// gdcmDicomDir.cxx
//-----------------------------------------------------------------------------
+#include <string>
+#include <algorithm>
+#include <sys/types.h>
+#include <errno.h>
+
+#ifdef _MSC_VER
+ #include <direct.h>
+#else
+ #include <unistd.h>
+#endif
+
#include "gdcmDicomDir.h"
-#include "gdcmPatient.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"
+
+//-----------------------------------------------------------------------------
+// For full DICOMDIR description, see:
+// PS 3.3-2003, pages 731-750
+//-----------------------------------------------------------------------------
-#include <string>
-gdcmDicomDir::gdcmDicomDir(std::string & FileName,
+// Constructor / Destructor
+
+/**
+ * \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, bool parseDir,
bool exception_on_error):
- gdcmParser(FileName.c_str(),exception_on_error, true ) {
+ gdcmParser(FileName,exception_on_error,true) // true : enable SeQuences
+{
+ // que l'on ai passe un root directory ou un DICOMDIR
+ // et quelle que soit la valeur de parseDir,
+ // on a lance gdcmParser
+
+ startMethod= NULL;
+ progressMethod= NULL;
+ endMethod= NULL;
+ startMethodArgDelete= NULL;
+ progressMethodArgDelete=NULL;
+ endMethodArgDelete= NULL;
+ startArg= NULL;
+ progressArg= NULL;
+ endArg= NULL;
+
+ progress=0.0;
+ abort=false;
+ metaElems=NULL;
- gdcmPatient *patCur;
- gdcmStudy *studCur;
- gdcmSerie *serCur;
- gdcmImage *imaCur;
-
- ListTag::iterator i, j;
+// gdcmParser already executed
+// if user passed a root directory, sure we didn't get anything
+
+ if( GetListEntry().begin()==GetListEntry().end() )
+ {
+ // if parseDir == false, it should be tagged as an error
+ dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list 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
+ }
+
+ if(parseDir)
+ {
+ dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory"
+ " and create the DicomDir");
+ ParseDirectory();
+ }
+ }
+ else {
+ CreateDicomDir();
+ CheckBoundaries(); // to maintain consistency between
+ // home-made gdcmDicomDir
+ // and the ones comming from a DICOMDIR file
+ }
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief Constructor : creates an empty gdcmDicomDir
+ * @param exception_on_error whether we want to throw an exception or not
+ */
+gdcmDicomDir::gdcmDicomDir(bool exception_on_error):
+ gdcmParser(exception_on_error)
+{
+ startMethod= NULL;
+ progressMethod= NULL;
+ endMethod= NULL;
+ startMethodArgDelete= NULL;
+ progressMethodArgDelete=NULL;
+ endMethodArgDelete= NULL;
+ startArg= NULL;
+ progressArg= NULL;
+ endArg= NULL;
+
+ progress=0.0;
+ abort=false;
+ std::string pathBidon = ""; // Sorry, NULL not allowed ...
+ SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements
+ AddDicomDirMetaToEnd(listEntries.begin(),--listEntries.end());
+}
+
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief Canonical destructor
+ */
+gdcmDicomDir::~gdcmDicomDir()
+{
+ SetStartMethod(NULL);
+ SetProgressMethod(NULL);
+ SetEndMethod(NULL);
+
+ if(metaElems)
+ delete metaElems;
- if ( GetListEntry().begin() == GetListEntry().end() ) {
- cout << "ListEntry vide " << endl;
- }
-
- i = GetListEntry().begin();
- while ( i != GetListEntry().end() ) {
-
- // std::cout << std::hex << (*i)->GetGroup() <<
- // " " << (*i)->GetElement() << endl;
-
- std::string v = (*i)->GetValue();
- if (v == "PATIENT ") {
- patCur=new gdcmPatient();
- //cout << "PATIENT" << endl,
- patCur->beginObj =i;
- GetPatients().push_back(patCur);
- }
-
- if (v == "STUDY ") {
- //cout << "STUDY" << endl,
- studCur=new gdcmStudy();
- studCur->beginObj = patCur->endObj = i;
- lPatient::iterator aa = GetPatients().end();
- --aa;
- (*aa)->GetStudies().push_back(studCur);
- }
- studCur=new gdcmStudy();
-
- if (v == "SERIES") {
- //cout << "SERIES" << endl,
- serCur=new gdcmSerie();
-
- serCur->beginObj = studCur->endObj= i;
- lPatient::iterator aa = GetPatients().end();
- --aa;
- lStudy::iterator bb = (*aa)->GetStudies().end();
- --bb;
- (*bb)->GetSeries().push_back(serCur);
- }
-
- if (v == "IMAGE ") {
- //cout << "IMAGE" << endl;
- imaCur=new gdcmImage();
- imaCur->beginObj = serCur->endObj= i;
-
- lPatient::iterator aa = GetPatients().end();
- --aa;
- lStudy::iterator bb = (*aa)->GetStudies().end();
- --bb;
- lSerie::iterator cc = (*bb)->GetSeries().end();
- --cc;
- (*cc)->GetImages().push_back(imaCur);
-
-
- /* ---
- // ce n'est pas sur une nouvelle IMAGE, qu'il faut intervenir
- // mais lorsqu'on rencontre un 'non IMAGE' apres des 'IMAGE'
- lImage::iterator dd = (*cc)->GetImages().end();
-
- if ( (*cc)->GetImages().begin() != dd ) {
- --dd;
- (*dd)->endObj = i;
- }
- --- */
- }
- ++i;
- }
-}
-
-
-gdcmDicomDir::~gdcmDicomDir() {
- lPatient::iterator cc = GetPatients().begin();
- while (cc != GetPatients().end() ) {
- //cout << "delete PATIENT" << endl;
+ for(ListDicomDirPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ {
delete *cc;
- ++cc;
}
}
+
+//-----------------------------------------------------------------------------
+// Print
+/**
+ * \ingroup gdcmDicomDir
+ * \brief Canonical Printer
+ */
+void gdcmDicomDir::Print(std::ostream &os)
+{
+ if(metaElems)
+ {
+ 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 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 gdcmParser is the one of a reasonable DicomDir,
+ * false otherwise.
+ */
+bool gdcmDicomDir::IsReadable(void)
+{
+ if(!gdcmParser::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 !
+ * \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 false only when fail to open
+ */
+
+bool gdcmDicomDir::Write(std::string fileName)
+{
+ FILE * fp1;
+
+ fp1=fopen(fileName.c_str(),"wb");
+ if(fp1==NULL)
+ {
+ printf("Failed to open(write) File [%s] \n",fileName.c_str());
+ return(false);
+ }
+
+ char * filePreamble = new char[128];
+ fwrite(filePreamble,128,1,fp1);
+ fwrite("DICM",4,1,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)
+
+ 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, ExplicitVR);
+ }
+
+ itPatient = GetDicomDirPatients().begin();
+ while ( itPatient != GetDicomDirPatients().end() ) {
+ for(i=(*itPatient)->debut();i!=(*itPatient)->fin();++i) {
+ WriteEntry(*i,_fp, ExplicitVR);
+ }
+ itStudy = ((*itPatient)->GetDicomDirStudies()).begin();
+ while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) {
+ for(i=(*itStudy)->debut();i!=(*itStudy)->fin();++i) {
+ WriteEntry(*i,_fp, ExplicitVR);
+ }
+ itSerie = ((*itStudy)->GetDicomDirSeries()).begin();
+ while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) {
+ for(i=(*itSerie)->debut();i!=(*itSerie)->fin();++i) {
+ WriteEntry(*i,_fp, ExplicitVR);
+ }
+ itImage = ((*itSerie)->GetDicomDirImages()).begin();
+ while (itImage != (*itSerie)->GetDicomDirImages().end() ) {
+ for(i=(*itImage)->debut();i!=(*itImage)->fin();++i) {
+ WriteEntry(*i,_fp, ExplicitVR);
+ }
+ ++itImage;
+ }
+ ++itSerie;
+ }
+ ++itStudy;
+ }
+ ++itPatient;
+ }
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief create a gdcmHeader-like chained list from a root Directory
+ * @param path entry point of the tree-like structure
+ */
+void gdcmDicomDir::CreateDicomDirChainedList(std::string path)
+{
+ CallStartMethod();
+
+ gdcmDirList fileList(path,1); // gets recursively the file list
+ unsigned int count=0;
+ ListHeader list;
+ gdcmHeader *header;
+
+ listEntries.clear();
+ patients.clear();
+
+ for(gdcmDirList::iterator it=fileList.begin();
+ it!=fileList.end();
+ ++it)
+ {
+ progress=(float)(count+1)/(float)fileList.size();
+ CallProgressMethod();
+ if(abort)
+ break;
+
+ header=new gdcmHeader(it->c_str());
+ if(header->IsReadable())
+ 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);
+
+ 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 modifies the limits of a gdcmObject, created from a DICOMDIR file
+ */
+
+void gdcmDicomDir::CheckBoundaries()
+{
+ ListDicomDirPatient::iterator itPatient;
+ ListDicomDirStudy::iterator itStudy;
+ ListDicomDirSerie::iterator itSerie;
+ ListDicomDirImage::iterator itImage;
+ ListTag::iterator i,j;
+
+ GetDicomDirMeta()->ResetBoundaries(0);
+
+ itPatient = GetDicomDirPatients().begin();
+ while ( itPatient != GetDicomDirPatients().end() ) {
+ (*itPatient)->ResetBoundaries(1);
+ itStudy = ((*itPatient)->GetDicomDirStudies()).begin();
+ while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) {
+ (*itStudy)->ResetBoundaries(1);
+ itSerie = ((*itStudy)->GetDicomDirSeries()).begin();
+ while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) {
+ (*itSerie)->ResetBoundaries(1);
+ itImage = ((*itSerie)->GetDicomDirImages()).begin();
+ while (itImage != (*itSerie)->GetDicomDirImages().end() ) {
+ (*itImage)->ResetBoundaries(1);
+ ++itImage;
+ }
+ ++itSerie;
+ }
+ ++itStudy;
+ }
+ ++itPatient;
+ }
+}
+
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief adds a new Patient to a partially created DICOMDIR
+ */
+gdcmDicomDirPatient * gdcmDicomDir::NewPatient(void) {
+ std::list<gdcmElement> elemList;
+ std::list<gdcmElement>::iterator it;
+ guint16 tmpGr,tmpEl;
+ gdcmDictEntry *dictEntry;
+ gdcmHeaderEntry *entry;
+
+ elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements();
+ std::list<gdcmHeaderEntry *>::iterator debInsertion, finInsertion, i,j;
+
+ debInsertion = metaElems->fin();
+ ++debInsertion;
+ finInsertion=debInsertion;
+
+ // 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 gdcmHeaderEntry(dictEntry);
+ entry->SetOffset(0); // just to avoid missprinting
+ entry->SetValue(it->value);
+
+ 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());
+ }
+
+ tagHT.insert( PairHT(entry->GetKey(),entry) ); // add in the (multimap) H Table
+ listEntries.insert(debInsertion ,entry); // en tete de liste des Patients
+ ++finInsertion;
+ }
+
+ i=metaElems->fin();
+ i++;
+
+ gdcmDicomDirPatient *p = new gdcmDicomDirPatient(i, --debInsertion,
+ &tagHT, &listEntries);
+ patients.push_front(p);
+ return p;
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \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 create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader
+ */
+void gdcmDicomDir::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 -
+
+ gdcmDicomDirType type=gdcmDicomDir::GDCM_DICOMDIR_META;
+ ListTag::iterator begin;
+ ListTag::iterator end, end2;
+
+ begin=listEntries.begin();
+ end=begin;
+ for(ListTag::iterator i=end;i !=listEntries.end();++i)
+ {
+ std::string v=(*i)->GetValue();
+ if(v=="PATIENT ")
+ {
+ end=end2=i;
+ AddObjectToEnd(type,begin,--end2);
+ type=gdcmDicomDir::GDCM_DICOMDIR_PATIENT;
+ begin=end;
+ }
+
+ if(v=="STUDY ")
+ {
+ end=end2=i;
+ AddObjectToEnd(type,begin,--end2);
+ type=gdcmDicomDir::GDCM_DICOMDIR_STUDY;
+ begin=end;
+ }
+
+ if(v=="SERIES")
+ {
+ end=end2=i;
+ AddObjectToEnd(type,begin,--end2);
+ type=gdcmDicomDir::GDCM_DICOMDIR_SERIE;
+ begin=end;
+ }
+
+ if(v=="IMAGE ")
+ {
+ end=end2=i;
+ AddObjectToEnd(type,begin,--end2);
+ type=gdcmDicomDir::GDCM_DICOMDIR_IMAGE;
+ begin=end;
+ }
+ }
+
+ end=end2=listEntries.end();
+ if(begin!=end)
+ AddObjectToEnd(type,begin,--end2);
+}
+/**
+ * \ingroup gdcmDicomDir
+ * \brief AddObjectToEnd
+ * @param type
+ * @param begin iterator on the first HeaderEntry within the chained List
+ * @param end iterator on the last HeaderEntry within the chained List
+ */
+void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end)
+{
+ if(begin==end)
+ return;
+
+ switch(type)
+ {
+ case gdcmDicomDir::GDCM_DICOMDIR_META:
+ AddDicomDirMetaToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_PATIENT:
+ AddDicomDirPatientToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_STUDY:
+ AddDicomDirStudyToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_SERIE:
+ AddDicomDirSerieToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_IMAGE:
+ AddDicomDirImageToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_NONE:
+ AddDicomDirImageToEnd(begin,end); //FIXME
+ break;
+ }
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief Well ... Not realy to end, there is only one occurence
+ * @param begin iterator on the first HeaderEntry within the chained List
+ * @param end iterator on the last HeaderEntry within the chained List
+*/
+void gdcmDicomDir::AddDicomDirMetaToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ if(metaElems)
+ delete metaElems;
+ metaElems = new gdcmDicomDirMeta(begin,end,&tagHT,&listEntries);
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief AddDicomDirPatientToEnd
+ * @param begin iterator on the first HeaderEntry within the chained List
+ * @param end iterator on the last HeaderEntry within the chained List
+*/
+void gdcmDicomDir::AddDicomDirPatientToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ patients.push_back(new gdcmDicomDirPatient(begin,end,&tagHT, &listEntries));
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief AddDicomDirStudyToEnd
+ * @param begin iterator on the first HeaderEntry within the chained List
+ * @param end iterator on the last HeaderEntry within the chained List
+ */
+ void gdcmDicomDir::AddDicomDirStudyToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ if(patients.size()>0)
+ {
+ ListDicomDirPatient::iterator itp=patients.end();
+ itp--;
+ (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(begin,end,&tagHT, &listEntries));
+ }
+}
+/**
+ * \ingroup gdcmDicomDir
+ * \brief AddDicomDirSerieToEnd
+ * @param begin iterator on the first HeaderEntry within the chained List
+ * @param end iterator on the last HeaderEntry within the chained List
+ */
+void gdcmDicomDir::AddDicomDirSerieToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ 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 gdcmDicomDirSerie(begin,end,&tagHT, &listEntries));
+ }
+ }
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief AddDicomDirImageToEnd
+ * @param begin iterator on the first HeaderEntry within the chained List
+ * @param end iterator on the last HeaderEntry within the chained List
+ */
+ void gdcmDicomDir::AddDicomDirImageToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ 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 gdcmDicomDirImage(begin,end,&tagHT, &listEntries));
+ }
+ }
+ }
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \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)
+{
+ std::string patPrevName="", patPrevID="";
+ std::string studPrevInstanceUID="", studPrevID="";
+ std::string serPrevInstanceUID="", serPrevID="";
+
+ std::string patCurName, patCurID;
+ std::string studCurInstanceUID, studCurID;
+ std::string serCurInstanceUID, serCurID;
+
+ SetElement(path,GDCM_DICOMDIR_META,NULL);
+
+ ListTag::iterator debPat=listEntries.begin();
+ for(ListHeader::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 gdcmDicomDir
+ * \brief adds to the HTable and at the end of the Chained List
+ * 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,gdcmHeader *header)
+{
+ std::list<gdcmElement> elemList;
+ std::list<gdcmElement>::iterator it;
+ guint16 tmpGr, tmpEl;
+ gdcmDictEntry *dictEntry;
+ gdcmHeaderEntry *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 gdcmHeaderEntry(dictEntry);
+ entry->SetOffset(0); // just to avoid 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());
+ }
+ }
+ //AddHeaderEntry(entry); // both in H Table and in chained list
+ tagHT.insert( PairHT( entry->GetKey(),entry) );
+ listEntries.push_back(entry);
+ //wasUpdated = 1; // is private
+ }
+}
+/**
+ * \ingroup gdcmDicomDir
+ * \brief compares two dgcmHeaders
+ */
+bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2)
+{
+ return(*header1<*header2);
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR
+ */
+
+void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() {
+ 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;
+}
+
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff