X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=35726eac96b77eb1e632e162b00347daed4cb68d;hb=40b909789581894e57a0d8f22d6f1f91f55e7f84;hp=111f0e0fa1d3d05bbc311cb1f6d44138d11fa69e;hpb=4d59e5e9778e5abff13d13d576ef92ce81498b6f;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 111f0e0f..35726eac 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,651 +1,968 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2004/10/12 04:35:44 $ + Version: $Revision: 1.73 $ + + 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 "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.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" #include - +#include #include -#include -//----------------------------------------------------------------------------- -class ELEMENTS +#ifdef _MSC_VER + #include +#else + #include +#endif +namespace gdcm { -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,"") -}; +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -/* - * \ingroup gdcmDicomDir - * \brief - * @param Filename - * @param exception_on_error + +/** + * \ingroup DicomDir + * \brief Constructor : creates an empty DicomDir + */ +DicomDir::DicomDir() + :Document( ) +{ + Initialize(); // sets all private fields to NULL + std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... + MetaElems = NewMeta(); +} + +/** + * \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 */ -gdcmDicomDir::gdcmDicomDir(const char *FileName, - bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) +DicomDir::DicomDir(std::string const & fileName, bool parseDir ): + Document( fileName ) { - if( GetListEntry().begin()==GetListEntry().end() ) + // Whatever user passed (a root directory or a DICOMDIR) + // and whatever the value of parseDir was, + // Document is already executed + Initialize(); // sets all private fields to NULL + + // if user passed a root directory, sure we didn't get anything + + if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); + dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty"); + + if ( fileName.size() == 1 && fileName[0] == '.' ) + { + // user passed '.' as Name + // we get current directory name + char dummy[1000]; + getcwd(dummy, (size_t)1000); + SetFileName( dummy ); // will be converted into a string + } - std::string path=FileName; - std::string file; + if ( parseDir ) // user asked for a recursive parsing of a root directory + { + MetaElems = NewMeta(); - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); + dbg.Verbose(0, "DicomDir::DicomDir : Parse directory" + " and create the DicomDir"); + ParseDirectory(); + } else - path.resize(pos2); - NewDicomDir(path); + { + /// \todo if parseDir == false, it should be tagged as an error + // NON ! il suffit d'appeler ParseDirectory() + // apres le constructeur + } + } + else // Only if user passed a DICOMDIR + { + // Directory record sequence + DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME : what do we do when the parsed file IS NOT a + /// DICOMDIR file ? + } + CreateDicomDir(); } - - CreateDicomDir(); -} - -/* - * \ingroup gdcmDicomDir - * \brief - * @param exception_on_error - */ -gdcmDicomDir::gdcmDicomDir(ListTag *l, - bool exception_on_error): - gdcmParser(exception_on_error ) -{ - listEntries=*l; - CreateDicomDir(); } -/* - * \ingroup gdcmDicomDir +/** * \brief Canonical destructor */ -gdcmDicomDir::~gdcmDicomDir() +DicomDir::~DicomDir() { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + SetStartMethod(NULL); + SetProgressMethod(NULL); + SetEndMethod(NULL); + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) { delete *cc; } + if ( MetaElems ) + { + delete MetaElems; + } } //----------------------------------------------------------------------------- // Print -void gdcmDicomDir::Print(std::ostream &os) +/** + * \brief Canonical Printer + */ +void DicomDir::Print(std::ostream &os) { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + if( MetaElems ) { - (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + MetaElems->SetPrintLevel(PrintLevel); + MetaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc) + { + (*cc)->SetPrintLevel( PrintLevel ); + (*cc)->Print( os ); } } //----------------------------------------------------------------------------- // Public /** - * \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 ! - * @param fileName file to be written to - * @return + * \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 Document is the one of a reasonable DicomDir, + * false otherwise. */ -bool gdcmDicomDir::Write(std::string fileName) +bool DicomDir::IsReadable() { - FILE * fp1; - - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) + if( !Document::IsReadable() ) { - printf("Failed to open(write) File [%s] \n",fileName.c_str()); - return(false); + return false; + } + if( !MetaElems ) + { + return false; + } + if( Patients.size() <= 0 ) + { + return false; } - - char * filePreamble; - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - free(filePreamble); - - WriteEntries(DICOMDIR,fp1); - - fclose(fp1); return true; } -//----------------------------------------------------------------------------- -// Protected -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief Sets all fields to NULL */ -void gdcmDicomDir::NewDicomDir(std::string path) + +void DicomDir::Initialize() { - gdcmDirList fileList(path,1); - ListHeader list; - gdcmHeader *header; + StartMethod = NULL; + ProgressMethod = NULL; + EndMethod = NULL; + StartMethodArgDelete = NULL; + ProgressMethodArgDelete = NULL; + EndMethodArgDelete = NULL; + StartArg = NULL; + ProgressArg = NULL; + EndArg = NULL; + + Progress = 0.0; + Abort = false; + + MetaElems = 0; +} - listEntries.clear(); - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) +/** + * \ingroup DicomDir + * \brief fills the whole structure, starting from a root Directory + */ +void DicomDir::ParseDirectory() +{ + CreateDicomDirChainedList( GetFileName() ); + CreateDicomDir(); +} + +/** + * \ingroup DicomDir + * \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 DicomDir::SetStartMethod(Method* method, void* arg, + Method* argDelete ) +{ + if( StartArg && StartMethodArgDelete ) { -// std::cout<<*it<c_str()); - if(header->IsReadable()) - list.push_back(header); - else - delete header; + StartMethodArgDelete( StartArg ); } - SetElements(path,list); + StartMethod = method; + StartArg = arg; + StartMethodArgDelete = argDelete; } -//----------------------------------------------------------------------------- -// Private -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \ingroup DicomDir + * \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::CreateDicomDir() +void DicomDir::SetStartMethodArgDelete(Method* method) { - // The list is parsed. When a tag 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; + StartMethodArgDelete = method; +} - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=listEntries.begin();i !=listEntries.end();++i) +/** + * \ingroup DicomDir + * \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 DicomDir::SetProgressMethod(Method* method, void* arg, + Method* argDelete ) +{ + if( ProgressArg && ProgressMethodArgDelete ) { - // std::cout << std::hex <<(*i)->GetGroup() << - // " " <<(*i)->GetElement() << endl; - - std::string v=(*i)->GetValue(); - if(v=="PATIENT ") - { - // std::cout<<"PATIENT"<0) + +bool DicomDir::WriteDicomDir(std::string const& fileName) +{ + uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; + + FILE* fp = fopen(fileName.c_str(), "wb"); + if( !fp ) { - ListPatient::iterator itp=patients.end(); - itp--; - (*itp)->AddStudy(new gdcmStudy(begin,end)); + printf("Failed to open(write) File [%s] \n", fileName.c_str()); + return false; } + + uint8_t filePreamble[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble,128,1,fp); + fwrite("DICM",4,1,fp); + + DicomDirMeta *ptrMeta = GetDicomDirMeta(); + ptrMeta->Write(fp, ExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta + fwrite(&sq[0],8,1,fp); // 0004 1220 ffff ffff + + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc ) + { + (*cc)->Write( fp, ExplicitVR ); + } + + // force writing Sequence Delimitation Item + fwrite(&sqt[0],8,1,fp); // fffe e0dd ffff ffff + + fclose( fp ); + return true; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param + +//----------------------------------------------------------------------------- +// Protected + +/** + * \ingroup DicomDir + * \brief create a Document-like chained list from a root Directory + * @param path entry point of the tree-like structure */ -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +void DicomDir::CreateDicomDirChainedList(std::string const & path) { - if(patients.size()>0) + CallStartMethod(); + DirList fileList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; + Header *header; + + TagHT.clear(); + Patients.clear(); + + for( DirList::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) { - ListPatient::iterator itp=patients.end(); - itp--; + Progress = (float)(count+1)/(float)fileList.size(); + CallProgressMethod(); + if( Abort ) + { + break; + } - if((*itp)->GetStudies().size()>0) + header = new Header( it->c_str() ); + if( !header ) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); - itst--; - (*itst)->AddSerie(new gdcmSerie(begin,end)); + dbg.Verbose( 1, + "DicomDir::CreateDicomDirChainedList: " + "failure in new Header ", + it->c_str() ); } + + if( header->IsReadable() ) + { + // Add the file header to the chained list: + list.push_back(header); + dbg.Verbose( 1, + "DicomDir::CreateDicomDirChainedList: readable ", + it->c_str() ); + + } + else + { + delete header; + } + count++; } + // sorts Patient/Study/Serie/ + std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); + + 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 - * @param +/** + * \ingroup DicomDir + * \brief adds *the* Meta to a partially created DICOMDIR */ - void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) + +DicomDirMeta * DicomDir::NewMeta() { - if(patients.size()>0) - { - ListPatient::iterator itp=patients.end(); - itp--; - - if((*itp)->GetStudies().size()>0) + DicomDirMeta *m = new DicomDirMeta( &TagHT ); + + if ( TagHT.begin() != TagHT.end() ) // after Document Parsing + { + TagDocEntryHT::iterator lastOneButSequence = TagHT.end(); + lastOneButSequence --; + // ALL the 'out of Sequence' Tags belong to Meta Elems + // (we skip 0004|1220 [Directory record sequence] ) + for ( TagDocEntryHT::iterator cc = TagHT.begin(); + cc != lastOneButSequence; + ++cc) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); - itst--; - - if((*itst)->GetSeries().size()>0) - { - ListSerie::iterator its=(*itst)->GetSeries().end(); - its--; - (*its)->AddImage(new gdcmImage(begin,end)); - } + m->AddDocEntry( cc->second ); } } + else // after root directory parsing + { + std::list elemList; + elemList=Global::GetDicomDirElements()->GetDicomDirMetaElements(); + m->FillObject(elemList); + } + m->SetSQItemNumber(0); // To avoid further missprinting + return m; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR */ -void gdcmDicomDir::SetElements(std::string &path,ListHeader &list) +DicomDirPatient * DicomDir::NewPatient() { - std::string patPrevName="", patPrevID=""; - std::string studPrevInstanceUID="", studPrevID=""; - std::string serPrevInstanceUID="", serPrevID=""; + std::list::iterator it; + uint16_t tmpGr,tmpEl; + DictEntry *dictEntry; + ValEntry *entry; - std::string patCurName, patCurID; - std::string studCurInstanceUID, studCurID; - std::string serCurInstanceUID, serCurID; + std::list elemList; + elemList=Global::GetDicomDirElements()->GetDicomDirPatientElements(); + SQItem *s = new SQItem(0); - SetElement(path,GDCM_NONE,NULL); - - ListTag::iterator debPat=listEntries.begin(); - for(ListHeader::iterator it=list.begin();it!=list.end();++it) + // for all the DicomDirPatient Elements + for( it = elemList.begin(); it != elemList.end(); ++it ) { - // 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); - - if(patCurName!=patPrevName || patCurID!=patPrevID) - SetElement(path,GDCM_PATIENT,*it); - - // if new Study Deal with 'STUDY' Elements - if(studCurInstanceUID!=studPrevInstanceUID || studCurID!=studPrevID) - SetElement(path,GDCM_STUDY,*it); - - // if new Serie Deal with 'SERIE' Elements - if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID) + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); + entry = new ValEntry( dictEntry ); + entry->SetOffset(0); // just to avoid further missprinting + entry->SetValue( it->Value ); + + // dealing with value length ... + + if( dictEntry->GetGroup() == 0xfffe) { - SetElement(path,GDCM_SERIE,*it); + entry->SetLength(entry->GetValue().length()); + } + else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) + { + entry->SetLength( 4 ); } - - // Always Deal with 'IMAGE' Elements - SetElement(path,GDCM_IMAGE,*it); - - patPrevName=patCurName; - patPrevID=patCurID; - studPrevInstanceUID=studCurInstanceUID; - studPrevID=studCurID; - serPrevInstanceUID=serCurInstanceUID; - serPrevID=serCurID; + 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 ); } + + DicomDirPatient *p = new DicomDirPatient(s, &TagHT); + Patients.push_front( p ); + + return p; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief adds to the HTable + * the Entries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header Header of the current file */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) +void DicomDir::SetElement(std::string &path,DicomDirType type, + Document *header) { - ELEMENTS *elemList; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; + std::list elemList; + std::list::iterator it; + uint16_t tmpGr, tmpEl; + DictEntry *dictEntry; + ValEntry *entry; std::string val; - - switch(type) + SQItem *si = new SQItem(0); // all the items will be at level 1 + switch( type ) { - case GDCM_PATIENT: - elemList=patientElem; + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); break; - case GDCM_STUDY: - elemList=studyElem; + + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); break; - case GDCM_SERIE: - elemList=serieElem; + + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); break; - case GDCM_IMAGE: - elemList=imageElem; + + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); break; - case GDCM_NONE: - elemList=metaElem; + + case GDCM_DICOMDIR_META: + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); break; + default: return; } - - for(int i=0;;i++) + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + // for all the relevant elements found in their own spot of the DicomDir.dic + // FIXME : troubles found when it's a SeqEntry + + for( it = elemList.begin(); it != elemList.end(); ++it) { - tmpGr=elemList[i].group; - tmpEl=elemList[i].elem; - if(tmpGr==0xffff) - break; + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); - dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); + entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! - entry=new gdcmHeaderEntry(dictEntry); - entry->SetOffset(0); // just to avoid missprinting + entry->SetOffset(0); // just to avoid further missprinting + entry->SetLength(0); // just to avoid further missprinting - if(header) - val=header->GetEntryByNumber(tmpGr,tmpEl); + if( header ) + { + // NULL when we Build Up (ex nihilo) a DICOMDIR + // or when we add the META elems + val = header->GetEntryByNumber(tmpGr, tmpEl); + } else - val=GDCM_UNFOUND; + { + val = GDCM_UNFOUND; + } - if(val==GDCM_UNFOUND) + if( val == GDCM_UNFOUND) { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) + if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID { - // TODO force the *end* File Name(remove path) - val=path; + // force to the *end* File Name + val = Util::GetName( path ); } - else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image + else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image { - if(header->GetFileName().substr(0,path.length())!=path) + if( header->GetFileName().substr(0, path.length()) != path ) { - dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path of file name is incorrect"); - val=header->GetFileName(); + dbg.Verbose(0, "DicomDir::SetElement : the base path" + " of file name is incorrect"); + val = header->GetFileName(); } else - val=&(header->GetFileName()[path.length()]); + { + val = &(header->GetFileName().c_str()[path.length()]); + } } else { - val=elemList[i].value; + val = it->Value; } } - entry->SetValue(val); + else + { + if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) + val = it->Value; + } + + // GDCM_UNFOUND or not ! - if(dictEntry) + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if( dictEntry ) { - if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) + if( dictEntry->GetGroup() == 0xfffe ) + { + entry->SetLength( entry->GetValue().length() ); // FIXME + } + else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) { entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) + } + else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" ) { entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") + } + else if( dictEntry->GetVR() == "SQ" ) { - entry->SetLength(0xffffffff); + entry->SetLength( 0xffffffff ); } else { - entry->SetLength(entry->GetValue().length()); + entry->SetLength( entry->GetValue().length() ); } } - listEntries.push_back(entry); - } + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + std::cout << "GDCM_DICOMDIR_META ?!? should never print that" + << std::endl; + } + si->AddEntry(entry); + } + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + AddDicomDirImageToEnd(si); + break; + + case GDCM_DICOMDIR_SERIE: + AddDicomDirSerieToEnd(si); + break; + + case GDCM_DICOMDIR_STUDY: + AddDicomDirStudyToEnd(si); + break; + + case GDCM_DICOMDIR_PATIENT: + AddDicomDirPatientToEnd(si); + break; + + default: + return; + } + //int count=1; // find a trick to increment + //s->AddEntry(si, count); // Seg Faults + +} + +/** + * \brief CallStartMethod + */ +void DicomDir::CallStartMethod() +{ + Progress = 0.0f; + Abort = false; + if( StartMethod ) + { + StartMethod( StartArg ); + } +} + +/** + * \ingroup DicomDir + * \brief CallProgressMethod + */ +void DicomDir::CallProgressMethod() +{ + if( ProgressMethod ) + { + ProgressMethod( ProgressArg ); + } +} + +/** + * \ingroup DicomDir + * \brief CallEndMethod + */ +void DicomDir::CallEndMethod() +{ + Progress = 1.0f; + if( EndMethod ) + { + EndMethod( EndArg ); + } +} + +//----------------------------------------------------------------------------- +// Private +/** + * \ingroup DicomDir + * \brief create a 'DicomDir' from a DICOMDIR Header + */ +void DicomDir::CreateDicomDir() +{ + // 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 - + + // Directory record sequence + DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? + return; + } + + SeqEntry* s = dynamic_cast(e); + if ( !s ) + { + dbg.Verbose(0, "DicomDir::CreateDicomDir: no SeqEntry present"); + // useless : (0x0004,0x1220) IS a Sequence ! + return; + } + + DicomDirType type = DicomDir::GDCM_DICOMDIR_META; + MetaElems = NewMeta(); + + ListSQItem listItems = s->GetSQItems(); + + DocEntry * d; + std::string v; + for( ListSQItem::iterator i = listItems.begin(); + i !=listItems.end(); ++i ) + { + d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) ) + { + v = valEntry->GetValue(); + } + else + { + dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry."); + continue; + } + + if( v == "PATIENT " ) + { + AddDicomDirPatientToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_PATIENT; + } + else if( v == "STUDY " ) + { + AddDicomDirStudyToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_STUDY; + } + else if( v == "SERIES" ) + { + AddDicomDirSerieToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_SERIE; + } + else if( v == "IMAGE " ) + { + AddDicomDirImageToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_IMAGE; + } + else + { + // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // neither an 'IMAGE' SQItem. Skip to next item. + continue; + } + } +} + +/** + * \ingroup DicomDir + * \brief Well ... there is only one occurence + */ +void DicomDir::AddDicomDirMeta() +{ + if( MetaElems ) + { + delete MetaElems; + } + MetaElems = new DicomDirMeta( &TagHT ); +} + +/** + * \ingroup DicomDir + * \brief AddDicomDirPatientToEnd + * @param s SQ Item to enqueue to the DicomPatient chained List + */ +void DicomDir::AddDicomDirPatientToEnd(SQItem *s) +{ + Patients.push_back(new DicomDirPatient(s, &TagHT)); +} + +/** + * \ingroup DicomDir + * \brief AddDicomDirStudyToEnd + * @param s SQ Item to enqueue to the DicomDirStudy chained List + */ + void DicomDir::AddDicomDirStudyToEnd(SQItem *s) +{ + if( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + (*itp)->AddDicomDirStudy(new DicomDirStudy(s, &TagHT)); + } +} + +/** + * \ingroup DicomDir + * \brief AddDicomDirSerieToEnd + * @param s SQ Item to enqueue to the DicomDirSerie chained List + */ +void DicomDir::AddDicomDirSerieToEnd(SQItem *s) +{ + if( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + + if( (*itp)->GetDicomDirStudies().size() > 0 ) + { + ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); + itst--; + (*itst)->AddDicomDirSerie(new DicomDirSerie(s, &TagHT)); + } + } +} + +/** + * \ingroup DicomDir + * \brief AddDicomDirImageToEnd + * @param s SQ Item to enqueue to the DicomDirImage chained List + */ + void DicomDir::AddDicomDirImageToEnd(SQItem *s) +{ + if( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + + if( (*itp)->GetDicomDirStudies().size() > 0 ) + { + ListDicomDirStudy::iterator itst = (*itp)->GetDicomDirStudies().end(); + itst--; + + if( (*itst)->GetDicomDirSeries().size() > 0 ) + { + ListDicomDirSerie::iterator its = (*itst)->GetDicomDirSeries().end(); + its--; + (*its)->AddDicomDirImage(new DicomDirImage(s, &TagHT)); + } + } + } +} + +/** + * \ingroup DicomDir + * \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 DicomDir::SetElements(std::string &path, VectDocument &list) +{ + std::string patPrevName = "", patPrevID = ""; + std::string studPrevInstanceUID = "", studPrevID = ""; + std::string serPrevInstanceUID = "", serPrevID = ""; + + std::string patCurName, patCurID; + std::string studCurInstanceUID, studCurID; + std::string serCurInstanceUID, serCurID; + + 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); + studCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000d); + studCurID = (*it)->GetEntryByNumber(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000e); + serCurID = (*it)->GetEntryByNumber(0x0020,0x0011); + + if( patCurName != patPrevName || patCurID != patPrevID) + { + SetElement(path, GDCM_DICOMDIR_PATIENT, *it); + } + + // if new Study Deal with 'STUDY' Elements + if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID ) + { + SetElement(path, GDCM_DICOMDIR_STUDY, *it); + } + + // if new Serie Deal with 'SERIE' Elements + if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID ) + { + SetElement(path, GDCM_DICOMDIR_SERIE, *it); + } + + // Always Deal with 'IMAGE' Elements + SetElement(path, GDCM_DICOMDIR_IMAGE, *it); + + patPrevName = patCurName; + patPrevID = patCurID; + studPrevInstanceUID = studCurInstanceUID; + studPrevID = studCurID; + serPrevInstanceUID = serCurInstanceUID; + serPrevID = serCurID; + } +} + +/** + * \ingroup DicomDir + * \brief compares two dgcmHeaders + */ +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) +{ + return *header1 < *header2; } +} // end namespace gdcm //-----------------------------------------------------------------------------