-// 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: 2004/08/02 16:42:14 $
+ Version: $Revision: 1.63 $
+
+ 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>
+
+#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 Constructor
- * @param Filename
- * @param exception_on_error
+ * \brief Constructor : creates an empty gdcmDicomDir
+ */
+gdcmDicomDir::gdcmDicomDir()
+ :gdcmDocument( )
+{
+ Initialize();
+
+ std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ...
+ SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements
+ AddDicomDirMeta();
+}
+
+/**
+ * \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 parseDir,
- bool exception_on_error):
- gdcmParser(FileName,exception_on_error,true)
+gdcmDicomDir::gdcmDicomDir(std::string const & fileName, bool parseDir ):
+ gdcmDocument( fileName )
{
- metaElems=NULL;
+ // que l'on ai passe un root directory ou un DICOMDIR
+ // et quelle que soit la valeur de parseDir,
+ // on a deja lance gdcmDocument
+ Initialize();
- if( GetListEntry().begin()==GetListEntry().end() )
+ // gdcmDocument already executed
+ // if user passed a root directory, sure we didn't get anything
+
+ if ( TagHT.begin() == TagHT.end() )
{
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty");
+ dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty");
+
+ if ( fileName.size() == 1 && fileName[0] == '.' )
+ {
+ // user passed '.' as Name
+ // we get current directory name
+ char* dummy = new char[1000];
+ getcwd(dummy, (size_t)1000);
+ std::cout << "Directory to parse : [" << dummy << "]" << std::endl;
+ SetFileName( dummy ); // will be converted into a string
+ delete[] dummy; // no longer needed
+ }
- if(parseDir)
+ if ( parseDir )
{
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir");
+ dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory"
+ " and create the DicomDir");
ParseDirectory();
}
+ else
+ {
+ /// \todo if parseDir == false, it should be tagged as an error
+ // NON ! il suffit d'appeler ParseDirectory()
+ // apres le constructeur
+ }
}
else
+ {
+ // Directory record sequence
+ gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
+ if ( !e )
+ {
+ dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record"
+ " sequence (0x0004,0x1220)");
+ /// \todo FIXME : what do we do when the parsed file IS NOT a
+ /// DICOMDIR file ?
+ }
CreateDicomDir();
+ }
}
-/*
- * \ingroup gdcmDicomDir
+/**
* \brief Canonical destructor
*/
gdcmDicomDir::~gdcmDicomDir()
{
- if(metaElems)
+ SetStartMethod(NULL);
+ SetProgressMethod(NULL);
+ SetEndMethod(NULL);
+
+ if ( metaElems )
+ {
delete metaElems;
+ }
- for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ for(ListDicomDirPatient::iterator cc = patients.begin();
+ cc!= patients.end();
+ ++cc)
{
delete *cc;
}
//-----------------------------------------------------------------------------
// Print
-/*
- * \ingroup gdcmDicomDir
+/**
* \brief Canonical Printer
*/
void gdcmDicomDir::Print(std::ostream &os)
{
if(metaElems)
{
- metaElems->SetPrintLevel(printLevel);
+ metaElems->SetPrintLevel(PrintLevel);
metaElems->Print(os);
- }
-
- for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ }
+ for(ListDicomDirPatient::iterator cc = patients.begin();
+ cc != patients.end();
+ ++cc)
{
- (*cc)->SetPrintLevel(printLevel);
- (*cc)->Print(os);
+ (*cc)->SetPrintLevel( PrintLevel );
+ (*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()
+{
+ if( !gdcmDocument::IsReadable() )
+ {
+ return false;
+ }
+ if( !metaElems )
+ {
+ return false;
+ }
+ if( patients.size() <= 0 )
+ {
+ return false;
+ }
+
+ return true;
+}
+
+/**
+ * \brief Sets all fields to NULL
+ */
+
+void gdcmDicomDir::Initialize()
+{
+ 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;
+}
+
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief fills the whole structure, starting from a root Directory
+ */
+void gdcmDicomDir::ParseDirectory()
+{
+ 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)
+
+bool gdcmDicomDir::Write(std::string const & fileName)
{
- FILE * fp1;
-
- fp1=fopen(fileName.c_str(),"wb");
- if(fp1==NULL)
+ FILE * fp1 = fopen(fileName.c_str(), "wb");
+ if( !fp1 )
{
- printf("Failed to open(write) File [%s] \n",fileName.c_str());
- return(false);
+ printf("Failed to open(write) File [%s] \n", fileName.c_str());
+ 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(fp1,DICOMDIR);
-
- fclose(fp1);
+ delete[] filePreamble;
+ UpdateDirectoryRecordSequenceLength();
+ WriteEntries(fp1);
+ fclose( fp1 );
return true;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief fills whole the structure
+/**
+ * \brief Writes in a file using the tree-like structure.
+ * @param _fp already open file pointer
*/
-void gdcmDicomDir::ParseDirectory(void)
-{
- NewDicomDir(GetPath());
- CreateDicomDir();
-}
+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 create a gdcmDicomDir from a root Directory
- * @param path entry point of the stree-like structure
+ * \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 const & 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)
+ for( gdcmDirList::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
{
- header=new gdcmHeader(it->c_str());
- if(header->IsReadable())
+ progress = (float)(count+1)/(float)fileList.size();
+ CallProgressMethod();
+ if( abort )
+ {
+ break;
+ }
+
+ header = new gdcmHeader( it->c_str() );
+ if( !header )
+ {
+ dbg.Verbose( 1,
+ "gdcmDicomDir::CreateDicomDirChainedList: "
+ "failure in new Header ",
+ it->c_str() );
+ }
+ if( header->IsReadable() )
+ {
+ // Add the file header to the chained list:
list.push_back(header);
- else
- delete header;
+ dbg.Verbose( 1,
+ "gdcmDicomDir::CreateDicomDirChainedList: readable ",
+ it->c_str() );
+ }
+ else
+ {
+ delete header;
+ }
+ count++;
}
- std::sort(list.begin(),list.end(),gdcmDicomDir::HeaderLessThan);
+ // sorts Patient/Study/Serie/
+ std::sort(list.begin(), list.end(), gdcmDicomDir::HeaderLessThan );
- std::string tmp=fileList.GetDirName();
- SetElements(tmp,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 Get the DicomDir path
- * @param
+ * \brief adds *the* Meta to a partially created DICOMDIR
*/
-std::string gdcmDicomDir::GetPath(void)
+
+ /// \todo FIXME : Heuuuuu ! Il prend les Entries du Document deja parse,
+ /// il ne fabrique rien !
+
+gdcmDicomDirMeta * gdcmDicomDir::NewMeta()
{
- std::string path=GetFileName();
+ gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &TagHT );
+ for ( TagDocEntryHT::iterator cc = TagHT.begin();
+ cc != TagHT.end(); ++cc)
+ {
+ m->AddDocEntry( cc->second );
+ }
+ return m;
+}
- int pos1=path.rfind("/");
- int pos2=path.rfind("\\");
- if(pos1>pos2)
- path.resize(pos1);
- else
- path.resize(pos2);
- return(path);
+/**
+ * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR
+ */
+gdcmDicomDirPatient * gdcmDicomDir::NewPatient()
+{
+ std::list<gdcmElement>::iterator it;
+ uint16_t tmpGr,tmpEl;
+ gdcmDictEntry *dictEntry;
+ gdcmValEntry *entry;
+
+ std::list<gdcmElement> elemList;
+ elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements();
+// Looks nice, but gdcmDicomDir IS NOT a gdcmObject ...
+// gdcmDicomDirPatient *p = new gdcmDicomDirPatient(ptagHT);
+// FillObject(elemList);
+// patients.push_front( p );
+// return p;
+/// \todo TODO : find a trick to use FillObject !!!
+
+ gdcmSQItem *s = new gdcmSQItem(0);
+
+ // 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;
+ uint16_t tmpGr, tmpEl;
+ gdcmDictEntry *dictEntry;
+ gdcmValEntry *entry;
+ std::string val;
+ //gdcmObject *o;
+ switch( type )
+ {
+ case GDCM_DICOMDIR_IMAGE:
+ elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements();
+ break;
+
+ case GDCM_DICOMDIR_SERIE:
+ elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements();
+ break;
+
+ case GDCM_DICOMDIR_STUDY:
+ elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements();
+ break;
+
+ case GDCM_DICOMDIR_PATIENT:
+ elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements();
+ 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 ) // 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;
+ }
+
+ 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() ); // FIXME
+ }
+ 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() );
+ }
+ }
+ std::cout << " was TagHT[entry->GetKey()] = entry " << std::endl;
+ if ( type == GDCM_DICOMDIR_META ) {
+ std::cout << " special Treatment for GDCM_DICOMDIR_META" << std::endl;
+
+ }
+ //TagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE !
+ }
+}
+
+/**
+ * \brief CallStartMethod
+ */
+void gdcmDicomDir::CallStartMethod()
+{
+ progress = 0.0f;
+ abort = false;
+ if( startMethod )
+ {
+ startMethod( startArg );
+ }
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief CallProgressMethod
+ */
+void gdcmDicomDir::CallProgressMethod()
+{
+ if( progressMethod )
+ {
+ progressMethod( progressArg );
+ }
+}
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief CallEndMethod
+ */
+void gdcmDicomDir::CallEndMethod()
+{
+ 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 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_META;
- ListTag::iterator begin;
- ListTag::iterator end;
-
- begin=listEntries.begin();
- end=begin;
- for(ListTag::iterator i=end;i !=listEntries.end();++i)
+ // Directory record sequence
+ gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
+ if ( !e )
{
- std::string v=(*i)->GetValue();
- if(v=="PATIENT ")
- {
- end=i;
- AddObjectToEnd(type,begin,end);
+ 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");
+ // useless : (0x0004,0x1220) IS a Sequence !
+ return;
+ }
- type=gdcmDicomDir::GDCM_PATIENT;
- begin=end;
- }
+ gdcmDicomDirType type = gdcmDicomDir::GDCM_DICOMDIR_META;
+ metaElems = NewMeta();
- if(v=="STUDY ")
+ ListSQItem listItems = s->GetSQItems();
+
+ 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) )
{
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_STUDY;
- begin=end;
+ v = ValEntry->GetValue();
}
-
- if(v=="SERIES")
+ else
{
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_SERIE;
- begin=end;
+ dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry.");
+ continue;
}
- if(v=="IMAGE ")
+ if( v == "PATIENT " )
{
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_IMAGE;
- begin=end;
+ AddDicomDirPatientToEnd( *i );
+ //AddObjectToEnd(type,*i);
+ type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT;
+ }
+ else if( v == "STUDY " )
+ {
+ AddDicomDirStudyToEnd( *i );
+ // AddObjectToEnd(type,*i);
+ type = gdcmDicomDir::GDCM_DICOMDIR_STUDY;
+ }
+ else if( v == "SERIES" )
+ {
+ AddDicomDirSerieToEnd( *i );
+ // AddObjectToEnd(type,*i);
+ type = gdcmDicomDir::GDCM_DICOMDIR_SERIE;
+ }
+ 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;
}
- }
-
- if(begin!=end)
- {
- end=GetListEntry().end();
- AddObjectToEnd(type,begin,end);
}
}
-/*
+
+/**
* \ingroup gdcmDicomDir
- * \brief
+ * \brief AddObjectToEnd
* @param type
- * @param begin
- * @param end
+ * @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_META:
- AddMetaToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_META:
+ AddDicomDirMeta();
break;
- case gdcmDicomDir::GDCM_PATIENT:
- AddPatientToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_PATIENT:
+ AddDicomDirPatientToEnd(s);
break;
- case gdcmDicomDir::GDCM_STUDY:
- AddStudyToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_STUDY:
+ AddDicomDirStudyToEnd(s);
break;
- case gdcmDicomDir::GDCM_SERIE:
- AddSerieToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_SERIE:
+ AddDicomDirSerieToEnd(s);
break;
- case gdcmDicomDir::GDCM_IMAGE:
- AddImageToEnd(begin,end);
+ case gdcmDicomDir::GDCM_DICOMDIR_IMAGE:
+ AddDicomDirImageToEnd(s);
+ break;
+ case gdcmDicomDir::GDCM_DICOMDIR_NONE:
+ AddDicomDirImageToEnd(s); //FIXME
break;
}
}
-/*
- * \ingroup gdcmDicomDir
- * \brief Well ... Not realy to end, there is only one occurence
- * @param begin
- * @param end
*/
-void gdcmDicomDir::AddMetaToEnd(ListTag::iterator begin,ListTag::iterator end)
+
+/**
+ * \ingroup gdcmDicomDir
+ * \brief Well ... there is only one occurence
+ */
+void gdcmDicomDir::AddDicomDirMeta()
{
- if(metaElems)
+ if( metaElems )
+ {
delete metaElems;
- metaElems = new gdcmMeta(begin,end);
+ }
+ metaElems = new gdcmDicomDirMeta( &TagHT );
}
-/*
+/**
* \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
-*/
-void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end)
+ * \brief AddDicomDirPatientToEnd
+ * @param s SQ Item to enqueue to the DicomPatient chained List
+ */
+void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s)
{
- patients.push_back(new gdcmPatient(begin,end));
+ patients.push_back(new gdcmDicomDirPatient(s, &TagHT));
}
-/*
+/**
* \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
+ * \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)
+ 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 begin
- * @param end
+ * \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)
+ 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
- * @param begin
- * @param end
- * @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)
+ 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 path
- * @param list
+ * \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 studPrevInstanceUID="", studPrevID="";
- std::string serPrevInstanceUID="", serPrevID="";
+ std::string patPrevName = "", patPrevID = "";
+ std::string studPrevInstanceUID = "", studPrevID = "";
+ 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);
- studCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000d);
- studCurID=(*it)->GetEntryByNumber(0x0020,0x0010);
- serCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000e);
- serCurID=(*it)->GetEntryByNumber(0x0020,0x0011);
+ 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( 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_STUDY,*it);
+ 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_SERIE,*it);
+ if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID )
+ {
+ SetElement(path, GDCM_DICOMDIR_SERIE, *it);
+ }
// Always Deal with 'IMAGE' Elements
- SetElement(path,GDCM_IMAGE,*it);
-
- patPrevName=patCurName;
- patPrevID=patCurID;
- studPrevInstanceUID=studCurInstanceUID;
- studPrevID=studCurID;
- serPrevInstanceUID=serCurInstanceUID;
- serPrevID=serCurID;
+ SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
+
+ patPrevName = patCurName;
+ patPrevID = patCurID;
+ studPrevInstanceUID = studCurInstanceUID;
+ studPrevID = studCurID;
+ serPrevInstanceUID = serCurInstanceUID;
+ serPrevID = serCurID;
}
}
-/*
+/**
* \ingroup gdcmDicomDir
- * \brief
- * @param path
- * @param type
- * @param header
+ * \brief compares two dgcmHeaders
*/
-void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header)
+bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1, gdcmDocument *header2)
{
- std::list<gdcmElement> elemList;
- std::list<gdcmElement>::iterator it;
- guint16 tmpGr, tmpEl;
- gdcmDictEntry *dictEntry;
- gdcmHeaderEntry *entry;
- std::string val;
-
- switch(type)
- {
- case GDCM_PATIENT:
- elemList=gdcmGlobal::GetDicomDirElements()->GetPatientElements();
- break;
- case GDCM_STUDY:
- elemList=gdcmGlobal::GetDicomDirElements()->GetStudyElements();
- break;
- case GDCM_SERIE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetSerieElements();
- break;
- case GDCM_IMAGE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetImageElements();
- break;
- case GDCM_NONE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetMetaElements();
- 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) )
- {
- // 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=it->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);
- }
+ return *header1 < *header2;
}
-bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2)
+/**
+ * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR
+ */
+void gdcmDicomDir::UpdateDirectoryRecordSequenceLength()
{
- return(*header1<*header2);
+
+/// \todo FIXME : to go on compiling
+///
+/// to be re written !
+/// int offset = 0;
+/// ListTag::iterator it;
+/// uint16_t 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