-// gdcmDicomDir.cxx
-//-----------------------------------------------------------------------------
-#include <string>
-#include <algorithm>
-#include <sys/types.h>
-#include <errno.h>
-
-#ifdef _MSC_VER
- #include <direct.h>
-#else
- #include <unistd.h>
-#endif
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDicomDir.cxx,v $
+ Language: C++
+ Date: $Date: 2008/02/13 18:53:33 $
+ Version: $Revision: 1.197 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+//-----------------------------------------------------------------------------
+// For full DICOMDIR description, see:
+// PS 3.3-2003, pages 731-750
+//-----------------------------------------------------------------------------
#include "gdcmDicomDir.h"
+#include "gdcmDicomDirObject.h"
#include "gdcmDicomDirStudy.h"
#include "gdcmDicomDirSerie.h"
+#include "gdcmDicomDirVisit.h"
#include "gdcmDicomDirImage.h"
+#include "gdcmDicomDirPrivate.h"
+#include "gdcmDicomDirPatient.h"
+#include "gdcmDicomDirMeta.h"
+#include "gdcmDicomDirElement.h"
#include "gdcmDirList.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
#include "gdcmGlobal.h"
-#include "gdcmHeader.h"
-
+#include "gdcmFile.h"
#include "gdcmSeqEntry.h"
#include "gdcmSQItem.h"
-#include "gdcmValEntry.h"
+#include "gdcmDataEntry.h"
+#include "gdcmCommandManager.h"
-//-----------------------------------------------------------------------------
-// For full DICOMDIR description, see:
-// PS 3.3-2003, pages 731-750
-//-----------------------------------------------------------------------------
+#include <fstream>
+#include <string>
+#include <algorithm>
+#include <sys/types.h>
+
+#ifdef _MSC_VER
+# define getcwd _getcwd
+#endif
+
+#if defined(_MSC_VER) || defined(__BORLANDC__)
+# include <direct.h>
+#else
+# include <unistd.h>
+#endif
+
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
+
+// ----------------------------------------------------------------------------
+// Note for future developpers
+// ----------------------------------------------------------------------------
+//
+// Dicom PS 3.3 describes the relationship between Directory Records, as follow
+// (see also PS 4.3, 2004, page 50 for Entity-Relationship model)
+//
+// Directory Record Type Directory Record Types which may be included
+// in the next lower-level directory Entity
+//
+// (Root directory Entity) PATIENT, TOPIC, PRIVATE
+//
+// PATIENT STUDY, PRIVATE
+//
+// STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT, PRIVATE
+//
+// SERIES IMAGE, OVERLAYS, MODALITY LUT, VOI LUT,
+// CURVE, STORED PRINT, RT DOSE, RT STRUCTURE SET
+// RT PLAN, RT TREAT RECORD, PRESENTATION, WAVEFORM,
+// SR DOCUMENT, KEY OBJECT DOC, SPECTROSCOPY,
+// RAW DATA, REGISTRATION, FIDUCIAL, PRIVATE,
+// ENCAP DOC
+// IMAGE
+// OVERLAY
+// MODALITY LUT
+// VOI LUT
+// CURVE
+// STORED PRINT
+// RT DOSE
+// RT STRUCTURE SET
+// RT PLAN
+// RT TREAT RECORD
+// PRESENTATION
+// WAVEFORM
+// SR DOCUMENT
+// KEY OBJECT DOC
+// SPECTROSCOPY
+// RAW DATA
+// REGISTRATION
+// FIDUCIAL
+// PRIVATE
+// ENCAP DOC
+//
+
+/*
+
+// see also : ftp://medical.nema.org/medical/dicom/final/cp343_ft.doc
+
+RELATIONSHIP BETWEEN DIRECTORY RECORDS
+
+Directory Record Type Directory Record Types which may be included
+ in the next lower-level directory Entity
+
+(Root Directory Entity) PATIENT, TOPIC, PRIVATE
+
+PATIENT STUDY, PRIVATE
+
+STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT, PRIVATE
+
+SERIES IMAGE, OVERLAY, MODALITY LUT, VOI LUT, CURVE,
+ STORED PRINT, RT DOSE, RT STRUCTURE SET, RT PLAN,
+ RT TREAT RECORD, PRESENTATION, WAVEFORM, SR DOCUMENT,
+ KEY OBJECT DOC, SPECTROSCOPY, RAW DATA, PRIVATE
+
+IMAGE PRIVATE
+OVERLAY PRIVATE
+MODALITY LUT PRIVATE
+VOI LUT PRIVATE
+CURVE PRIVATE
+STORED PRINT PRIVATE
+RT DOSE PRIVATE
+RT STRUCTURE SET PRIVATE
+RT PLAN PRIVATE
+RT TREAT RECORD PRIVATE
+PRESENTATION PRIVATE
+WAVEFORM PRIVATE
+SR DOCUMENT PRIVATE
+KEY OBJECT DOC PRIVATE
+SPECTROSCOPY PRIVATE
+RAW DATA PRIVATE
+TOPIC STUDY, SERIES, IMAGE, OVERLAY, MODALITY LUT, VOI LUT,
+ CURVE, STORED PRINT, RT DOSE, RT STRUCTURE SET,
+ RT PLAN, RT TREAT RECORD, PRESENTATION, WAVEFORM,
+ SR DOCUMENT, KEY OBJECT DOC, SPECTROSCOPY, RAW DATA,
+ PRIVATE
+VISIT PRIVATE
+
+RESULTS INTERPRETATION, PRIVATE
+
+INTERPRETATION PRIVATE
+STUDY COMPONENT PRIVATE
+PRIVATE PRIVATE, (any of the above as privately defined)
+MRDR (Not applicable)
+
+Note : Directory Record Types PRINT QUEUE, FILM SESSION, FILM BOX, and
+ IMAGE BOX were previously defined in DICOM. They have been retired.
+ See PS 3.3-1998.
+*/
+
+// ----------------------
+// The current gdcm version only deals with :
+//
+// (Root directory Entity) PATIENT
+// PATIENT STUDY
+// STUDY SERIES
+// STUDY VISIT
+// SERIES IMAGE
+// IMAGE /
+//
+// DicomDir::CreateDicomDir will have to be completed
+// Treelike structure management will have to be upgraded
+// ----------------------------------------------------------------------------
+
+namespace GDCM_NAME_SPACE
+{
+//-----------------------------------------------------------------------------
// Constructor / Destructor
+/**
+ * \brief Constructor : creates an empty DicomDir
+ */
+DicomDir::DicomDir()
+{
+ Initialize(); // sets all private fields to NULL
+ ParseDir = false;
+ NewMeta();
+}
+//#ifndef GDCM_LEGACY_REMOVE
/**
* \brief Constructor Parses recursively the directory and creates the DicomDir
* or uses an already built DICOMDIR, depending on 'parseDir' value.
- * @param FileName name
+ * @param fileName name
* - of the root directory (parseDir = true)
* - of the DICOMDIR (parseDir = false)
* @param parseDir boolean
* 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
+ * @deprecated use : new DicomDir() + [ SetLoadMode(lm) + ] SetDirectoryName(name)
+ * or : new DicomDir() + SetFileName(name)
*/
-gdcmDicomDir::gdcmDicomDir(const char *FileName, bool parseDir,
- bool exception_on_error):
- gdcmDocument(FileName,exception_on_error,true) // true : enable SeQuences
+ /*
+DicomDir::DicomDir(std::string const &fileName, bool parseDir ):
+ Document( )
{
- // que l'on ai passe un root directory ou un DICOMDIR
- // et quelle que soit la valeur de parseDir,
- // on a lance gdcmDocument
-
- 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;
-
-// gdcmDocument already executed
-// if user passed a root directory, sure we didn't get anything
-
- if( GetEntry().begin()==GetEntry().end() )
- {
- // if parseDir == false, it should be tagged as an error
- 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
- }
-
- if(parseDir)
- {
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory"
- " and create the DicomDir");
- ParseDirectory();
- }
- }
- else {
- gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); // Directory record sequence
- if (e==NULL) {
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record sequence (0x0004,0x1220)"
- );
- // FIXME : what to do when the parsed file IS NOT a DICOMDIR file ?
- }
- CreateDicomDir();
- }
+ // At this step, Document constructor is already executed,
+ // whatever user passed (either a root directory or a DICOMDIR)
+ // and whatever the value of parseDir was.
+ // (nothing is checked in Document constructor, to avoid overhead)
+
+ ParseDir = parseDir;
+ SetLoadMode (LD_ALL); // concerns only dicom files
+ SetFileName( fileName );
+ Load( );
}
+*/
+//#endif
/**
- * \ingroup gdcmDicomDir
- * \brief Constructor : creates an empty gdcmDicomDir
- * @param exception_on_error whether we want to throw an exception or not
+ * \brief Canonical destructor
*/
-gdcmDicomDir::gdcmDicomDir(bool exception_on_error):
- gdcmDocument(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
- AddDicomDirMeta();
+DicomDir::~DicomDir()
+{
+ ClearPatient();
+ if ( MetaElems )
+ {
+ MetaElems->Delete();
+ }
}
+//-----------------------------------------------------------------------------
+// Public
/**
- * \ingroup gdcmDicomDir
- * \brief Canonical destructor
+ * \brief Loader. use SetFileName(fn)
+ * or SetLoadMode(lm) + SetDirectoryName(dn) before !
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool DicomDir::Load( )
+{
+ if (!ParseDir)
+ {
+ if ( ! this->Document::Load( ) )
+ return false;
+ }
+ return DoTheLoadingJob( );
+}
+//#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Loader. (DEPRECATED : kept not to break the API)
+ * @param fileName file to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ * @deprecated use SetFileName(n) + Load() instead
*/
-gdcmDicomDir::~gdcmDicomDir()
+ /*
+bool DicomDir::Load(std::string const &fileName )
{
- SetStartMethod(NULL);
- SetProgressMethod(NULL);
- SetEndMethod(NULL);
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
- if(metaElems)
- delete metaElems;
-
- for(ListDicomDirPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ SetFileName( fileName );
+ if (!ParseDir)
{
- delete *cc;
+ if ( ! this->Document::Load( ) )
+ return false;
}
+ return DoTheLoadingJob( );
}
+*/
+//#endif
-//-----------------------------------------------------------------------------
-// Print
/**
- * \ingroup gdcmDicomDir
- * \brief Canonical Printer
+ * \brief Does the Loading Job (internal use only)
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
*/
-void gdcmDicomDir::Print(std::ostream &os)
+bool DicomDir::DoTheLoadingJob( )
{
- if(metaElems)
+ Progress = 0.0f;
+ Abort = false;
+
+ if (!ParseDir)
{
- metaElems->SetPrintLevel(printLevel);
- metaElems->Print(os);
- }
- for(ListDicomDirPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ // Only if user passed a DICOMDIR
+ // ------------------------------
+ Fp = 0;
+ if (!Document::Load() )
+ {
+ return false;
+ }
+
+ if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse
+ {
+ gdcmWarningMacro( "Entry HT empty for file: "<< GetFileName());
+ return false;
+ }
+ // Directory record sequence
+ DocEntry *e = GetDocEntry(0x0004, 0x1220);
+ if ( !e )
+ {
+ gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)"
+ << " in file " << GetFileName());
+ return false;
+ }
+ else
+ {
+ CreateDicomDir();
+ }
+ }
+ else
{
- (*cc)->SetPrintLevel(printLevel);
- (*cc)->Print(os);
+ // Only if user passed a root directory
+ // ------------------------------------
+ if ( GetFileName() == "." )
+ {
+ // user passed '.' as Name
+ // we get current directory name
+ char buf[2048];
+ const char *cwd = getcwd(buf, 2048);
+ if( cwd )
+ {
+ SetFileName( buf ); // will be converted into a string
+ }
+ else
+ {
+ gdcmErrorMacro( "Path was too long to fit on 2048 bytes" );
+ }
+ }
+ NewMeta();
+ gdcmDebugMacro( "Parse directory and create the DicomDir : "
+ << GetFileName() );
+ ParseDirectory();
}
+ return true;
}
-//-----------------------------------------------------------------------------
-// Public
/**
- * \ingroup gdcmDicomDir
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current header was properly parsed
+ * decides whether or not the current document 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,
+ * @return true when Document is the one of a reasonable DicomDir,
* false otherwise.
*/
-bool gdcmDicomDir::IsReadable(void)
+bool DicomDir::IsReadable()
{
- if(!gdcmDocument::IsReadable())
- return(false);
- if(!metaElems)
- return(false);
- if(patients.size()<=0)
- return(false);
-
- return(true);
-}
+ if ( Filetype == Unknown )
+ {
+ gdcmErrorMacro( "Wrong filetype for " << GetFileName());
+ return false;
+ }
+ if ( !MetaElems )
+ {
+ gdcmWarningMacro( "Meta Elements missing in DicomDir");
+ return false;
+ }
+ if ( Patients.size() <= 0 )
+ {
+ gdcmWarningMacro( "NO Patient in DicomDir");
+ return false;
+ }
-/**
- * \ingroup gdcmDicomDir
- * \brief fills the whole structure, starting from a root Directory
- */
-void gdcmDicomDir::ParseDirectory(void)
-{
- CreateDicomDirChainedList(GetFileName());
- CreateDicomDir();
+ return true;
}
/**
- * \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)
+ * \brief adds *the* Meta to a partially created DICOMDIR
+ */
+DicomDirMeta *DicomDir::NewMeta()
{
- if((startArg)&&(startMethodArgDelete))
- startMethodArgDelete(startArg);
+ if ( MetaElems )
+ {
+ MetaElems->Delete();
+ }
+ DocEntry *entry = GetFirstEntry();
+ if ( entry )
+ {
+ MetaElems = DicomDirMeta::New(true); // true = empty
- startMethod=method;
- startArg=arg;
- startMethodArgDelete=argDelete;
+ entry = GetFirstEntry();
+ while( entry )
+ {
+ if ( dynamic_cast<SeqEntry *>(entry) )
+ break;
+
+ MetaElems->AddEntry(entry);
+ RemoveEntry(entry);
+
+ entry = GetFirstEntry();
+ }
+ }
+ else // after root directory parsing
+ {
+ MetaElems = DicomDirMeta::New(false); // false = not empty
+ }
+ MetaElems->SetSQItemNumber(0); // To avoid further missprinting
+ return MetaElems;
}
/**
- * \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
+ * \brief adds a new Patient (with the basic elements) to a partially created
+ * DICOMDIR
*/
-void gdcmDicomDir::SetStartMethodArgDelete(gdcmMethod *method)
+DicomDirPatient *DicomDir::NewPatient()
{
- startMethodArgDelete=method;
+ DicomDirPatient *dd = DicomDirPatient::New();
+ AddPatientToEnd( dd );
+ return dd;
}
/**
- * \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
+ * \brief Remove all Patients
*/
-void gdcmDicomDir::SetProgressMethod(gdcmMethod *method,void *arg,gdcmMethod *argDelete)
+void DicomDir::ClearPatient()
{
- if((progressArg)&&(progressMethodArgDelete))
- progressMethodArgDelete(progressArg);
-
- progressMethod=method;
- progressArg=arg;
- progressMethodArgDelete=argDelete;
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc!= Patients.end();
+ ++cc)
+ {
+ (*cc)->Unregister();
+ }
+ Patients.clear();
}
/**
- * \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)
+ * \brief Get the first entry while visiting the DicomDirPatients
+ * \return The first DicomDirPatient if found, otherwhise NULL
+ */
+DicomDirPatient *DicomDir::GetFirstPatient()
{
- progressMethodArgDelete=method;
+ ItPatient = Patients.begin();
+ if ( ItPatient != Patients.end() )
+ return *ItPatient;
+ return NULL;
}
/**
- * \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
+ * \brief Get the next entry while visiting the DicomDirPatients
+ * \note : meaningfull only if GetFirstEntry already called
+ * \return The next DicomDirPatient if found, otherwhise NULL
*/
-void gdcmDicomDir::SetEndMethod(gdcmMethod *method, void *arg, gdcmMethod *argDelete)
+DicomDirPatient *DicomDir::GetNextPatient()
{
- if((endArg)&&(endMethodArgDelete))
- endMethodArgDelete(endArg);
+ gdcmAssertMacro (ItPatient != Patients.end());
- endMethod=method;
- endArg=arg;
- endMethodArgDelete=argDelete;
+ ++ItPatient;
+ if ( ItPatient != Patients.end() )
+ return *ItPatient;
+ return NULL;
}
/**
- * \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
+ * \brief fills the whole structure, starting from a root Directory
*/
-void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method)
+void DicomDir::ParseDirectory()
{
- endMethodArgDelete=method;
+ CreateDicomDirChainedList( GetFileName() );
+ CreateDicomDir();
}
/**
- * \ingroup gdcmDicomDir
- * \brief writes on disc a DICOMDIR
+ * \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;
+bool DicomDir::Write(std::string const &fileName)
+{
+ int i;
+ uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff };
+ uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0x0000, 0x0000 };
+
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if ( !fp )
+ {
+ gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
+ return false;
+ }
- fp1=fopen(fileName.c_str(),"wb");
- if(fp1==NULL)
+ char filePreamble[128];
+ memset(filePreamble, 0, 128);
+ fp->write(filePreamble, 128);
+ binary_write( *fp, "DICM");
+
+ DicomDirMeta *ptrMeta = GetMeta();
+ ptrMeta->WriteContent(fp, ExplicitVR, true, false);
+
+ // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
+ for(i=0;i<6;++i)
+ {
+ binary_write(*fp, sq[i]);
+ }
+
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc != Patients.end();
+ ++cc )
+ {
+ (*cc)->WriteContent( fp, ExplicitVR, false, true );
+ }
+
+ // force writing Sequence Delimitation Item
+ for(i=0;i<4;++i)
{
- printf("Failed to open(write) File [%s] \n",fileName.c_str());
- return(false);
+ binary_write(*fp, sqt[i]); // fffe e0dd 0000 0000
}
- char * filePreamble = new char[128];
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
- delete[] filePreamble;
- UpdateDirectoryRecordSequenceLength();
- WriteEntries(fp1);
+ fp->close();
+ delete fp;
- fclose(fp1);
return true;
}
/**
- * \brief Writes in a file using the tree-like structure.
- * @param _fp already open file pointer
+ * \brief Anonymize a DICOMDIR
+ * @return true
*/
+
+bool DicomDir::Anonymize()
+{
+ DataEntry *v;
+ // Something clever to be found to forge the Patient names
+ std::ostringstream s;
+ int i = 1;
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc!= Patients.end();
+ ++cc)
+ {
+ s << i;
+ v = (*cc)->GetDataEntry(0x0010, 0x0010) ; // Patient's Name
+ if (v)
+ {
+ v->SetString(s.str());
+ }
-void gdcmDicomDir::WriteEntries(FILE *_fp)
-{
- /// \todo (?) tester les echecs en ecriture
- /// (apres chaque fwrite, dans le WriteEntry)
+ v = (*cc)->GetDataEntry(0x0010, 0x0020) ; // Patient ID
+ if (v)
+ {
+ v->SetString(" ");
+ }
+ v = (*cc)->GetDataEntry(0x0010, 0x0030) ; // Patient's BirthDate
+ if (v)
+ {
+ v->SetString(" ");
+ }
+ s << "";
+ i++;
+ }
+ return true;
+}
-/* TODO : to go on compiling
+/**
+ * \brief Copies all the attributes from an other DocEntrySet
+ * @param set entry to copy from
+ * @remarks The contained DocEntries are not copied, only referenced
+ */
+void DicomDir::Copy(DocEntrySet *set)
+{
+ // Remove all previous childs
+ ClearPatient();
- 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;
+ Document::Copy(set);
+
+ DicomDir *dd = dynamic_cast<DicomDir *>(set);
+ if( dd )
+ {
+ if(MetaElems)
+ MetaElems->Unregister();
+ MetaElems = dd->MetaElems;
+ if(MetaElems)
+ MetaElems->Register();
+
+ Patients = dd->Patients;
+ for(ItPatient = Patients.begin();ItPatient != Patients.end();++ItPatient)
+ (*ItPatient)->Register();
}
- */
-}
-
+}
+
//-----------------------------------------------------------------------------
// Protected
-
/**
- * \ingroup gdcmDicomDir
- * \brief create a gdcmDocument-like chained list from a root Directory
+ * \brief create a Document-like chained list from a root Directory
* @param path entry point of the tree-like structure
*/
-void gdcmDicomDir::CreateDicomDirChainedList(std::string path)
+void DicomDir::CreateDicomDirChainedList(std::string const &path)
{
CallStartMethod();
-
- gdcmDirList fileList(path,1); // gets recursively the file list
- unsigned int count=0;
+ DirList dirList(path,1); // gets recursively the file list
+ unsigned int count = 0;
VectDocument list;
- gdcmHeader *header;
-
- tagHT.clear();
- patients.clear();
+ File *f;
- for(gdcmDirList::iterator it=fileList.begin();
- it!=fileList.end();
- ++it)
+ DirListType fileList = dirList.GetFilenames();
+ unsigned int nbFile = fileList.size();
+ for( DirListType::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
{
- progress=(float)(count+1)/(float)fileList.size();
+ Progress = (float)(count+1)/(float)nbFile;
CallProgressMethod();
- if(abort)
+ 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;
+ f = File::New( );
+ f->SetLoadMode(LoadMode); // we allow user not to load Sequences,
+ // or Shadow groups, or ......
