwap : C est du DICOM actuel \n"); - } else { - filetype = Unknown; - if (DEBUG) printf ("_IdDcmCheckSwap : Ce n'est PAS du DICOM actuel\n"); +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. + * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * other cases. + */ +bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.53" ) + return true; + return false; +} + +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a RLE Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. + */ +bool gdcmHeader::IsRLELossLessTransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.5" ) { + return true; + } + return false; +} + +/** + * \ingroup gdcmHeader + * \brief Determines if Transfer Syntax was already encountered + * and if it corresponds to a JPEG Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. + */ +bool gdcmHeader::IsJPEGLossless(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + // faire qq chose d'intelligent a la place de ça + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + const char * Transfert = Element->GetValue().c_str(); + if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; + if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; + if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; + + return false; +} + +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEG2000 one + * @return True when JPEG2000 (Lossly or LossLess) found. False in all + * other cases. + */ +bool gdcmHeader::IsJPEG2000(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( (Transfer == "1.2.840.10008.1.2.4.90") + || (Transfer == "1.2.840.10008.1.2.4.91") ) + return true; + return false; +} + +/** + * \ingroup gdcmHeader + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool gdcmHeader::IsDicomV3(void) { + // Checking if Transfert Syntax exists is enough + // Anyway, it's to late check if the 'Preamble' was found ... + // And ... would it be a rich idea to check ? + // (some 'no Preamble' DICOM images exist !) + return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); +} + +/** + * \ingroup gdcmHeader + * \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 + */ +int gdcmHeader::GetXSize(void) { + std::string StrSize; + StrSize = GetEntryByNumber(0x0028,0x0011); + if (StrSize == GDCM_UNFOUND) + return 0; + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of lines of image. + * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() + * @return The encountered size when found, 1 by default + * (The ACR-MEMA file contains a Signal, not an Image). + */ +int gdcmHeader::GetYSize(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0010); + if (StrSize != GDCM_UNFOUND) + return atoi(StrSize.c_str()); + if ( IsDicomV3() ) + return 0; + else + // 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; +} + +/** + * \ingroup gdcmHeader + * \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 absent 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 gdcmHeader::GetZSize(void) { + // Both DicomV3 and ACR/Nema consider the "Number of Frames" + // as the third dimension. + std::string StrSize = GetEntryByNumber(0x0028,0x0008); + if (StrSize != GDCM_UNFOUND) + return atoi(StrSize.c_str()); + + // We then consider the "Planes" entry as the third dimension + StrSize = GetEntryByNumber(0x0028,0x0012); + if (StrSize != GDCM_UNFOUND) + return atoi(StrSize.c_str()); + return 1; +} + +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetBitsStored(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0101); + if (StrSize == GDCM_UNFOUND) + return 0; // It's supposed to be mandatory + // the caller will have to check + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetBitsAllocated(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0100); + if (StrSize == GDCM_UNFOUND) + return 0; // It's supposed to be mandatory + // the caller will have to check + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetSamplesPerPixel(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0002); + if (StrSize == GDCM_UNFOUND) + return 1; // Well, it's supposed to be mandatory ... + // but sometimes it's missing : *we* assume Gray pixels + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetPlanarConfiguration(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0006); + if (StrSize == GDCM_UNFOUND) + return 0; + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetPixelSize(void) { + 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; + dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + return 0; +} + +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetPixelType(void) { + std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated + if (BitsAlloc == GDCM_UNFOUND) { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + BitsAlloc = std::string("16"); + } + if (BitsAlloc == "64") // ) + return ("FD"); + if (BitsAlloc == "12") // It will be unpacked + BitsAlloc = std::string("16"); + else if (BitsAlloc == "24") // (in order no to be messed up + BitsAlloc = std::string("8"); // by old RGB images) + + std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" + if (Signed == GDCM_UNFOUND) { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + BitsAlloc = std::string("0"); } + if (Signed == "0") + Signed = std::string("U"); + else + Signed = std::string("S"); - if(filetype == TrueDicom) { - // on saute le File Preamble (souvent a ZERO) : 128 Octets - // + le DICM (4), et le (0002, 0000) soit 4 (136 = 128 + 4 + 4) - entCur = deb+136; - if(memcmp(entCur, "UL", (size_t)2) == 0) { - // les 2 premiers octets de la lgr peuvent valoir UL --> Explicit VR - filetype = ExplicitVR; - if (DEBUG) printf ("_IdDcmCheckSwap : Explicit VR\n"); - } else { - filetype = ImplicitVR; - if (DEBUG) printf ("_IdDcmCheckSwap : PAS Explicit VR\n"); - } + return( BitsAlloc + Signed); +} - if (net2host) { // HostByteOrder is different from NetworkByteOrder - sw = 0; // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire - if (DEBUG) printf("HostByteOrder = NetworkByteOrder\n"); - } else { /* on est sur une Sun ou une SGI */ - sw = 4321; - if (DEBUG) printf("HostByteOrder != NetworkByteOrder\n"); - } +/** + * \ingroup gdcmHeader + * \brief Recover the offset (from the beginning of the file) + * of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset + */ +size_t gdcmHeader::GetPixelOffset(void) { + // + // If the element (0x0088,0x0200) 'icone image sequence' is found + // (grPixel,numPixel) is stored twice : the first one for the icon + // the second one for the image ... + // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything* + // see gdcmData/MxTwinLossLess.dcm ... + + //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence + + IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); + gdcmHeaderEntry* PixelElement; + if (countGrPixel == 1) + PixelElement = (it.first)->second; + else { + PixelElement = (++it.first)->second; // hope there are no more than 2 ! + } + if (PixelElement) { + return PixelElement->GetOffset(); + } else { +/* std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; */ + return 0; + } +} +// TODO : unify those two (previous one and next one) +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetPixelAreaLength(void) { + + IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); + gdcmHeaderEntry* PixelElement; + + if (countGrPixel==1) + PixelElement = (it.first)->second; + else + PixelElement = (++it.first)->second; - rewind(e->fp); - fseek (e->fp, 132L, SEEK_SET); //On se positionne sur le debut des info - e->offsetCourant=132; - return sw; - - } /* fin TrueDicom */ - - // Pas du TrueDicom : permiere hypothese c'est de l'ACR 'propre', auquel - // cas la lgr du premier element du groupe est FORCEMENT 4 - - entCur=deb + 4; - s=str2num(entCur,int); - - switch (s) { - case 0x00040000 : - sw=3412; if(DEBUG) printf("s : %08x sw : %d\n",s,sw); - filetype = ACR; - break; - case 0x04000000 : - sw=4321; if(DEBUG) printf("s : %08x sw : %d\n",s,sw); - filetype = ACR; - break; - case 0x00000400 : - sw=2143; if(DEBUG) printf("s : %08x sw : %d\n",s,sw); - filetype = ACR; - break; - case 0x00000004 : - sw=0; if(DEBUG) printf("s : %08x sw : %d\n",s,sw); - filetype = ACR; - break; - default : - sw = -1; - if (DEBUG) printf (" Pas trouve l info de Swap; On va parier\n"); - } - - // Deuxieme hypothese : c'est de l'ACR 'pas propre' i.e. il manque - // la lgr du groupe - - if(sw==-1) { - /* On n'a pas trouve l'info de swap 28/11/2000 JPR */ - // Si c'est du VRAI ACR NEMA si on est sur une DEC ou un PC swap=0, - // SUN ou SGI SWAP=4321 - /* si c'est du RAW, ca degagera + tard */ - - if (DEBUG) printf("On force la chance \n"); - - if (x!=ntohs(x)) // HostByteOrder is different from NetworkByteOrder - sw = 0; // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire - else - sw = 4321; // on est sur Sun ou SGI - } + if (PixelElement) { + return PixelElement->GetLength(); + } else { +/* std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl;*/ + return 0; + } +} - rewind(e->fp); // les info commencent au debut - e->offsetCourant=0; - return (sw); +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::HasLUT(void) { + + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) + return false; + // LutDescriptorGreen + if ( !GetHeaderEntryByNumber(0x0028,0x1102) ) + return false; + // LutDescriptorBlue + if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) + return false; + // Red Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) + return false; + // Green Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1202) ) + return false; + // Blue Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1203) ) + return false; + return true; } -void gdcmHeader::_setAcrLibido() { - - _ID_DCM_ELEM * ple; - PLIST_ELEMENT plelem; - PLIST pl; - - // Positionnement ACR_LIBIDO - if(DEBUG) printf("Entree ds _setAcrLibido\n"); - - filetype = ACR_LIBIDO = 0; - if ( filetype != TrueDicom) { - // Recognition Code --> n'existe plus en DICOM V3 ... - - pl = e->plist; - plelem = IdLstFirst(pl); - while (plelem) { - ple= IdLstPtrObj(plelem); - if(DEBUG) printf("gr %04x Num %04x\n", ple->Gr, ple->Num); - if(ple->Gr > 0x0008) break; // On a depasse - if(ple->Gr == 0x0008) { - if(ple->Num > 0x0010) break; // On a depasse - if(ple->Num == 0x0010) { - if ( (memcmp(ple->valeurElem,"ACRNEMA_LIBIDO",14)==0) - // si c'est egal - || (memcmp(ple->valeurElem,"CANRME_AILIBOD",14)==0)) { - // en cas d'objet ACRLibido fait sr 1 autre machine) - e->ACR_LIBIDO =1; - } // fin if memcmp - break; - } // fin if ple->Num==0x0010 - } // fin ple->Gr==0x0008 - plelem = IdLstNext(plelem); - } // fin while - } // fin if TrueDicom - - return; +/** + * \ingroup gdcmHeader + * \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 gdcmHeader::GetLUTNbits(void) { + std::vector tokens; + //int LutLength; + //int LutDepth; + int LutNbits; + //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + // Consistency already checked in GetLUTLength + std::string LutDescription = GetEntryByNumber(0x0028,0x1101); + if (LutDescription == GDCM_UNFOUND) + return 0; + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + 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; } -/* ======================================================================= -* _IdDcmRecupLgr -* -* ACR-NEMA : On a toujours -* GroupNumber (2 Octets) -* ElementNumber (2 Octets) -* ElementSize (4 Octets) -* -* -* DICOM : On peut avoir (implicit Value Representation) -* GroupNumber (2 Octets) -* ElementNumber (2 Octets) -* ElementSize (4 Octets) -* -* On peut avoir (explicit Value Representation) -* GroupNumber (2 Octets) -* ElementNumber (2 Octets) -* ValueRepresentation (2 Octets) -* ElementSize (2 Octets) -* -* ATTENTION : dans le cas ou ValueRepresentation = OB, OW, SQ, UN -* GroupNumber (2 Octets) -* ElementNumber (2 Octets) -* ValueRepresentation (2 Octets) -* zone reservee (2 Octets) -* ElementSize (4 Octets) -* -* -* ======================================================================= */ /** - * \ingroup dcm - * \brief recupere la longueur d'un champ DICOM. - * (le fichier doit deja avoir ete ouvert, - * _IdAcrCheckSwap(ID_DCM_HDR *e) avoir ete appele) - * et la partie 'group' ainsi que la partie 'elem' - * de l'acr_element doivent avoir ete lues. - * @param sw code swap - * @param skippedLength pointeur sur nombre d'octets que l'on a saute qd la lecture est finie - * @param longueurLue pointeur sur longueur (en nombre d'octets) effectivement lue - - * @return longueur retenue pour le champ + * \ingroup gdcmHeader + * \brief builts Red/Green/Blue/Alpha LUT from Header + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * and (0028,1101),(0028,1102),(0028,1102) + * - xxx Palette Color Lookup Table Descriptor - are found + * and (0028,1201),(0028,1202),(0028,1202) + * - xxx Palette Color Lookup Table Data - are found + * \warning does NOT deal with : + * 0028 1100 Gray Lookup Table Descriptor (Retired) + * 0028 1221 Segmented Red Palette Color Lookup Table Data + * 0028 1222 Segmented Green Palette Color Lookup Table Data + * 0028 1223 Segmented Blue Palette Color Lookup Table Data + * no known Dicom reader deals with them :-( + * @return a RGBA Lookup Table + */ +unsigned char * gdcmHeader::GetLUTRGBA(void) { +// Not so easy : see +// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables + +// if Photometric Interpretation # PALETTE COLOR, no LUT to be done + if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") { + return NULL; + } + int lengthR, debR, nbitsR; + int lengthG, debG, nbitsG; + int lengthB, debB, nbitsB; + +// Get info from Lut Descriptors +// (the 3 LUT descriptors may be different) + std::string LutDescriptionR = GetEntryByNumber(0x0028,0x1101); + if (LutDescriptionR == GDCM_UNFOUND) + return NULL; + std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102); + if (LutDescriptionG == GDCM_UNFOUND) + return NULL; + std::string LutDescriptionB = GetEntryByNumber(0x0028,0x1103); + if (LutDescriptionB == GDCM_UNFOUND) + return NULL; + + std::vector tokens; + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionR, tokens, "\\"); + lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes + debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value + nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits) + tokens.clear(); + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionG, tokens, "\\"); + lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes + debG =atoi(tokens[1].c_str()); // subscript of the first Lut Value + nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits) + tokens.clear(); + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionB, tokens, "\\"); + lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes + debB =atoi(tokens[1].c_str()); // subscript of the first Lut Value + nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits) + tokens.clear(); + + // Load LUTs into memory, (as they were stored on disk) + unsigned char *lutR = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1201); + unsigned char *lutG = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1202); + unsigned char *lutB = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1203); + + if (!lutR || !lutG || !lutB ) { + return NULL; + } + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + + unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) + if (!LUTRGBA) { + return NULL; + } + memset(LUTRGBA, 0, 1024); + // Bits Allocated + int nb; + std::string str_nb = GetEntryByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { + nb = 16; + } else { + nb = atoi(str_nb.c_str() ); + } + int mult; + + if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size + mult=2; // high byte must be = low byte + else // See PS 3.3-2003 C.11.1.1.2 p 619 + mult=1; + + // if we get a black image, let's just remove the '+1' + // from 'i*mult+1' and check again + // if it works, we shall have to check the 3 Palettes + // to see which byte is ==0 (first one, or second one) + // and fix the code + // We give up the checking to avoid some (useless ?)overhead + // (optimistic asumption) + unsigned char *a; + int i; + + a = LUTRGBA+0; + for(i=0;iGetValue(TransfertSyntax); + //delete ts; // Seg Fault when deleted ?! + return tsName; +} -static guint32 _IdDcmRecupLgr(ID_DCM_HDR *e, int sw, int *skippedLength, int *longueurLue) { -guint32 l_gr; -unsigned short int l_gr_2; -int i, trouve; -char VR[5]; -int lgrLue; - -/* - * ATTENTION : -*/ - -int nbCode=26; // nombre d'elements dans la table de type DICOM_VR definie dans dicom.c - -/* ================ */ - -// ID_DCM_HDR *e sert uniquement de passe-plat pour __ExplicitVR - - -if (e->__ExplicitVR == 1) { - lgrLue=fread (&VR, (size_t)2,(size_t)1, e->fp); - VR[2]=0; - - // ATTENTION : - // Ce n'est pas parce qu'on a trouve UL la premiere fois qu'on respecte - // Explicit VR tout le temps - // (cf e=film ...) - - for(i=0,trouve=0;ipleCourant)->VR=_ID_dicom_vr[i].dicom_VR; - trouve=1; - break; - } - } - - if ( trouve == 0) { - - // On est mal : implicit VR repere - // mais ce n'est pas un code connu ... - // On reconstitue la longueur - - if(DEBUG) printf("IdDcmRecupLgr : Explicit VR, mais pas trouve de code connu\n"); - memcpy(&l_gr, VR,(size_t)2); - - lgrLue=fread ( ((char*)&l_gr)+2, (size_t)2, (size_t)1, e->fp); - - if(sw) l_gr = _IdDcmSWAP_LONG(((guint32)l_gr),sw); - - if(DEBUG) printf("IdDcmRecupLgr : lgr deduite : %08x , %d\n",l_gr,l_gr); - - *longueurLue=l_gr; - if ( (int)l_gr == -1) { - l_gr=0; - } - *skippedLength = 4; - if (DEBUG) printf(" 1 : lgr %08x (%d )skippedLength %d\n",l_gr,l_gr, *skippedLength); - return(l_gr); - } - - // On repart dans la sequence 'sensee' - - if(DEBUG) printf("VR : [%01x , %01x] (%c%c) en position %d du tableau\n", VR[0],VR[1],VR[0],VR[1],i); - //printf(" %d , %s\n", i,_ID_dicom_vr[i].dicom_VR); - - if ( - (!memcmp( VR,"OB",(size_t)2 )) || - (!memcmp( VR,"OW",(size_t)2 )) || - (!memcmp( VR,"SQ",(size_t)2 )) || - (!memcmp( VR,"UN",(size_t)2 )) ) { - - // les 2 octets suivants sont reserves - - if(DEBUG) printf("IdDcmRecupLgr : les 2 octets suivants sont reserves\n"); - //on les saute - fseek(e->fp, 2L,SEEK_CUR); - - //on lit la lgr sur QUATRE octets - - lgrLue=fread (&l_gr, (size_t)4,(size_t)1, e->fp); - - if(sw) l_gr = _IdDcmSWAP_LONG(((guint32)l_gr),sw); - *skippedLength = 8; - - } else { - //on lit la lgr sur DEUX octets - - lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, e->fp); - - if(sw) l_gr_2 = _IdDcmSWAP_SHORT((unsigned short)l_gr_2,sw); - - *longueurLue=l_gr_2; - - - if ( l_gr_2 == 0xffff) { - l_gr = 0; - } else { - l_gr = l_gr_2; - } - *skippedLength = 4; - } - } else { // Explicit VR = 0 - - //on lit la lgr sur QUATRE octets - - lgrLue=fread (&l_gr, (size_t)4,(size_t)1, e->fp); +/** + * \ingroup gdcmHeader + * \brief Sets the Pixel Area size in the Header + * --> not-for-rats function + * @param ImageDataSize new Pixel Area Size + * warning : nothing else is checked + */ +void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { + std::string content1; + char car[20]; + + // Assumes HeaderEntry (GrPixel, NumPixel) is unique ... + // TODO deal with multiplicity (see gdcmData/icone.dcm) + sprintf(car,"%d",ImageDataSize); + + gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel); + a->SetLength(ImageDataSize); + + ImageDataSize+=8; + sprintf(car,"%d",ImageDataSize); + content1=car; + SetEntryByNumber(content1, GrPixel, NumPixel); +} - if(sw)l_gr=_IdDcmSWAP_LONG(((long)l_gr),sw); - *skippedLength = 4; - } + +/** + * \ingroup gdcmHeader + * \brief compares 2 Headers, according to DICOMDIR rules + * --> not-for-rats function + * \warning does NOT work with ACR-NEMA files + * \todo find a trick to solve the pb (use RET fields ?) + * @param header + * @return true if 'smaller' + */ + bool gdcmHeader::operator<(gdcmHeader &header){ + std::string s1,s2; + + // Patient Name + s1=this->GetEntryByNumber(0x0010,0x0010); + s2=header.GetEntryByNumber(0x0010,0x0010); + if(s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Patient ID + s1=this->GetEntryByNumber(0x0010,0x0020); + s2=header.GetEntryByNumber(0x0010,0x0020); + if (s1 < s2) + return(true); + else if (s1 > s2) + return(1); + else + { + // Study Instance UID + s1=this->GetEntryByNumber(0x0020,0x000d); + s2=header.GetEntryByNumber(0x0020,0x000d); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Serie Instance UID + s1=this->GetEntryByNumber(0x0020,0x000e); + s2=header.GetEntryByNumber(0x0020,0x000e); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + } + } + } + return(false); +} + +//----------------------------------------------------------------------------- +// Protected + +/** + * \ingroup gdcmHeader + * \brief anonymize a Header (removes Patient's personal info) + * (read the code to see which ones ...) + * @param + */ +bool gdcmHeader::anonymizeHeader() { + + gdcmHeaderEntry *patientNameHE = GetHeaderEntryByNumber (0x0010, 0x0010); + // gdcmHeaderEntry *patientIDHE = GetHeaderEntryByNumber (0x0010, 0x0020); + + ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone + ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress + ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID - *longueurLue=l_gr; + if (patientNameHE) { + std::string StudyInstanceUID = GetEntryByNumber (0x0020, 0x000d); + if (StudyInstanceUID !=GDCM_UNFOUND) + ReplaceOrCreateByNumber(StudyInstanceUID, 0x0010, 0x0010); + else + ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010); + } - // Traitement des curiosites sur la longueur + // Just for fun :-( + // (if any) remove or replace all the stuff that contains a Date - if ( (int)l_gr == 0xffffffff) - l_gr=0; - - if(!memcmp( VR,"SQ",(size_t)2 )) { // ca annonce une SEQUENCE d'items ?! - l_gr=0; // on lira donc les items de la sequence - if (DEBUG) printf(" SQ trouve : lgr %d \n",l_gr); - } - -if (DEBUG) printf(" 2 : lgr %08x (%d) skippedLength %d\n",l_gr,l_gr, *skippedLength); - return(l_gr); -} +//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; + } +//----------------------------------------------------------------------------- +// Private + +//-----------------------------------------------------------------------------