X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=7fbc137c187952a3e690a05ee07aa930f246ef4d;hb=05f9a9731209a5c98895a57c6abca609f8e9b312;hp=111f0e0fa1d3d05bbc311cb1f6d44138d11fa69e;hpb=4d59e5e9778e5abff13d13d576ef92ce81498b6f;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 111f0e0f..7fbc137c 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,251 +1,161 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- -#include "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.h" -#include "gdcmDirList.h" -#include "gdcmUtil.h" +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2004/06/23 13:02:36 $ + Version: $Revision: 1.52 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ #include - +#include #include #include -//----------------------------------------------------------------------------- -class ELEMENTS -{ -public : - ELEMENTS(unsigned short int _group,unsigned short int _elem,std::string _value) - {group=_group;elem=_elem;value=_value;} - - unsigned short int group; - unsigned short int elem; - std::string value; -}; - -ELEMENTS metaElem[]={ - //Meta Group Length : to be computed later - ELEMENTS(0x0002,0x0000,"12345"), - //File Meta Information Version - ELEMENTS(0x0002,0x0001,"\2\0\0\0"), - //Media Stored SOP Class UID i.e. : 'Media Storage Directory Storage' - ELEMENTS(0x0002,0x0002,"1.2.840.10008.1.3.10"), - //Media Stored SOP Instance UID : may be forged later - ELEMENTS(0x0002,0x0003,""), - //Transfer Syntax UID i.e. : Explicit VR - Little Endian - ELEMENTS(0x0002,0x0010,"1.2.840.10008.1.2.1"), - //Implementation Class UID : may be forged later - ELEMENTS(0x0002,0x0012,""), - //Implementation Version Name - ELEMENTS(0x0002,0x0013,"gdcmLib"), - //File-set ID : - ELEMENTS(0x0004,0x1130,""), - //Offset of the first dir of root dir entity : to be computed later - ELEMENTS(0x0004,0x1200,"0"), - //Offset of the last dir of root dir entity : to be computed later - ELEMENTS(0x0004,0x1202,"0"), - //File-set consistency flag - ELEMENTS(0x0004,0x1212,"0"), - //Directory record sequence : *length* to be set later - ELEMENTS(0x0004,0x1220,"0"), - ELEMENTS(0xffff,0xffff,"") -} ; - -ELEMENTS patientElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"PATIENT "), // don't remove trailing space ! - - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Patient's Name - ELEMENTS(0x0010,0x0010,""), - // Patient ID - ELEMENTS(0x0010,0x0020,""), - // Patient's Birthdate - ELEMENTS(0x0010,0x0030,""), - // Patient's Sex - ELEMENTS(0x0010,0x0040,""), - ELEMENTS(0xffff,0xffff,"") - }; - -ELEMENTS studyElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"STUDY "), // don't remove trailing space ! - - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Study Date - ELEMENTS(0x0008,0x0020,""), - // Study Time - ELEMENTS(0x0008,0x0030,""), - // Accession Number - ELEMENTS(0x0008,0x0050,""), - // Study Description - ELEMENTS(0x0008,0x1030,""), - // Study Instance UID : may be forged later - ELEMENTS(0x0020,0x000d,""), - // Study ID : may be forged later - ELEMENTS(0x0020,0x0010,""), - ELEMENTS(0xffff,0xffff,"") -}; - - -ELEMENTS serieElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"SERIES"), // don't add trailing space ! - - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Series Date - ELEMENTS(0x0008,0x0021,""), - // Series Time - ELEMENTS(0x0008,0x0031,""), - // Modality - ELEMENTS(0x0008,0x0060,""), - // Institution Name : may be forged later - ELEMENTS(0x0008,0x0080,""), - // Institution Address : may be forged later - ELEMENTS(0x0008,0x0081,""), - // Series Description : may be forged later - ELEMENTS(0x0008,0x103e,""), - // Series Instance UID : may be forged later - ELEMENTS(0x0020,0x000e,""), - // Series Number : may be forged later - ELEMENTS(0x0020,0x0011,"0"), - ELEMENTS(0xffff,0xffff,"") -}; - -ELEMENTS imageElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"IMAGE "), // don't remove trailing space ! - - // Referenced File ID : to be set later(relative File Name) - ELEMENTS(0x0004,0x1500,""), - // Referenced SOP Class UID in File : may be forged later - ELEMENTS(0x0004,0x1510,""), - // Referenced SOP Class UID in File : may be forged later - ELEMENTS(0x0004,0x1511,""), - // Referenced Transfer Syntax in File - ELEMENTS(0x0004,0x1512,""), - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Image Type - ELEMENTS(0x0008,0x0008,""), - // SOP Class UID : to be set/forged later - ELEMENTS(0x0008,0x0016,""), - // SOP Instance UID : to be set/forged later - ELEMENTS(0x0008,0x0018,""), - // Content Date - ELEMENTS(0x0008,0x0023,""), - // Content Time - ELEMENTS(0x0008,0x0033,""), - // Referenced Image Sequence : to be set/forged later - ELEMENTS(0x0008,0x1040,""), - ELEMENTS(0xfffe,0xe000,"0"), - // Referenced SOP Class UID : to be set/forged later - ELEMENTS(0x0008,0x1150,""), - // Referenced SOP Instance UID : to be set/forged later - ELEMENTS(0x0008,0x1155,""), - // Image Number - ELEMENTS(0x0020,0x0013,"0"), - // Image Position Patient - ELEMENTS(0x0020,0x0032,"0"), - // Image Orientation(Patient) - ELEMENTS(0x0020,0x0037,"0"), - // Frame of Reference UID - ELEMENTS(0x0020,0x0052,"0"), - // Rows - ELEMENTS(0x0028,0x0010,"0"), - // Columns - ELEMENTS(0x0028,0x0011,"0"), - // Pixel Spacing - ELEMENTS(0x0028,0x0030,"0"), - // Calibration Image - ELEMENTS(0x0050,0x0004,"0"), - ELEMENTS(0xffff,0xffff,"") -}; +#ifdef _MSC_VER + #include +#else + #include +#endif + +#include "gdcmDicomDir.h" +#include "gdcmDicomDirStudy.h" +#include "gdcmDicomDirSerie.h" +#include "gdcmDicomDirImage.h" +#include "gdcmDirList.h" +#include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmGlobal.h" +#include "gdcmHeader.h" +#include "gdcmSeqEntry.h" +#include "gdcmSQItem.h" +#include "gdcmValEntry.h" +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -/* - * \ingroup gdcmDicomDir - * \brief - * @param Filename - * @param exception_on_error + +void gdcmDicomDir::Initialize(void) +{ + startMethod = NULL; + progressMethod = NULL; + endMethod = NULL; + startMethodArgDelete = NULL; + progressMethodArgDelete = NULL; + endMethodArgDelete = NULL; + startArg = NULL; + progressArg = NULL; + endArg = NULL; + + progress = 0.0; + abort = false; + + metaElems = (gdcmDicomDirMeta *)0; +} + + +/** + * \brief Constructor Parses recursively the directory and creates the DicomDir + * or uses an already built DICOMDIR, depending on 'parseDir' value. + * @param FileName name + * - of the root directory (parseDir = true) + * - of the DICOMDIR (parseDir = false) + * @param parseDir boolean + * - true if user passed an entry point + * and wants to explore recursively the directories + * - false if user passed an already built DICOMDIR file + * and wants to use it + * @param exception_on_error whether we want to throw an exception or not */ -gdcmDicomDir::gdcmDicomDir(const char *FileName, +gdcmDicomDir::gdcmDicomDir(const char *FileName, bool parseDir, bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) + gdcmDocument(FileName,exception_on_error,true) // true : enable SeQuences { - if( GetListEntry().begin()==GetListEntry().end() ) - { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); + // que l'on ai passe un root directory ou un DICOMDIR + // et quelle que soit la valeur de parseDir, + // on a lance gdcmDocument + Initialize(); - std::string path=FileName; - std::string file; + // gdcmDocument already executed + // if user passed a root directory, sure we didn't get anything - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); - else - path.resize(pos2); - NewDicomDir(path); - } + if( GetEntry().begin() == GetEntry().end() ) + { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); + + if(strlen(FileName)==1 && FileName[0]=='.') { // user passed '.' as Name + // we get current directory name + char* dummy= new char[1000]; + getcwd(dummy, (size_t)1000); + SetFileName(dummy); // will be converted into a string + delete[] dummy; // no longer needed + } - CreateDicomDir(); + if(parseDir) + { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory" + " and create the DicomDir"); + ParseDirectory(); + } else { + /// \todo if parseDir == false, it should be tagged as an error + } + } + else + { + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if (e==NULL) { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME : what to do when the parsed file IS NOT a + /// DICOMDIR file ? + } + CreateDicomDir(); + } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param exception_on_error + * \brief Constructor : creates an empty gdcmDicomDir + * @param exception_on_error whether we want to throw an exception or not */ -gdcmDicomDir::gdcmDicomDir(ListTag *l, - bool exception_on_error): - gdcmParser(exception_on_error ) -{ - listEntries=*l; - CreateDicomDir(); +gdcmDicomDir::gdcmDicomDir(bool exception_on_error): + gdcmDocument(exception_on_error) +{ + + Initialize(); + + std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... + SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements + AddDicomDirMeta(); } -/* - * \ingroup gdcmDicomDir +/** * \brief Canonical destructor */ gdcmDicomDir::~gdcmDicomDir() { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + SetStartMethod(NULL); + SetProgressMethod(NULL); + SetEndMethod(NULL); + + if(metaElems) + delete metaElems; + + for(ListDicomDirPatient::iterator cc = patients.begin(); + cc!= patients.end(); + ++cc) { delete *cc; } @@ -253,25 +163,159 @@ gdcmDicomDir::~gdcmDicomDir() //----------------------------------------------------------------------------- // Print +/** + * \brief Canonical Printer + */ void gdcmDicomDir::Print(std::ostream &os) { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + if(metaElems) + { + metaElems->SetPrintLevel(printLevel); + metaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = patients.begin(); + cc != patients.end(); + ++cc) { (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + (*cc)->Print(os); } } //----------------------------------------------------------------------------- // 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 DicomDir. + * @return true when gdcmDocument is the one of a reasonable DicomDir, + * false otherwise. + */ +bool gdcmDicomDir::IsReadable(void) +{ + if(!gdcmDocument::IsReadable()) + return(false); + if(!metaElems) + return(false); + if(patients.size()<=0) + return(false); + + return(true); +} + +/** + * \ingroup gdcmDicomDir + * \brief fills the whole structure, starting from a root Directory + */ +void gdcmDicomDir::ParseDirectory(void) +{ + CreateDicomDirChainedList(GetFileName()); + CreateDicomDir(); +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the start method to call when the parsing of the directory starts + * @param method Method to call + * @param arg Argument to pass to the method + * @param argDelete Argument + * \warning In python : the arg parameter isn't considered + */ +void gdcmDicomDir::SetStartMethod(gdcmMethod *method,void *arg,gdcmMethod *argDelete) +{ + if((startArg)&&(startMethodArgDelete)) + startMethodArgDelete(startArg); + + startMethod=method; + startArg=arg; + startMethodArgDelete=argDelete; +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the method to delete the argument + * The argument is destroyed when the method is changed or when the + * class is destroyed + * @param method Method to call to delete the argument + */ +void gdcmDicomDir::SetStartMethodArgDelete(gdcmMethod *method) +{ + startMethodArgDelete=method; +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the progress method to call when the parsing of the directory progress + * @param method Method to call + * @param arg Argument to pass to the method + * @param argDelete Argument + * \warning In python : the arg parameter isn't considered + */ +void gdcmDicomDir::SetProgressMethod(gdcmMethod *method,void *arg,gdcmMethod *argDelete) +{ + if((progressArg)&&(progressMethodArgDelete)) + progressMethodArgDelete(progressArg); + + progressMethod=method; + progressArg=arg; + progressMethodArgDelete=argDelete; +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the method to delete the argument + * The argument is destroyed when the method is changed or when the + * class is destroyed + * @param method Method to call to delete the argument + */ +void gdcmDicomDir::SetProgressMethodArgDelete(gdcmMethod *method) +{ + progressMethodArgDelete=method; +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the end method to call when the parsing of the directory ends + * @param method Method to call + * @param arg Argument to pass to the method + * @param argDelete Argument + * \warning In python : the arg parameter isn't considered + */ +void gdcmDicomDir::SetEndMethod(gdcmMethod *method, void *arg, gdcmMethod *argDelete) +{ + if((endArg)&&(endMethodArgDelete)) + endMethodArgDelete(endArg); + + endMethod=method; + endArg=arg; + endMethodArgDelete=argDelete; +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the method to delete the argument + * The argument is destroyed when the method is changed or when the class + * is destroyed + * @param method Method to call to delete the argument + */ +void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) +{ + endMethodArgDelete=method; +} + /** * \ingroup gdcmDicomDir * \brief writes on disc a DICOMDIR * \ warning does NOT add the missing elements in the header : - * \ it's up to the user doing it ! + * it's up to the user doing it ! + * \todo : to be re-written using the DICOMDIR tree-like structure + * *not* the chained list + * (does NOT exist if the DICOMDIR is user-forged !) * @param fileName file to be written to - * @return + * @return false only when fail to open */ + bool gdcmDicomDir::Write(std::string fileName) { FILE * fp1; @@ -283,369 +327,640 @@ bool gdcmDicomDir::Write(std::string fileName) return(false); } - char * filePreamble; - filePreamble=(char*)calloc(128,1); + char * filePreamble = new char[128]; fwrite(filePreamble,128,1,fp1); fwrite("DICM",4,1,fp1); - free(filePreamble); - - WriteEntries(DICOMDIR,fp1); + delete[] filePreamble; + UpdateDirectoryRecordSequenceLength(); + WriteEntries(fp1); fclose(fp1); - return true; } +/** + * \brief Writes in a file using the tree-like structure. + * @param _fp already open file pointer + */ + +void gdcmDicomDir::WriteEntries(FILE *) //_fp +{ + /// \todo (?) tester les echecs en ecriture + /// (apres chaque fwrite, dans le WriteEntry) + + +/* TODO : to go on compiling + + gdcmDicomDirMeta *ptrMeta; + ListDicomDirPatient::iterator itPatient; + ListDicomDirStudy::iterator itStudy; + ListDicomDirSerie::iterator itSerie; + ListDicomDirImage::iterator itImage; + ListTag::iterator i; + + ptrMeta= GetDicomDirMeta(); + for(i=ptrMeta->debut();i!=ptrMeta->fin();++i) { + WriteEntry(*i,_fp, gdcmExplicitVR); + } + + itPatient = GetDicomDirPatients().begin(); + while ( itPatient != GetDicomDirPatients().end() ) { + for(i=(*itPatient)->debut();i!=(*itPatient)->fin();++i) { + WriteEntry(*i,_fp, gdcmExplicitVR); + } + itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); + while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { + for(i=(*itStudy)->debut();i!=(*itStudy)->fin();++i) { + WriteEntry(*i,_fp, gdcmExplicitVR); + } + itSerie = ((*itStudy)->GetDicomDirSeries()).begin(); + while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) { + for(i=(*itSerie)->debut();i!=(*itSerie)->fin();++i) { + WriteEntry(*i,_fp, gdcmExplicitVR); + } + itImage = ((*itSerie)->GetDicomDirImages()).begin(); + while (itImage != (*itSerie)->GetDicomDirImages().end() ) { + for(i=(*itImage)->debut();i!=(*itImage)->fin();++i) { + WriteEntry(*i,_fp, gdcmExplicitVR); + } + ++itImage; + } + ++itSerie; + } + ++itStudy; + } + ++itPatient; + } + */ +} + //----------------------------------------------------------------------------- // Protected -/* + +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief create a gdcmDocument-like chained list from a root Directory + * @param path entry point of the tree-like structure */ -void gdcmDicomDir::NewDicomDir(std::string path) +void gdcmDicomDir::CreateDicomDirChainedList(std::string path) { - gdcmDirList fileList(path,1); - ListHeader list; + CallStartMethod(); + + gdcmDirList fileList(path,1); // gets recursively the file list + unsigned int count=0; + VectDocument list; gdcmHeader *header; - listEntries.clear(); + tagHT.clear(); + patients.clear(); for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) + it!=fileList.end(); + ++it) { -// std::cout<<*it<c_str()); if(header->IsReadable()) - list.push_back(header); + list.push_back(header); // adds the file header to the chained list else delete header; + + count++; } + // sorts Patient/Study/Serie/ + std::sort(list.begin(),list.end(),gdcmDicomDir::HeaderLessThan); - SetElements(path,list); + std::string tmp=fileList.GetDirName(); + + //for each Header of the chained list, add/update the Patient/Study/Serie/Image info + SetElements(tmp,list); + + CallEndMethod(); +} + +/** + * \ingroup gdcmDicomDir + * \brief adds *the* Meta to a partially created DICOMDIR + */ + + // FIXME : Heuuuuu ! Il prend les Entries du Document deja parse, + // il ne fabrique rien ! + +gdcmDicomDirMeta * gdcmDicomDir::NewMeta(void) { + gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); + for (TagDocEntryHT::iterator cc = tagHT.begin();cc != tagHT.end();++cc) { + m->AddDocEntry(cc->second); + } + return m; +} + + +/** + * \ingroup gdcmDicomDir + * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + */ +gdcmDicomDirPatient * gdcmDicomDir::NewPatient(void) { + std::list elemList; + std::list::iterator it; + guint16 tmpGr,tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + + gdcmSQItem *s = new gdcmSQItem(0); + + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + + // TODO : use FillObject !!! + + // for all the DicomDirPatient Elements + + for(it=elemList.begin();it!