+ f->SetFileName( it->c_str() );
+ f->Load( );
- count++;
+ if ( f->IsReadable() )
+ {
+ // Add the file to the chained list:
+ list.push_back(f);
+ gdcmDebugMacro( "Readable " << it->c_str() );
+ }
+ else
+ {
+ f->Delete();
+ }
+ 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);
-
+ std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
+
+ std::string tmp = dirList.GetDirName();
+ //for each File 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);
+ for(VectDocument::iterator itDoc=list.begin();
+ itDoc!=list.end();
+ ++itDoc)
+ {
+ dynamic_cast<File *>(*itDoc)->Delete();
}
- return m;
}
+//-----------------------------------------------------------------------------
+// Private
/**
- * \ingroup gdcmDicomDir
- * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR
+ * \brief Sets all fields to NULL
*/
-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);
- }
+void DicomDir::Initialize()
+{
+ Progress = 0.0;
+ Abort = false;
- gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &tagHT);
- patients.push_front(p);
- return p;
+ MetaElems = NULL;
}
-
/**
- * \ingroup gdcmDicomDir
- * \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
+ * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header
*/
-void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,
- gdcmDocument *header)
+void DicomDir::CreateDicomDir()
{
- std::list<gdcmElement> elemList;
- std::list<gdcmElement>::iterator it;
- guint16 tmpGr, tmpEl;
- gdcmDictEntry *dictEntry;
- gdcmDocEntry *entry;
- std::string val;
+ // The SeqEntries of "Directory Record Sequence" are parsed.
+ // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
+ // N.B. : VISIT, PRIVATE not fully dealt with
+ // 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 -
+ gdcmDebugMacro("Create DicomDir");
- switch(type)
+ // Directory record sequence
+ DocEntry *e = GetDocEntry(0x0004, 0x1220);
+ if ( !e )
{
- 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;
+ gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found");
+ return;
}
-
- for(it=elemList.begin();it!=elemList.end();++it)
+
+ SeqEntry *s = dynamic_cast<SeqEntry *>(e);
+ if ( !s )
{
- tmpGr=it->group;
- tmpEl=it->elem;
- dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl);
- entry=new gdcmDocEntry(dictEntry);
- entry->SetOffset(0); // just to avoid further missprinting
+ gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?");
+ return;
+ }
+
+ NewMeta();
+
+ DocEntry *d;
+ std::string v;
+ SQItem *si;
- if(header)
- val=header->GetEntryByNumber(tmpGr,tmpEl);
+ SQItem *tmpSI=s->GetFirstSQItem();
+ while(tmpSI)
+ {
+ d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type
+ if ( DataEntry *dataEntry = dynamic_cast<DataEntry *>(d) )
+ {
+ v = dataEntry->GetString();
+ }
else
- val=GDCM_UNFOUND;
+ {
+ gdcmWarningMacro( "(0004,1430) not a DataEntry ?!?");
+ continue;
+ }
+
+ // A decent DICOMDIR has much more images than series,
+ // more series than studies, and so on.
