X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmElValSet.cxx;h=d9e8c39d34f029d759563ce880ad0d72986b3ed2;hb=f04b9ef9bad66e1847e8139db9cd4126e4340301;hp=dc2093e28b01c671d058a73985a97eac8587f9eb;hpb=551b84c1dc82294c4fc7356da0b5b1b3d74f7645;p=gdcm.git diff --git a/src/gdcmElValSet.cxx b/src/gdcmElValSet.cxx index dc2093e2..d9e8c39d 100644 --- a/src/gdcmElValSet.cxx +++ b/src/gdcmElValSet.cxx @@ -1,268 +1,550 @@ // gdcmElValSet.cxx -#include "gdcm.h" #include "gdcmUtil.h" +#include "gdcmElValSet.h" +#include "gdcmTS.h" +#include -TagElValueHT & ElValSet::GetTagHt(void) { +gdcmElValSet::~gdcmElValSet() { + for (TagElValueHT::iterator tag = tagHt.begin(); tag != tagHt.end(); ++tag) { + gdcmElValue* EntryToDelete = tag->second; + if ( EntryToDelete ) + delete EntryToDelete; + } + tagHt.clear(); + // Since Add() adds symetrical in both tagHt and NameHt we can + // assume all the pointed gdcmElValues are already cleaned-up when + // we cleaned tagHt. + NameHt.clear(); +} + +TagElValueHT & gdcmElValSet::GetTagHt(void) { return tagHt; } -void ElValSet::Add(ElValue * newElValue) { + +ListTag & gdcmElValSet::GetListElem(void) { + return listElem; +} + +/** + * \ingroup gdcmElValSet + * \brief + * @param newElValue + * @return + */ +void gdcmElValSet::Add(gdcmElValue * newElValue) { tagHt [newElValue->GetKey()] = newElValue; NameHt[newElValue->GetName()] = newElValue; + +// WARNING : push_bash in listElem ONLY during ParseHeader +// TODO : something to allow further Elements addition +// position to be taken care of ! + listElem.push_back(newElValue); } -void ElValSet::Print(ostream & os) { - for (TagElValueHT::iterator tag = tagHt.begin(); - tag != tagHt.end(); - ++tag){ - os << tag->first << ": "; - os << "[" << tag->second->GetValue() << "]"; - os << "[" << tag->second->GetName() << "]"; - os << "[" << tag->second->GetVR() << "]" << endl; - } +/** + * \ingroup gdcmElValSet + * \brief Checks if a given Dicom element exists + * \ within a ElValSet + * @param Group + * @param Elem + * @return + */ +int gdcmElValSet::CheckIfExistByNumber(guint16 Group, guint16 Elem ) { + std::string key = TranslateToKey(Group, Elem ); + return (tagHt.count(key)); +} + +/** + * \ingroup gdcmElValSet + * \brief + */ +void gdcmElValSet::Print(std::ostream & os) { + + size_t o; + short int g, e; + TSKey v; + std::string d2; + gdcmTS * ts = gdcmGlobal::GetTS(); + + for (TagElValueHT::iterator tag = tagHt.begin(); + tag != tagHt.end(); + ++tag){ + g = tag->second->GetGroup(); + e = tag->second->GetElement(); + v = tag->second->GetValue(); + o = tag->second->GetOffset(); + d2 = _CreateCleanString(v); // replace non printable characters by '.' + + os << tag->first << ": "; + os << " lgr : " << tag->second->GetLength(); + os << ", Offset : " << o; + os << " x(" << std::hex << o << std::dec << ") "; + os << "\t[" << tag->second->GetVR() << "]"; + os << "\t[" << tag->second->GetName() << "]"; + os << "\t[" << d2 << "]"; + + // Display the UID value (instead of displaying the rough code) + if (g == 0x0002) { // Some more to be displayed ? + if ( (e == 0x0010) || (e == 0x0002) ) + os << " ==>\t[" << ts->GetValue(v) << "]"; + } else { + if (g == 0x0008) { + if ( (e == 0x0016) || (e == 0x1150) ) + os << " ==>\t[" << ts->GetValue(v) << "]"; + } + } + os << std::endl; + } + + std::cout << "----------------------------------------------" << std::endl; + + //for (ListTag::iterator i = listElem.begin(); + + char tag[9]; + + for (std::list::iterator i = listElem.begin(); + i != listElem.end(); + ++i){ + sprintf(tag,"%04x|%04x",(*i)->GetGroup(),(*i)->GetElement()); + g = (*i)->GetGroup(); + e = (*i)->GetElement(); + v = (*i)->GetValue(); + o = (*i)->GetOffset(); + d2 = _CreateCleanString(v); // replace non printable characters by '.' + //os << std::hex <GetLength(); + os << ", Offset : " << o; + os << " x(" << std::hex << o << std::dec << ") "; + os << "\t[" << (*i)->GetVR() << "]"; + os << "\t[" << (*i)->GetName() << "]"; + os << "\t[" << d2 << "]"; + + // Display the UID value (instead of displaying the rough code) + if (g == 0x0002) { // Any more to be displayed ? + if ( (e == 0x0010) || (e == 0x0002) ) + os << " ==>\t[" << ts->GetValue(v) << "]"; + } else { + if (g == 0x0008) { + if ( (e == 0x0016) || (e == 0x1150) ) + os << " ==>\t[" << ts->GetValue(v) << "]"; + } + } + os << std::endl; + + } + } -void ElValSet::PrintByName(ostream & os) { - for (TagElValueNameHT::iterator tag = NameHt.begin(); - tag != NameHt.end(); - ++tag){ - os << tag->first << ": "; - os << "[" << tag->second->GetValue() << "]"; - os << "[" << tag->second->GetKey() << "]"; - os << "[" << tag->second->GetVR() << "]" << endl; - } +/** + * \ingroup gdcmElValSet + * \brief + */ +void gdcmElValSet::PrintByName(std::ostream & os) { + for (TagElValueNameHT::iterator tag = NameHt.begin(); + tag != NameHt.end(); + ++tag){ + os << tag->first << ": "; + os << "[" << tag->second->GetValue() << "]"; + os << "[" << tag->second->GetKey() << "]"; + os << "[" << tag->second->GetVR() << "]" << std::endl; + } } -ElValue* ElValSet::GetElementByNumber(guint32 group, guint32 element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHt.count(key)) - return (ElValue*)0; - if (tagHt.count(key) > 1) - dbg.Verbose(0, "ElValSet::GetElementByNumber", - "multiple entries for this key (FIXME) !"); - return tagHt.find(key)->second; +/** + * \ingroup gdcmElValSet + * \brief + * @param group + * @param element + * @return + */ +gdcmElValue* gdcmElValSet::GetElementByNumber(guint16 group, guint16 element) { + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( ! tagHt.count(key)) + return (gdcmElValue*)0; + return tagHt.find(key)->second; } -ElValue* ElValSet::GetElementByName(string TagName) { +/** + * \ingroup gdcmElValSet + * \brief + * @return + */ +gdcmElValue* gdcmElValSet::GetElementByName(std::string TagName) { if ( ! NameHt.count(TagName)) - return (ElValue*)0; - if (NameHt.count(TagName) > 1) - dbg.Verbose(0, "ElValSet::GetElement", - "multipe entries for this key (FIXME) !"); + return (gdcmElValue*)0; return NameHt.find(TagName)->second; } -string ElValSet::GetElValueByNumber(guint32 group, guint32 element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHt.count(key)) - return "gdcm::Unfound"; - if (tagHt.count(key) > 1) - dbg.Verbose(0, "ElValSet::GetElValueByNumber", - "multiple entries for this key (FIXME) !"); - return tagHt.find(key)->second->GetValue(); +/** + * \ingroup gdcmElValSet + * \brief + * @param group + * @param element + * @return + */ +std::string gdcmElValSet::GetElValueByNumber(guint16 group, guint16 element) { + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( ! tagHt.count(key)) + return GDCM_UNFOUND; + return tagHt.find(key)->second->GetValue(); } -string ElValSet::GetElValueByName(string TagName) { - if ( ! NameHt.count(TagName)) - return "gdcm::Unfound"; - if (NameHt.count(TagName) > 1) - dbg.Verbose(0, "ElValSet::GetElValue", - "multipe entries for this key (FIXME) !"); - return NameHt.find(TagName)->second->GetValue(); +/** + * \ingroup gdcmElValSet + * \brief + * @return + */ +std::string gdcmElValSet::GetElValueByName(std::string TagName) { + if ( ! NameHt.count(TagName)) + return GDCM_UNFOUND; + return NameHt.find(TagName)->second->GetValue(); } -int ElValSet::SetElValueByNumber(string content, guint32 group, guint32 element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHt.count(key)) - return 0; - if (tagHt.count(key) > 1) { - dbg.Verbose(0, "ElValSet::SetElValueByNumber", - "multiple entries for this key (FIXME) !"); - return (0); - } - tagHt[key]->SetValue(content); +/** + * \ingroup gdcmElValSet + * \brief + * @param content + * @param group + * @param element + * @return + */ +int gdcmElValSet::SetElValueByNumber(std::string content, + guint16 group, guint16 element) { + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( ! tagHt.count(key)) + return 0; + int l = content.length(); + if(l%2) { // Odd length are padded with a space (020H). + l++; + content = content + '\0'; + } + tagHt[key]->SetValue(content); - // Question : m à j LgrElem ? - tagHt[key]->SetLength(strlen(content.c_str())); + std::string vr = tagHt[key]->GetVR(); + guint32 lgr; - // FIXME should we really update the element length ? - tagHt[key]->SetLength(content.length()); + if( (vr == "US") || (vr == "SS") ) + lgr = 2; + else if( (vr == "UL") || (vr == "SL") ) + lgr = 4; + else + lgr = l; + tagHt[key]->SetLength(lgr); - return(1); + + + return 1; +} + +/** + * \ingroup gdcmElValSet + * \brief + * @param content + * @param TagName + * @return + */ +int gdcmElValSet::SetElValueByName(std::string content, std::string TagName) { + if ( ! NameHt.count(TagName)) + return 0; + int l = content.length(); + if(l%2) { // Odd length are padded with a space (020H). + l++; + // Well. I know that '/0' is NOT a space + // but it doesn't work with a space. + // Use hexedit and see 0002|0010 value (Transfer Syntax UID) + content = content + '\0'; + } + NameHt[TagName]->SetValue(content); + + std::string vr = NameHt[TagName]->GetVR(); + guint32 lgr; + + if( (vr == "US") || (vr == "SS") ) + lgr = 2; + else if( (vr == "UL") || (vr == "SL") ) + lgr = 4; + else + lgr = content.length(); + +// TODO : WARNING: le cas de l'element des pixels (7fe0,0010) n'est pas traite +// par SetElValueByName +// il faudra utiliser SetElValueByNumber + + NameHt[TagName]->SetLength(lgr); + return 1; } -int ElValSet::SetElValueByName(string content, string TagName) { - if ( ! NameHt.count(TagName)) - return 0; - if (NameHt.count(TagName) > 1) { - dbg.Verbose(0, "ElValSet::SetElValueByName", - "multipe entries for this key (FIXME) !"); - return 0; - } - NameHt.find(TagName)->second->SetValue(content); - NameHt.find(TagName)->second->SetLength(strlen(content.c_str())); - return(1); +/** + * \ingroup gdcmElValSet + * \brief Generate a free TagKey i.e. a TagKey that is not present + * in the TagHt dictionary. + * @param group The generated tag must belong to this group. + * @return The element of tag with given group which is fee. + */ +guint32 gdcmElValSet::GenerateFreeTagKeyInGroup(guint16 group) { + for (guint32 elem = 0; elem < UINT32_MAX; elem++) { + TagKey key = gdcmDictEntry::TranslateToKey(group, elem); + if (tagHt.count(key) == 0) + return elem; + } + return UINT32_MAX; } +/** + * \ingroup gdcmElValSet + * \brief + * @param area + * @param group + * @param element + * @return + */ +int gdcmElValSet::SetVoidAreaByNumber(void * area, + guint16 group, guint16 element) { + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( ! tagHt.count(key)) + return 0; + tagHt[key]->SetVoidArea(area); + return 1 ; +} -int ElValSet::SetElValueLengthByNumber(guint32 l, guint32 group, guint32 element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHt.count(key)) - return 0; - if (tagHt.count(key) > 1) { - dbg.Verbose(0, "ElValSet::SetElValueLengthByNumber", - "multiple entries for this key (FIXME) !"); - return (0); - } - // m à j LgrElem - tagHt[key]->SetLength(l); - return(1); +/** + * \ingroup gdcmElValSet + * \brief + * @param length + * @param group + * @param element + * @return int acts as a boolean + */ +int gdcmElValSet::SetElValueLengthByNumber(guint32 length, + guint16 group, guint16 element) { + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( ! tagHt.count(key)) + return 0; + if (length%2) length++; // length must be even + tagHt[key]->SetLength(length); + return 1 ; +} +/** + * \ingroup gdcmElValSet + * \brief + * @param length + * @param TagName + * @return + */ +int gdcmElValSet::SetElValueLengthByName(guint32 length, std::string TagName) { + if ( ! NameHt.count(TagName)) + return 0; + if (length%2) length++; // length must be even + NameHt.find(TagName)->second->SetLength(length); + return 1 ; } +/** + * \ingroup gdcmElValSet + * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader + * @param SkipSequence TRUE if we don't want to write Sequences (ACR-NEMA Files) + * @param type + */ +void gdcmElValSet::UpdateGroupLength(bool SkipSequence, FileType type) { + guint16 gr, el; + std::string vr; + + gdcmElValue *elem; + char trash[10]; + std::string str_trash; + + GroupKey key; + GroupHT groupHt; // to hold the length of each group + TagKey tk; + // remember : + // typedef std::map GroupHT; + + gdcmElValue *elemZ; + + // for each Tag in the DCM Header + + for (TagElValueHT::iterator tag2 = tagHt.begin(); + tag2 != tagHt.end(); + ++tag2){ -int ElValSet::SetElValueLengthByName(guint32 l, string TagName) { - if ( ! NameHt.count(TagName)) - return 0; - if (NameHt.count(TagName) > 1) { - dbg.Verbose(0, "ElValSet::SetElValueByName", - "multipe entries for this key (FIXME) !"); - return 0; - } - NameHt.find(TagName)->second->SetLength(l); - return(1); + elem = tag2->second; + gr = elem->GetGroup(); + el = elem->GetElement(); + vr = elem->GetVR(); + + sprintf(trash, "%04x", gr); + key = trash; // generate 'group tag' + + // if the caller decided not to take SEQUENCEs into account + // e.g : he wants to write an ACR-NEMA File + + if (SkipSequence && vr == "SQ") continue; + + // Still unsolved problem : + // we cannot find the 'Sequence Delimitation Item' + // since it's at the end of the Hash Table + // (fffe,e0dd) + + // pas SEQUENCE en ACR-NEMA + // WARNING : + // --> la descente a l'interieur' des SQ + // devrait etre faite avec une liste chainee, pas avec une HTable... + + if ( groupHt.count(key) == 0) { // we just read the first elem of a given group + if (el == 0x0000) { // the first elem is 0x0000 + groupHt[key] = 0; // initialize group length + } else { + groupHt[key] = 2 + 2 + 4 + elem->GetLength(); // non 0x0000 first group elem + } + } else { // any elem but the first + if (type == ExplicitVR) { + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) { + groupHt[key] += 4; // explicit VR AND OB, OW, SQ : 4 more bytes + } + } + groupHt[key] += 2 + 2 + 4 + elem->GetLength(); + } + } + + unsigned short int gr_bid; + + for (GroupHT::iterator g = groupHt.begin(); // for each group we found + g != groupHt.end(); + ++g){ + // FIXME: g++ -Wall -Wstrict-prototypes reports on following line: + // warning: unsigned int format, different type arg + sscanf(g->first.c_str(),"%x",&gr_bid); + tk = g->first + "|0000"; // generate the element full tag + + if ( tagHt.count(tk) == 0) { // if element 0x0000 not found + gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL"); + elemZ = new gdcmElValue(tagZ); + elemZ->SetLength(4); + Add(elemZ); // create it + } else { + elemZ=GetElementByNumber(gr_bid, 0x0000); + } + sprintf(trash ,"%d",g->second); + str_trash=trash; + elemZ->SetValue(str_trash); + } } +/** + * \ingroup gdcmElValSet + * \brief + * @param type + * @param _fp + * @return + */ +void gdcmElValSet::WriteElements(FileType type, FILE * _fp) { + guint16 gr, el; + guint32 lgr; + const char * val; + std::string vr; + guint32 val_uint32; + guint16 val_uint16; + + std::vector tokens; -int ElValSet::Write(FILE * _fp) { + void *ptr; -// ATTENTION : fonction non terminée (commitée a titre de precaution) + // Tout ceci ne marche QUE parce qu'on est sur un proc Little Endian + // restent a tester les echecs en ecriture (apres chaque fwrite) - guint16 gr, el; - guint32 lgr; - const char * val; - string vr; - guint32 val_int32; - guint16 val_int16; - void *ptr; - char str_lgrCalcGroupe[10]; - - string implicitVRTransfertSyntax = "1.2.840.10008.1.2"; - - // Utilisées pour le calcul Group Length - int deja = 0; - guint32 lgrCalcGroupe=0; - ElValue *elem, *elemZ, *elemZPrec; - guint16 grCourant = 0; - - // Question : - // Comment pourrait-on tester si on est TrueDicom ou non , + for (TagElValueHT::iterator tag2=tagHt.begin(); + tag2 != tagHt.end(); + ++tag2){ + + gr = tag2->second->GetGroup(); + el = tag2->second->GetElement(); + lgr = tag2->second->GetLength(); + val = tag2->second->GetValue().c_str(); + vr = tag2->second->GetVR(); + + // std::cout << "Tag "<< std::hex << gr << " " << el << std::endl; + + if ( type == ACR ) { + if (gr < 0x0008) continue; // ignore pure DICOM V3 groups + if (gr %2) continue; // ignore shadow groups + if (vr == "SQ" ) continue; // ignore Sequences + if (gr == 0xfffe ) continue; // ignore delimiters + } + + fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group + fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element + + if ( (type == ExplicitVR) && (gr <= 0x0002) ) { + // EXPLICIT VR + guint16 z=0, shortLgr; + fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); + + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) { + fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); + fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); + + } else { + shortLgr=lgr; + fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); + } + } else { // IMPLICIT VR + fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); + } + + if (vr == "US" || vr == "SS") { + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (tag2->second->GetValue(), tokens, "\\"); + for (unsigned int i=0; isecond->GetValue(), tokens, "\\"); + for (unsigned int i=0; isecond; - printf("gr %04x el %04x lgr %d\n",elem->GetGroup(), elem->GetElement(), elem->GetLength()); - - if ( (elem->GetGroup() != grCourant) && - (elem->GetGroup() != 0xfffe) ) { // On arrive sur un nv Groupe - - printf("Nouv Groupegr %04x el %04x \n",elem->GetGroup(), elem->GetElement()); - - elemZ = elem; - - if(elemZ->GetElement() != 0x0000) { // pas d'element 'Lgr groupe' - // On crée - gdcmDictEntry * tagZ = new gdcmDictEntry(grCourant, 0x0000, "UL"); - elemZ = new ElValue(tagZ); // on le cree - elemZ->SetLength(4); - Add(elemZ); // On l'accroche à sa place - } - - if (deja) { - sprintf(str_lgrCalcGroupe,"%d",lgrCalcGroupe); - elemZPrec->SetValue(str_lgrCalcGroupe); - lgrCalcGroupe = 0; - } - deja = 1; - - lgrCalcGroupe = 12; //2 + 2 + 4 + 4; // Gr + Num + Lgr + LgrGroupe - printf ("lgrCalcGroupe %d\n",lgrCalcGroupe); - - elemZPrec = elemZ; - grCourant = elem->GetGroup(); - - } else { // On n'EST PAS sur un nv Groupe - - printf ("lgrCalcGroupe avant : %d LgrElem %d\n",lgrCalcGroupe,elem->GetLength()); - - lgrCalcGroupe += 2 + 2 + 4 + elem->GetLength(); // Gr + Num + Lgr + LgrElem - - printf ("lgrCalcGroupe apres %d\n",lgrCalcGroupe); - - } - } - - // Si on fait de l'implicit VR little Endian - // (pour moins se fairche sur processeur INTEL) - // penser a forcer le TRANSFERT SYNTAX UID - - SetElValueByNumber(implicitVRTransfertSyntax, 0x0002, 0x0010); - SetElValueLengthByNumber(18, 0x0002, 0x0010); // Le 0 de fin de chaine doit etre stocké, dans ce cas - - // restent à tester les echecs en écriture (apres chaque fwrite) - - for (TagElValueHT::iterator tag = tagHt.begin(); - tag != tagHt.end(); - ++tag){ - - // Question : - // peut-on se passer des affectations? - // - passer l'adresse du resultat d'une fonction (???) - // - acceder au champ sans passer par un accesseur ? - - gr = tag->second->GetGroup(); - el = tag->second->GetElement(); - lgr = tag->second->GetLength(); - val = tag->second->GetValue().c_str(); - vr = tag->second->GetVR(); - - fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group - fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - - //fwrite ( vr,(size_t)2 ,(size_t)1 ,_fp); //VR - - // si on n'est pas en IMPLICIT VR voir pb (lgr + VR) - - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); //lgr - - if (vr == "US" || vr == "SS") { - val_int16 = atoi(val); - ptr = &val_int16; - fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp); - continue; - } - if (vr == "UL" || vr == "SL") { - val_int32 = atoi(val); - ptr = &val_int32; - fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp); - continue; - } - - // Les pixels ne sont pas chargés dans l'element ! - if ((gr == 0x7fe0) && (el == 0x0010) ) break; - - fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); //valeur Elem - } - - return(1); + // WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA + // no way + // a moins de se livrer a un tres complique ajout des champs manquants. + // faire un CheckAndCorrectHeader (?) + + if ( (type == ImplicitVR) || (type == ExplicitVR) ) + UpdateGroupLength(false,type); + if ( type == ACR) + UpdateGroupLength(true,ACR); + + WriteElements(type, _fp); + return(1); }