=elemList.end();++it) + { + tmpGr=it->group; + tmpEl=it->elem; + dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); + entry=new gdcmValEntry(dictEntry); + entry->SetOffset(0); // just to avoid further missprinting + entry->SetValue(it->value); + + // dealing with value length ... + + if(dictEntry->GetGroup()==0xfffe) + { + entry->SetLength(entry->GetValue().length()); + } + else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) + { + entry->SetLength(4); + } + else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) + { + entry->SetLength(2); + } + else if(dictEntry->GetVR()=="SQ") + { + entry->SetLength(0xffffffff); + } + else + { + entry->SetLength(entry->GetValue().length()); + } + s->AddDocEntry(entry); + } + + gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &tagHT); + patients.push_front(p); + return p; +} + +/** + * \brief adds to the HTable + * the gdcmEntries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type gdcmObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header gdcmHeader of the current file + */ +void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, + gdcmDocument *header) +{ + std::list elemList; + std::list::iterator it; + guint16 tmpGr, tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + std::string val; + + switch(type){ + case GDCM_DICOMDIR_PATIENT: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + break; + case GDCM_DICOMDIR_STUDY: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); + break; + case GDCM_DICOMDIR_SERIE: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + break; + case GDCM_DICOMDIR_IMAGE: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + break; + case GDCM_DICOMDIR_META: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + break; + default: + return; + } + + for(it=elemList.begin();it!=elemList.end();++it) { + tmpGr=it->group; + tmpEl=it->elem; + dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); + entry=new gdcmValEntry(dictEntry); // Be sure it's never a BinEntry ! + + entry->SetOffset(0); // just to avoid further missprinting + + if(header) + val=header->GetEntryByNumber(tmpGr,tmpEl); + else + val=GDCM_UNFOUND; + + if(val==GDCM_UNFOUND) + { + if((tmpGr==0x0004) &&(tmpEl==0x1130) ) // File-set ID + { + // force to the *end* File Name + val=GetName(path); + } + else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image + { + if(header->GetFileName().substr(0,path.length())!=path) + { + dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path" + " of file name is incorrect"); + val=header->GetFileName(); + } + else + { + val=&(header->GetFileName().c_str()[path.length()]); + } + } + else + { + val=it->value; + } + } + else + { + if (header->GetEntryLengthByNumber(tmpGr,tmpEl)== 0) + val=it->value; + } + + entry->SetValue(val); + + if(dictEntry) + { + if(dictEntry->GetGroup()==0xfffe) { + entry->SetLength(entry->GetValue().length()); + } + else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) + { + entry->SetLength(4); + } + else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) + { + entry->SetLength(2); + } + else if(dictEntry->GetVR()=="SQ") + { + entry->SetLength(0xffffffff); + } + else + { + entry->SetLength(entry->GetValue().length()); + } + } + //AddDocEntry(entry); // both in H Table and in chained list + tagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE ! + } +} + +/** + * \brief CallStartMethod + */ +void gdcmDicomDir::CallStartMethod(void) +{ + progress=0.0f; + abort=false; + if(startMethod) + startMethod(startArg); +} +/** + * \ingroup gdcmDicomDir + * \brief CallProgressMethod + */ +void gdcmDicomDir::CallProgressMethod(void) +{ + if(progressMethod) + progressMethod(progressArg); +} +/** + * \ingroup gdcmDicomDir + * \brief CallEndMethod + */ +void gdcmDicomDir::CallEndMethod(void) +{ + progress=1.0f; + if(endMethod) + endMethod(endArg); } //----------------------------------------------------------------------------- // Private -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader */ void gdcmDicomDir::CreateDicomDir() { - // The list is parsed. When a tag is found : + // The list is parsed. + // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found : // 1 - we save the beginning iterator // 2 - we continue to parse // 3 - we find an other tag // + we create the object for the precedent tag // + loop to 1 - - gdcmDicomDirType type=gdcmDicomDir::GDCM_NONE; - ListTag::iterator begin; - ListTag::iterator end; - - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=listEntries.begin();i !=listEntries.end();++i) + gdcmDicomDirType type=gdcmDicomDir::GDCM_DICOMDIR_META; + + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if (e==NULL) { - // std::cout << std::hex <<(*i)->GetGroup() << - // " " <<(*i)->GetElement() << endl; + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? + return; + } + + gdcmSeqEntry* s = dynamic_cast(e); + if (!s) + { + dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); + return; + } - std::string v=(*i)->GetValue(); - if(v=="PATIENT ") + ListSQItem listItems = s->GetSQItems(); + gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); + (void)m; //?? + + gdcmDocEntry * d; + std::string v; + for(ListSQItem::iterator i=listItems.begin(); i !=listItems.end();++i) + { + d=(*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type + if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(d) ) { - // std::cout<<"PATIENT"<GetValue(); + } + else { - // std::cout<<"STUDY"<0) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp=patients.end(); itp--; - (*itp)->AddStudy(new gdcmStudy(begin,end)); + (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(s, &tagHT)); } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirSerieToEnd + * @param s SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) { if(patients.size()>0) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp=patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + if((*itp)->GetDicomDirStudies().size()>0) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); + ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddSerie(new gdcmSerie(begin,end)); + (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &tagHT)); } } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirImageToEnd + * @param s SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) { if(patients.size()>0) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp=patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + if((*itp)->GetDicomDirStudies().size()>0) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); + ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); itst--; - if((*itst)->GetSeries().size()>0) + if((*itst)->GetDicomDirSeries().size()>0) { - ListSerie::iterator its=(*itst)->GetSeries().end(); + ListDicomDirSerie::iterator its=(*itst)->GetDicomDirSeries().end(); its--; - (*its)->AddImage(new gdcmImage(begin,end)); + (*its)->AddDicomDirImage(new gdcmDicomDirImage(s, &tagHT)); } } } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info + * @param path path of the root directory + * @param list chained list of Headers */ -void gdcmDicomDir::SetElements(std::string &path,ListHeader &list) +void gdcmDicomDir::SetElements(std::string &path, VectDocument &list) { - std::string patPrevName="", patPrevID=""; + std::string patPrevName="", patPrevID=""; std::string studPrevInstanceUID="", studPrevID=""; - std::string serPrevInstanceUID="", serPrevID=""; + std::string serPrevInstanceUID="", serPrevID=""; - std::string patCurName, patCurID; + std::string patCurName, patCurID; std::string studCurInstanceUID, studCurID; - std::string serCurInstanceUID, serCurID; + std::string serCurInstanceUID, serCurID; - SetElement(path,GDCM_NONE,NULL); + SetElement(path,GDCM_DICOMDIR_META,NULL); - ListTag::iterator debPat=listEntries.begin(); - for(ListHeader::iterator it=list.begin();it!=list.end();++it) + for(VectDocument::iterator it=list.begin();it!=list.end();++it) { - // get the current file characteristics - patCurName=(*it)->GetEntryByNumber(0x0010,0x0010); - patCurID=(*it)->GetEntryByNumber(0x0010,0x0011); + // get the current file characteristics + patCurName= (*it)->GetEntryByNumber(0x0010,0x0010); + patCurID= (*it)->GetEntryByNumber(0x0010,0x0011); studCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000d); - studCurID=(*it)->GetEntryByNumber(0x0020,0x0010); - serCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000e); - serCurID=(*it)->GetEntryByNumber(0x0020,0x0011); + studCurID= (*it)->GetEntryByNumber(0x0020,0x0010); + serCurInstanceUID= (*it)->GetEntryByNumber(0x0020,0x000e); + serCurID= (*it)->GetEntryByNumber(0x0020,0x0011); if(patCurName!=patPrevName || patCurID!=patPrevID) - SetElement(path,GDCM_PATIENT,*it); + SetElement(path,GDCM_DICOMDIR_PATIENT,*it); // if new Study Deal with 'STUDY' Elements if(studCurInstanceUID!=studPrevInstanceUID || studCurID!=studPrevID) - SetElement(path,GDCM_STUDY,*it); + SetElement(path,GDCM_DICOMDIR_STUDY,*it); // if new Serie Deal with 'SERIE' Elements if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID) - { - SetElement(path,GDCM_SERIE,*it); - } + SetElement(path,GDCM_DICOMDIR_SERIE,*it); // Always Deal with 'IMAGE' Elements - SetElement(path,GDCM_IMAGE,*it); + SetElement(path,GDCM_DICOMDIR_IMAGE,*it); - patPrevName=patCurName; - patPrevID=patCurID; + patPrevName= patCurName; + patPrevID= patCurID; studPrevInstanceUID=studCurInstanceUID; - studPrevID=studCurID; - serPrevInstanceUID=serCurInstanceUID; - serPrevID=serCurID; + studPrevID= studCurID; + serPrevInstanceUID= serCurInstanceUID; + serPrevID= serCurID; } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief compares two dgcmHeaders */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) +bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1,gdcmDocument *header2) { - ELEMENTS *elemList; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; - std::string val; - - switch(type) - { - case GDCM_PATIENT: - elemList=patientElem; - break; - case GDCM_STUDY: - elemList=studyElem; - break; - case GDCM_SERIE: - elemList=serieElem; - break; - case GDCM_IMAGE: - elemList=imageElem; - break; - case GDCM_NONE: - elemList=metaElem; - break; - default: - return; - } - - for(int i=0;;i++) - { - tmpGr=elemList[i].group; - tmpEl=elemList[i].elem; - if(tmpGr==0xffff) - break; - - dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); - - entry=new gdcmHeaderEntry(dictEntry); - entry->SetOffset(0); // just to avoid missprinting + return(*header1<*header2); +} - if(header) - val=header->GetEntryByNumber(tmpGr,tmpEl); - else - val=GDCM_UNFOUND; +/** + * \ingroup gdcmDicomDir + * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR + */ - if(val==GDCM_UNFOUND) - { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) - { - // TODO force the *end* File Name(remove path) - val=path; - } - else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image - { - if(header->GetFileName().substr(0,path.length())!=path) - { - dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path of file name is incorrect"); - val=header->GetFileName(); - } - else - val=&(header->GetFileName()[path.length()]); - } - else - { - val=elemList[i].value; - } - } - entry->SetValue(val); +void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() { - if(dictEntry) - { - if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) - { - entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) - { - entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") - { - entry->SetLength(0xffffffff); - } - else - { - entry->SetLength(entry->GetValue().length()); - } - } +// FIXME : to go on compiling - listEntries.push_back(entry); - } +// to be re written ! +/* + int offset = 0; + ListTag::iterator it; + guint16 gr, el; + std::string vr; + for(it=listEntries.begin();it!=listEntries.end();++it) { + gr = (*it)->GetGroup(); + el = (*it)->GetElement(); + vr = (*it)->GetVR(); + if (gr !=0xfffe) { + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) { + offset += 4; // explicit VR AND OB, OW, SQ : 4 more bytes + } + offset += 2 + 2 + 4 + (*it)->GetLength(); + } else { + offset += 4; // delimiters don't have a value. + } + } + //bool res=SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps. + SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps. + return; + */ } //-----------------------------------------------------------------------------