-// 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 <string>
-
+#include <algorithm>
#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,"")
-};
+#ifdef _MSC_VER
+ #include <direct.h>
+#else
+ #include <unistd.h>
+#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;
}
//-----------------------------------------------------------------------------
// 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;
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<<std::endl;
+ progress=(float)(count+1)/(float)fileList.size();
+ CallProgressMethod();
+ if(abort)
+ break;
+
header=new gdcmHeader(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<gdcmElement> elemList;
+ std::list<gdcmElement>::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<gdcmElement> elemList;
+ std::list<gdcmElement>::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<gdcmSeqEntry*>(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"<<std::endl;
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_PATIENT;
- begin=end;
- }
-
- if(v=="STUDY ")
+ v = ValEntry->GetValue();
+ }
+ else
{
- // std::cout<<"STUDY"<<std::endl;
- end=i;
- AddObjectToEnd(type,begin,end);
+ dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry.");
+ continue;
+ }
- type=gdcmDicomDir::GDCM_STUDY;
- begin=end;
+ if(v=="PATIENT ")
+ {
+ AddDicomDirPatientToEnd(*i);
+ //AddObjectToEnd(type,*i);
+ type=gdcmDicomDir::GDCM_DICOMDIR_PATIENT;
}
- if(v=="SERIES")
+ else if(v=="STUDY ")
{
- // std::cout<<"SERIES"<<std::endl;
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_SERIE;
- begin=end;
+ AddDicomDirStudyToEnd(*i);
+ // AddObjectToEnd(type,*i);
+ type=gdcmDicomDir::GDCM_DICOMDIR_STUDY;
}
- if(v=="IMAGE ")
+ else if(v=="SERIES")
{
- // std::cout<<"IMAGE"<<std::endl;
- end=i;
- AddObjectToEnd(type,begin,end);
+ AddDicomDirSerieToEnd(*i);
+ // AddObjectToEnd(type,*i);
+ type=gdcmDicomDir::GDCM_DICOMDIR_SERIE;
+ }
- type=gdcmDicomDir::GDCM_IMAGE;
- begin=end;
+ else if(v=="IMAGE ")
+ {
+ AddDicomDirImageToEnd(*i);
+ // AddObjectToEnd(type,*i);
+ type=gdcmDicomDir::GDCM_DICOMDIR_IMAGE;
}
+
+ else
+ // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
+ // neither an 'IMAGE' SQItem. Skip to next item.
+ continue;
}
-
- end=GetListEntry().end();
- AddObjectToEnd(type,begin,end);
}
-/*
+/**
* \ingroup gdcmDicomDir
- * \brief
- * @param
+ * \brief AddObjectToEnd
+ * @param type
+ * @param begin iterator on the first DocEntry within the chained List
+ * @param end iterator on the last DocEntry within the chained List
*/
-void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end)
+
+// now useless ?
+
+/*void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,gdcmSQItem *s)
{
- if(begin==end)
+ if(s==NULL) // ??
return;
switch(type)
{
- case gdcmDicomDir::GDCM_PATIENT:
- AddPatientToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_META:
+ AddDicomDirMeta();
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_PATIENT:
+ AddDicomDirPatientToEnd(s);
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_STUDY:
+ AddDicomDirStudyToEnd(s);
break;
- case gdcmDicomDir::GDCM_STUDY:
- AddStudyToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_SERIE:
+ AddDicomDirSerieToEnd(s);
break;
- case gdcmDicomDir::GDCM_SERIE:
- AddSerieToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_IMAGE:
+ AddDicomDirImageToEnd(s);
break;
- case gdcmDicomDir::GDCM_IMAGE:
- AddImageToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_NONE:
+ AddDicomDirImageToEnd(s); //FIXME
break;
}
}
-/*
+*/
+
+/**
* \ingroup gdcmDicomDir
- * \brief
- * @param
- */
-void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end)
+ * \brief Well ... there is only one occurence
+*/
+void gdcmDicomDir::AddDicomDirMeta()
{
- patients.push_back(new gdcmPatient(begin,end));
+ if(metaElems)
+ delete metaElems;
+ metaElems = new gdcmDicomDirMeta(&tagHT);
}
-/*
+/**
+ * \ingroup gdcmDicomDir
+ * \brief AddDicomDirPatientToEnd
+ * @param s SQ Item to enqueue to the DicomPatient chained List
+*/
+void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s)
+{
+ patients.push_back(new gdcmDicomDirPatient(s, &tagHT));
+}
+
+/**
* \ingroup gdcmDicomDir
- * \brief
- * @param
+ * \brief AddDicomDirStudyToEnd
+ * @param s SQ Item to enqueue to the DicomDirStudy chained List
*/
- void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end)
+ void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s)
{
if(patients.size()>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;
+ */
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff