// gdcmDicomDir.cxx
//-----------------------------------------------------------------------------
#include "gdcmDicomDir.h"
-#include "gdcmPatient.h"
#include "gdcmStudy.h"
#include "gdcmSerie.h"
#include "gdcmImage.h"
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
#include <string>
-gdcmDicomDir::gdcmDicomDir(std::string & FileName,
+#include <sys/types.h>
+#include <errno.h>
+
+//-----------------------------------------------------------------------------
+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,"")
+};
+
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param Filename
+ * @param exception_on_error
+ */
+gdcmDicomDir::gdcmDicomDir(const char *FileName,
bool exception_on_error):
- gdcmParser(FileName.c_str(),exception_on_error, true ) {
-
-
- gdcmPatient *patCur;
- gdcmStudy *studCur;
- gdcmSerie *serCur;
- gdcmImage *imaCur;
-
- ListTag::iterator i, j;
-
-
- 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;
- }
+ gdcmParser(FileName,exception_on_error,true)
+{
+ if( GetListEntry().begin()==GetListEntry().end() )
+ {
+ dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty");
+ dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir");
+
+ std::string path=FileName;
+ std::string file;
+
+ int pos1=path.rfind("/");
+ int pos2=path.rfind("\\");
+ if(pos1>pos2)
+ path.resize(pos1);
+ else
+ path.resize(pos2);
+ NewDicomDir(path);
+ }
+
+ CreateDicomDir();
}
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param exception_on_error
+ */
+gdcmDicomDir::gdcmDicomDir(ListTag *l,
+ bool exception_on_error):
+ gdcmParser(exception_on_error )
+{
+ listEntries=*l;
+ CreateDicomDir();
+}
-gdcmDicomDir::~gdcmDicomDir() {
- lPatient::iterator cc = GetPatients().begin();
- while (cc != GetPatients().end() ) {
- //cout << "delete PATIENT" << endl;
+/*
+ * \ingroup gdcmDicomDir
+ * \brief Canonical destructor
+ */
+gdcmDicomDir::~gdcmDicomDir()
+{
+ for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ {
delete *cc;
- ++cc;
}
}
+
+//-----------------------------------------------------------------------------
+// Print
+void gdcmDicomDir::Print(std::ostream &os)
+{
+ for(ListPatient::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
+ */
+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;
+ 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
+ */
+void gdcmDicomDir::NewDicomDir(std::string path)
+{
+ gdcmDirList fileList(path,1);
+ ListHeader list;
+ gdcmHeader *header;
+
+ listEntries.clear();
+
+ for(gdcmDirList::iterator it=fileList.begin();
+ it!=fileList.end(); ++it)
+ {
+// std::cout<<*it<<std::endl;
+ header=new gdcmHeader(it->c_str());
+ if(header->IsReadable())
+ list.push_back(header);
+ else
+ delete header;
+ }
+
+ SetElements(path,list);
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+void gdcmDicomDir::CreateDicomDir()
+{
+ // 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;
+
+ begin=listEntries.begin();
+ end=begin;
+ for(ListTag::iterator i=listEntries.begin();i !=listEntries.end();++i)
+ {
+ // std::cout << std::hex <<(*i)->GetGroup() <<
+ // " " <<(*i)->GetElement() << endl;
+
+ std::string v=(*i)->GetValue();
+ if(v=="PATIENT ")
+ {
+ // std::cout<<"PATIENT"<<std::endl;
+ end=i;
+ AddObjectToEnd(type,begin,end);
+
+ type=gdcmDicomDir::GDCM_PATIENT;
+ begin=end;
+ }
+
+ if(v=="STUDY ")
+ {
+ // std::cout<<"STUDY"<<std::endl;
+ end=i;
+ AddObjectToEnd(type,begin,end);
+
+ type=gdcmDicomDir::GDCM_STUDY;
+ begin=end;
+ }
+
+ if(v=="SERIES")
+ {
+ // std::cout<<"SERIES"<<std::endl;
+ end=i;
+ AddObjectToEnd(type,begin,end);
+
+ type=gdcmDicomDir::GDCM_SERIE;
+ begin=end;
+ }
+
+ if(v=="IMAGE ")
+ {
+ // std::cout<<"IMAGE"<<std::endl;
+ end=i;
+ AddObjectToEnd(type,begin,end);
+
+ type=gdcmDicomDir::GDCM_IMAGE;
+ begin=end;
+ }
+ }
+
+ end=GetListEntry().end();
+ AddObjectToEnd(type,begin,end);
+}
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end)
+{
+ if(begin==end)
+ return;
+
+ switch(type)
+ {
+ case gdcmDicomDir::GDCM_PATIENT:
+ AddPatientToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_STUDY:
+ AddStudyToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_SERIE:
+ AddSerieToEnd(begin,end);
+ break;
+ case gdcmDicomDir::GDCM_IMAGE:
+ AddImageToEnd(begin,end);
+ break;
+ }
+}
+
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ patients.push_back(new gdcmPatient(begin,end));
+}
+
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+ void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ if(patients.size()>0)
+ {
+ ListPatient::iterator itp=patients.end();
+ itp--;
+ (*itp)->AddStudy(new gdcmStudy(begin,end));
+ }
+}
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ if(patients.size()>0)
+ {
+ ListPatient::iterator itp=patients.end();
+ itp--;
+
+ if((*itp)->GetStudies().size()>0)
+ {
+ ListStudy::iterator itst=(*itp)->GetStudies().end();
+ itst--;
+ (*itst)->AddSerie(new gdcmSerie(begin,end));
+ }
+ }
+}
+
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+ void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end)
+{
+ if(patients.size()>0)
+ {
+ ListPatient::iterator itp=patients.end();
+ itp--;
+
+ if((*itp)->GetStudies().size()>0)
+ {
+ 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));
+ }
+ }
+ }
+}
+
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+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_NONE,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_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)
+ {
+ SetElement(path,GDCM_SERIE,*it);
+ }
+
+ // Always Deal with 'IMAGE' Elements
+ SetElement(path,GDCM_IMAGE,*it);
+
+ patPrevName=patCurName;
+ patPrevID=patCurID;
+ studPrevInstanceUID=studCurInstanceUID;
+ studPrevID=studCurID;
+ serPrevInstanceUID=serCurInstanceUID;
+ serPrevID=serCurID;
+ }
+}
+
+/*
+ * \ingroup gdcmDicomDir
+ * \brief
+ * @param
+ */
+void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header)
+{
+ 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
+
+ if(header)
+ val=header->GetEntryByNumber(tmpGr,tmpEl);
+ else
+ val=GDCM_UNFOUND;
+
+ 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);
+
+ 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());
+ }
+ }
+
+ listEntries.push_back(entry);
+ }
+}
+
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff