X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=c46ddb0f91c78decda2c1e17121b5c7d911625d7;hb=edfc14dd195f9759cf02da0959d96d1499d572be;hp=6899e505b07794f68160c6c6f4b8c995733f406c;hpb=0fea0679c6061128104e6a357d20653baa274884;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 6899e505..c46ddb0f 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,360 +1,1388 @@ -#include "gdcmlib.h" -extern "C" { -#include "glib.h" -} -#include -// For nthos: -#ifdef _MSC_VER -#include -#else -#include -#endif - -#define LGR_ENTETE_A_LIRE 256 // on ne lit plus que le debut -#define DEBUG 1 - -//FIXME: this looks dirty to me... -#define str2num(str, typeNum) *((typeNum *)(str)) - -/** - * \ingroup gdcmHeader - * \brief 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 - * - * 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. - * - * (il faudrait avoir des fonctions auxquelles - * on passe le code Swap en parametre, pour faire des essais 'manuels') - */ -void gdcmHeader::CheckSwap() -{ - guint32 s; - guint32 x=4; // x : pour ntohs - bool net2host; // true when HostByteOrder is the same as NetworkByteOrder - - int lgrLue; - char * entCur; - char deb[LGR_ENTETE_A_LIRE]; - - // On teste le processeur - if (x==ntohs(x)) { - net2host = true; - } else { - net2host = false; - } - - // On commence par verifier si c'est du DICOM 'actuel' - // ------------- - lgrLue = fread(deb,1,LGR_ENTETE_A_LIRE, fp); - - 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"); - } - - 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"); - } - - 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"); - } - - rewind(fp); - fseek (fp, 132L, SEEK_SET); //On se positionne sur le debut des info - offsetCourant=132; - } // End of 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"); - } - if(sw!=-1) { - rewind(fp); // les info commencent au debut - offsetCourant=0; - return; - } - - // Deuxieme hypothese : c'est de l'ACR 'pas propre' i.e. il manque - // la lgr du groupe - - // On n'a pas trouve l'info de swap. - // Si c'est du VRAI ACR NEMA et - // * si on est sur une DEC ou un PC alors swap=0, - // * si on est sur SUN ou SGI, alors 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 - // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire - sw = 0; - else - // on est sur Sun ou SGI - sw = 4321; - rewind(fp); // les info commencent au debut - offsetCourant=0; - return; -} - -/** - * \ingroup gdcmHeader - * \brief Pour les fichiers non TrueDicom, si le recognition - * code (0008,0010) s'avere etre "ACR_LIBIDO", alors - * valide la reconnaissance du fichier en positionnant - * filetype. - */ -void gdcmHeader::setAcrLibido() { - string RecCode; - - if ( filetype != TrueDicom) { - printf("_setAcrLibido expects a presumably ACR file\n"); - // Recognition Code --> n'existe plus en DICOM V3 ... - RecCode = GetPubElValByNumber(0x0008, 0x0010); - // FIXME NOW - if (RecCode == "ACRNEMA_LIBIDO" || - RecCode == "CANRME_AILIBOD" ) - filetype = ACR_LIBIDO; - else - filetype = ACR; - } - return; -} - -/** - * \ingroup gdcmHeader - * \brief recupere la longueur d'un champ DICOM. - * Preconditions: - * 1/ le fichier doit deja avoir ete ouvert, - * 2/ CheckSwap() doit avoir ete appele - * 3/ la partie 'group' ainsi que la partie 'elem' - * de l'acr_element doivent avoir ete lues. - * - * ACR-NEMA : we allways get - * GroupNumber (2 Octets) - * ElementNumber (2 Octets) - * ElementSize (4 Octets) - * DICOM en implicit Value Representation : - * GroupNumber (2 Octets) - * ElementNumber (2 Octets) - * ElementSize (4 Octets) - * - * DICOM en 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) - * - * @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 - */ - -// FIXME sw n'est plus un argument necessaire -long int gdcmHeader::RecupLgr( - _ID_DCM_ELEM *pleCourant, int sw, int *skippedLength, int *longueurLue) -{ - guint32 l_gr; - unsigned short int l_gr_2; - int i, trouve; - char VR[5]; - int lgrLue; - - // FIX ME - // ATTENTION : nbCode correspond au nombre d'elements dans la table - // de type DICOM_VR. A nettoyer. - // - int nbCode=26; - - if (filetype == ExplicitVR) { - lgrLue=fread (&VR, (size_t)2,(size_t)1, 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;iVR=_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 de code connu\n"); - memcpy(&l_gr, VR,(size_t)2); - - lgrLue=fread ( ((char*)&l_gr)+2, (size_t)2, (size_t)1, fp); - - l_gr = SWAP_LONG((guint32)l_gr); - - 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); - - 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: on les saute - if(DEBUG) - printf("IdDcmRecupLgr : les 2 octets suivants sont reserves\n"); - fseek(fp, 2L,SEEK_CUR); - - //on lit la lgr sur QUATRE octets - lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp); - l_gr = SWAP_LONG((guint32)l_gr); - *skippedLength = 8; - - } else { - //on lit la lgr sur DEUX octets - lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, 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, fp); - - l_gr= SWAP_LONG((long)l_gr); - *skippedLength = 4; - } - - *longueurLue=l_gr; - - // Traitement des curiosites sur la longueur - - 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); -} - -/** - * \ingroup gdcmHeader - * \brief remet les octets dans un ordre compatible avec celui du processeur - - * @return longueur retenue pour le champ - */ - -guint32 gdcmHeader::SWAP_LONG(guint32 a) { - // FIXME: il pourrait y avoir un pb pour les entiers negatifs ... - switch (sw) { - case 4321 : - a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | - ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); - break; - - case 3412 : - a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); - break; - - case 2143 : - a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); - break; - default : - printf("\n\n\n *******\n erreur code swap ?!?\n\n\n"); - a=0; - } - return(a); +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmHeader.cxx,v $ + Language: C++ + Date: $Date: 2004/11/30 16:24:31 $ + Version: $Revision: 1.209 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#include "gdcmHeader.h" +#include "gdcmGlobal.h" +#include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmValEntry.h" +#include //sscanf + +#include + +namespace gdcm +{ +//----------------------------------------------------------------------------- +// Constructor / Destructor +/** + * \brief Constructor + * @param filename name of the file whose header we want to analyze + */ +Header::Header( 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 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. + // Note: this IS the right place for the code + + // Image Location + const std::string &imgLocation = GetEntryByNumber(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 endianity. + // 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; + } +} + +/** + * \brief Constructor used when we want to generate dicom files from scratch + */ +Header::Header() + :Document() +{ + InitializeDefaultHeader(); +} + +/** + * \brief Canonical destructor. + */ +Header::~Header () +{ +} + +/** + * \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 fp file pointer on an already open file + * @param filetype Type of the File to be written + * (ACR-NEMA, ExplicitVR, ImplicitVR) + */ +bool Header::Write(std::string fileName,FileType filetype) +{ + std::ofstream* fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (fp == NULL) + { + dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); + return false; + } + + // Bits Allocated + if ( GetEntryByNumber(0x0028,0x0100) == "12") + { + SetEntryByNumber("16", 0x0028,0x0100); + } + + /// \todo correct 'Pixel group' Length if necessary + + int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel); + if (i_lgPix != -2) + { + // no (GrPixel, NumPixel) element + std::string s_lgPix = Util::Format("%d", i_lgPix+12); + s_lgPix = Util::DicomString( s_lgPix.c_str() ); + ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); + } + + // FIXME : should be nice if we could move it to File + // (or in future gdcmPixelData class) + + // Drop Palette Color, if necessary + + if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' ) + { + // if SamplesPerPixel = 3, sure we don't need any LUT ! + // Drop 0028|1101, 0028|1102, 0028|1103 + // Drop 0028|1201, 0028|1202, 0028|1203 + + DocEntry* e = GetDocEntryByNumber(0x0028,0x01101); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1102); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1103); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x01201); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1202); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1203); + if (e) + { + RemoveEntryNoDestroy(e); + } + } + Document::WriteContent(fp,filetype); + + fp->close(); + delete fp; + + return true; +} + +//----------------------------------------------------------------------------- +// Print + + +//----------------------------------------------------------------------------- +// Public + +/** + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current Header was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable Dicom/Acr File. + * @return true when Header is the one of a reasonable Dicom/Acr file, + * false otherwise. + */ +bool Header::IsReadable() +{ + if( !Document::IsReadable() ) + { + return false; + } + + const std::string &res = GetEntryByNumber(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { + return false; // Image Dimensions + } + if ( !GetDocEntryByNumber(0x0028, 0x0100) ) + { + return false; // "Bits Allocated" + } + if ( !GetDocEntryByNumber(0x0028, 0x0101) ) + { + return false; // "Bits Stored" + } + if ( !GetDocEntryByNumber(0x0028, 0x0102) ) + { + return false; // "High Bit" + } + if ( !GetDocEntryByNumber(0x0028, 0x0103) ) + { + return false; // "Pixel Representation" i.e. 'Sign' + } + + return true; +} + +/** + * \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 Header::GetXSize() +{ + const std::string &strSize = GetEntryByNumber(0x0028,0x0011); + if ( strSize == GDCM_UNFOUND ) + { + return 0; + } + + return atoi( strSize.c_str() ); +} + +/** + * \brief Retrieve the number of lines of image. + * \warning The defaulted value is 1 as opposed to Header::GetXSize() + * @return The encountered size when found, 1 by default + * (The ACR-NEMA file contains a Signal, not an Image). + */ +int Header::GetYSize() +{ + const std::string &strSize = GetEntryByNumber(0x0028,0x0010); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } + if ( IsDicomV3() ) + { + return 0; + } + + // 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 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 Header::GetZSize() +{ + // Both DicomV3 and ACR/Nema consider the "Number of Frames" + // as the third dimension. + const 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 + const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) + { + 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 Header::GetXSpacing() +{ + float xspacing, yspacing; + const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + return 1.; + } + + int nbValues; + if( ( nbValues = sscanf( strSpacing.c_str(), + "%f\\%f", &yspacing, &xspacing)) != 2 ) + { + // if single value is found, xspacing is defaulted to yspacing + if ( nbValues == 1 ) + { + return yspacing; + } + } + if ( xspacing == 0.) + { + dbg.Verbose(0, "Header::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + // seems to be a bug in the header ... + sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + } + + return xspacing; +} + +/** + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float Header::GetYSpacing() +{ + float yspacing = 0; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetYSpacing: 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); + + 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 Header::GetZSpacing() +{ + // 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 absent, + // on suppose que les coupes sont jointives + + std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); + + if ( strSpacingBSlices == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices"); + std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); + if ( strSliceThickness == GDCM_UNFOUND ) + { + 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() ); + } + } + else + { + return (float)atof( strSpacingBSlices.c_str() ); + } + return 1.; +} + +/** + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept + */ +float Header::GetRescaleIntercept() +{ + float resInter = 0.; + /// 0028 1052 DS IMG Rescale Intercept + std::string strRescInter = GetEntryByNumber(0x0028,0x1052); + if ( strRescInter != GDCM_UNFOUND ) + { + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + { + // bug in the element 0x0028,0x1052 + dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope " + "is empty"); + } + } + + return resInter; +} + +/** + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope + */ +float Header::GetRescaleSlope() +{ + float resSlope = 1.; + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) + { + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + { + // bug in the element 0x0028,0x1053 + dbg.Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty"); + } + } + + return resSlope; +} + +/** + * \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) + */ +int Header::GetNumberOfScalarComponents() +{ + if ( GetSamplesPerPixel() == 3 ) + { + return 3; + } + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryByNumber(0x0028,0x0100) == "24" ) + { + return 3; + } + + std::string strPhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) + { + if ( HasLUT() )// PALETTE COLOR is NOT enough + { + return 3; + } + else + { + return 1; + } + } + + // 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 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' -) + */ +int Header::GetNumberOfScalarComponentsRaw() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" ) + { + return 3; + } + + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); } + +// +// -------------- 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 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 + */ +float Header::GetXOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + "Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + "Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? + return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + + 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 Header::GetYOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) + { + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + "Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + "Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? + return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + + return yImPos; +} + +/** + * \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 + */ +float Header::GetZOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) + { + dbg.Verbose(0, "Header::GetZImagePosition: wrong Image " + "Position Patient (0020,0032)"); + return 0.; // bug in the element 0x0020,0x0032 + } + else + { + return zImPos; + } + } + + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), + "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) + { + dbg.Verbose(0, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); + return 0.; // bug in the element 0x0020,0x0032 + } + else + { + return zImPos; + } + } + + std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images + if ( strSliceLocation != GDCM_UNFOUND ) + { + if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) + { + dbg.Verbose(0, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 + } + else + { + return zImPos; + } + } + dbg.Verbose(0, "Header::GetZImagePosition: unfound Slice Location (0020,1041)"); + + std::string strLocation = GetEntryByNumber(0x0020,0x0050); + if ( strLocation != GDCM_UNFOUND ) + { + if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) + { + dbg.Verbose(0, "Header::GetZImagePosition: wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 + } + else + { + return zImPos; + } + } + dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)"); + + return 0.; // Hopeless +} + +/** + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +int Header::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 = GetEntryByNumber(0x0020,0x0013); + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); + } + return 0; //Hopeless +} + +/** + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type + */ +ModalityType Header::GetModality() +{ + // 0008 0060 CS ID Modality + std::string strModality = GetEntryByNumber(0x0008,0x0060); + if ( strModality != GDCM_UNFOUND ) + { + 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; + + else + { + /// \todo throw error return value ??? + /// specified <> unknow in our database + return Unknow; + } + } + + return Unknow; +} + +/** + * \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 Header::GetBitsStored() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0101 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + "be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); +} + +/** + * \brief Retrieve the high bit position. + * \warning The method defaults to 0 when information is absent. + * The responsability of checking this value is left to the caller. + * @return The high bit positin when present. 0 when absent. + */ +int Header::GetHighBitPosition() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0102 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetHighBitPosition: this is supposed " + "to be mandatory"); + return 0; + } + return atoi( strSize.c_str() ); +} + +/** + * \brief Check wether the pixels are signed or UNsigned data. + * \warning The method defaults to false (UNsigned) when information is absent. + * The responsability of checking this value is left to the caller. + * @return True when signed, false when UNsigned + */ +bool Header::IsSignedPixelData() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0103 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed " + "to be mandatory"); + return false; + } + int sign = atoi( strSize.c_str() ); + if ( sign == 0 ) + { + return false; + } + return true; +} + +/** + * \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 Header::GetBitsAllocated() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + "be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); +} + +/** + * \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 Header::GetSamplesPerPixel() +{ + const std::string& strSize = GetEntryByNumber(0x0028,0x0002); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetBitsStored: this 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() ); +} + +/** + * \brief Check wether this a monochrome picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. + */ +bool Header::IsMonochrome() +{ + const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsMonochrome: absent Photometric " + "Interpretation"); + } + return false; +} + +/** + * \brief Check wether this a "PALETTE COLOR" picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "PALETTE COLOR". False otherwise. + */ +bool Header::IsPaletteColor() +{ + std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( PhotometricInterp == "PALETTE COLOR " ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric " + "Interpretation"); + } + return false; +} + +/** + * \brief Check wether this a "YBR_FULL" color picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "YBR_FULL". False otherwise. + */ +bool Header::IsYBRFull() +{ + std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( PhotometricInterp == "YBR_FULL" ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsYBRFull: absent Photometric " + "Interpretation"); + } + return false; +} + +/** + * \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 Header::GetPlanarConfiguration() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0006); + if ( strSize == GDCM_UNFOUND ) + { + return 0; + } + return atoi( strSize.c_str() ); +} + +/** + * \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 Header::GetPixelSize() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + // if (Header::GetEntryByNumber(0x0028,0x0100) == "24") + // return 3; + + 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, "Header::GetPixelSize: Unknown pixel type"); + return 0; +} + +/** + * \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 Header::GetPixelType() +{ + std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated"); + bitsAlloc = "16"; + } + + if ( bitsAlloc == "64" ) + { + return "FD"; + } + 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 = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation" + + if (sign == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); + bitsAlloc = "0"; + } + if ( sign == "0" ) + { + sign = "U"; + } + else + { + sign = "S"; + } + return bitsAlloc + sign; +} + + +/** + * \brief Recover the offset (from the beginning of the file) + * of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset + */ +size_t Header::GetPixelOffset() +{ + DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + if ( pxlElement ) + { + 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; + } +} + +/// \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 Header::GetPixelAreaLength() +{ + DocEntry* pxlElement = GetDocEntryByNumber(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; + } +} + +/** + * \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 Header::HasLUT() +{ + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntryByNumber(0x0028,0x1101) ) + { + return false; + } + // LutDescriptorGreen + if ( !GetDocEntryByNumber(0x0028,0x1102) ) + { + return false; + } + // LutDescriptorBlue + if ( !GetDocEntryByNumber(0x0028,0x1103) ) + { + return false; + } + // Red Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1201) ) + { + return false; + } + // Green Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1202) ) + { + return false; + } + // Blue Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(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; +} + +/** + * \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 Header::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 = GetEntryByNumber(0x0028,0x1101); + if ( lutDescription == GDCM_UNFOUND ) + { + return 0; + } + + 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; +} + +/** + * \brief Accesses the info from 0002,0010 : Transfert Syntax and TS + * else 1. + * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID) + */ +std::string Header::GetTransfertSyntaxName() +{ + // use the TS (TS : Transfert Syntax) + std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); + + if ( transfertSyntax == GDCM_NOTLOADED ) + { + std::cout << "Transfert Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" + << std::endl; + return "Uncompressed ACR-NEMA"; + } + if ( transfertSyntax == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetTransfertSyntaxName:" + " unfound Transfert Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } + + while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) ) + { + transfertSyntax.erase(transfertSyntax.length()-1, 1); + } + // we do it only when we need it + TS* ts = Global::GetTS(); + std::string tsName = ts->GetValue( transfertSyntax ); + + //delete ts; /// \todo Seg Fault when deleted ?! + return tsName; +} + +//----------------------------------------------------------------------------- +// Protected + +/** + * \brief anonymize a Header (removes Patient's personal info) + * (read the code to see which ones ...) + */ +bool Header::AnonymizeHeader() +{ + // If exist, replace by spaces + SetEntryByNumber (" ",0x0010, 0x2154); // Telephone + SetEntryByNumber (" ",0x0010, 0x1040); // Adress + SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID + + DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + + if ( patientNameHE ) // we replace it by Study Instance UID (why not) + { + std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010); + } + else + { + ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010); + } + } + + // 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; +} + +/** + * \brief gets the info from 0020,0037 : Image Orientation Patient + * @param iop adress of the (6)float aray to receive values + * @return cosines of image orientation patient + */ +void Header::GetImageOrientationPatient( float iop[6] ) +{ + std::string strImOriPat; + //iop is supposed to be float[6] + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; + + // 0020 0037 DS REL Image Orientation (Patient) + if ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + dbg.Verbose(0, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0037)"); + } + } + //For ACR-NEMA + // 0020 0035 DS REL Image Orientation (RET) + else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + dbg.Verbose(0, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0035)"); + } + } +} + +/** + * \brief Initialize a default DICOM header that should contain all the + * field require by other reader. DICOM standart does not + * explicitely defines thoses fields, heuristic has been choosen. + * This is not perfect as we are writting a CT image... + */ +void Header::InitializeDefaultHeader() +{ + typedef struct + { + const char *value; + uint16_t group; + uint16_t elem; + } DICOM_DEFAULT_VALUE; + + const char *date = Util::GetCurrentDate().c_str(); + const char *time = Util::GetCurrentTime().c_str(); + const char *uid = Util::CreateUniqueUID().c_str(); + + static DICOM_DEFAULT_VALUE defaultvalue[] = { + "76", 0x0002, 0x0000, // MetaElementGroup Length // FIXME: how to recompute ? + "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002, // MediaStorageSOPInstanceUID (CT Image Storage) + uid, 0x0002, 0x0012, // META Implementation Class UID + "ISO_IR 100", 0x0008, 0x0005, // Specific Character Set + "DERIVED\\SECONDARY\\OTHER\\GDCM", 0x0008, 0x0008, // Image Type + "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016, // SOP Class UID + "", 0x0008, 0x0050, // Accession Number + "GDCM", 0x0008, 0x0070, // Manufacturer + "GDCM", 0x0008, 0x0080, // Institution Name + "http://www-creatis.insa-lyon.fr/Public/Gdcm/", 0x0008, 0x0081, // Institution Address + "", 0x0008, 0x0090, // Refering Physician Name + "", 0x0008, 0x1030, // Study Description + "", 0x0008, 0x1050, // Performing Physician's Name + "", 0x0008, 0x1060, // Name of Physician(s) Reading Study + "", 0x0010, 0x0040, // Patient's Sex + uid, 0x0020, 0x000d, // StudyInstanceUID + uid, 0x0020, 0x000e, // SeriesInstanceUID + "", 0x0020, 0x0011, // AcquisitionNumber + "1\\0\\0\\0\\1\\0", 0x0020, 0x0037, // Image Orientation Patient + "1", 0x0028, 0x0002, // Samples per pixel 1 or 3 + "MONOCHROME2", 0x0028, 0x0004, // photochromatic interpretation + +// Date and time + + date, 0x0008, 0x0012, // Instance Creation Date + time, 0x0008, 0x0013, // Instance Creation Time + date, 0x0008, 0x0020, // Study Date + date, 0x0008, 0x0022, // Acquisition Date + date, 0x0008, 0x0023, // Content Date + time, 0x0008, 0x0030, // Study Time + "CT", 0x0008, 0x0060, // Modality + "GDCM", 0x0010, 0x0010, // Patient's Name + "GDCMID", 0x0010, 0x0020, // Patient ID + "1", 0x0020, 0x0010, // StudyID + "1", 0x0020, 0x0011, // SeriesNumber + "1.0", 0x0018, 0x0050, // slice Thickness + "1.0", 0x0018, 0x0088, // space between slices + "1.0\\1.0", 0x0028, 0x0030, // pixelSpacing + "64", 0x0028, 0x0010, // nbRows + "64", 0x0028, 0x0011, // nbCols + "16", 0x0028, 0x0100, // BitsAllocated 8 or 16 + "12", 0x0028, 0x0101, // BitsStored 8 or 12 + "11", 0x0028, 0x0102, // HighBit 7 or 11 + "0", 0x0028, 0x0103, // Pixel Representation 0(unsigned) or 1(signed) + "1000.0", 0x0028, 0x1051, // Window Width + "500.0", 0x0028, 0x1050, // Window Center + 0, 0, 0 + }; + + // default value + // Special case this is the image (not a string) + GrPixel = 0x7fe0; + NumPixel = 0x0010; + ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel); + + // All remaining strings: + unsigned int i = 0; + DICOM_DEFAULT_VALUE current = defaultvalue[i]; + while( current.value ) + { + std::string value = Util::DicomString( current.value ); //pad the string properly + ReplaceOrCreateByNumber(value, current.group, current.elem); + current = defaultvalue[++i]; + } +} + +//----------------------------------------------------------------------------- +// Private + +//----------------------------------------------------------------------------- + +} // end namespace gdcm