+ // This is the right order to perform the tests
- if(val==GDCM_UNFOUND)
+ if ( v == "IMAGE " )
{
- 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
+ si = DicomDirImage::New(true); // true = empty
+ if ( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
{
- 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()]);
- }
+ si->Delete();
+ si = NULL;
+ gdcmErrorMacro( "Add AddImageToEnd failed");
}
- else
+ }
+ else if ( v == "SERIES" )
+ {
+ si = DicomDirSerie::New(true); // true = empty
+ if ( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
{
- val=it->value;
+ si->Delete();
+ si = NULL;
+ gdcmErrorMacro( "Add AddSerieToEnd failed");
}
- }
- else
- {
- if (header->GetEntryLengthByNumber(tmpGr,tmpEl)== 0)
- val=it->value;
}
-
- ((gdcmValEntry *)entry)->SetValue(val);
-
- if(dictEntry)
+ else if ( v == "VISIT " )
{
- if(dictEntry->GetGroup()==0xfffe)
- {
- entry->SetLength(((gdcmValEntry *)entry)->GetValue().length());
- }
- else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") )
+ si = DicomDirVisit::New(true); // true = empty
+ if ( !AddVisitToEnd( static_cast<DicomDirVisit *>(si)) )
{
- entry->SetLength(4);
- }
- else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") )
+ si->Delete();
+ si = NULL;
+ gdcmErrorMacro( "Add AddVisitToEnd failed");
+ }
+ }
+ else if ( v == "STUDY " )
+ {
+ si = DicomDirStudy::New(true); // true = empty
+ if ( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
{
- entry->SetLength(2);
- }
- else if(dictEntry->GetVR()=="SQ")
+ si->Delete();
+ si = NULL;
+ gdcmErrorMacro( "Add AddStudyToEnd failed");
+ }
+ }
+ else if ( v == "PATIENT " )
+ {
+ si = DicomDirPatient::New(true); // true = empty
+ if ( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
{
- entry->SetLength(0xffffffff);
+ si->Delete();
+ si = NULL;
+ gdcmErrorMacro( "Add PatientToEnd failed");
}
- else
+ }
+ /// \todo : deal with PRIVATE (not so easy, since PRIVATE appears
+ /// at different levels ?!? )
+
+ else if ( v == "PRIVATE " ) // for SIEMENS 'CSA Non Image'
+ {
+
+ gdcmWarningMacro( " -------------------------------------------"
+ << "a PRIVATE SQItem was found : " << v);
+ si = DicomDirPrivate::New(true); // true = empty
+ if ( !AddPrivateToEnd( static_cast<DicomDirPrivate *>(si)) )
{
- entry->SetLength(((gdcmValEntry *)entry)->GetValue().length());
+ si->Delete();
+ si = NULL;
+ gdcmErrorMacro( "Add PrivateToEnd failed");
}
+ }
+ else
+ {
+ // It was neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
+ // nor an 'IMAGE' SQItem. Skip to next item.
+ gdcmWarningMacro( " -------------------------------------------"
+ << "a non PATIENT/STUDY/SERIE/IMAGE /VISIT/PRIVATE SQItem was found : "
+ << v);
+
+ // FIXME : deal with other item types !
+ tmpSI=s->GetNextSQItem(); // To avoid infinite loop
+ continue;
}
- //AddDocEntry(entry); // both in H Table and in chained list
- tagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE !
- }
-}
-/**
- * \ingroup gdcmDicomDir
- * \brief CallStartMethod
- */
-void gdcmDicomDir::CallStartMethod(void)
-{
- progress=0.0f;
- abort=false;
- if(startMethod)
- startMethod(startArg);
+ if ( si )
+ si->Copy(tmpSI);
+
+ tmpSI=s->GetNextSQItem();
+ }
+ ClearEntry();
}
+
/**
- * \ingroup gdcmDicomDir
- * \brief CallProgressMethod
+ * \brief AddPatientToEnd
+ * @param dd SQ Item to enqueue to the DicomPatient chained List
*/
-void gdcmDicomDir::CallProgressMethod(void)
+bool DicomDir::AddPatientToEnd(DicomDirPatient *dd)
{
- if(progressMethod)
- progressMethod(progressArg);
+ Patients.push_back(dd);
+ return true;
}
+
/**
- * \ingroup gdcmDicomDir
- * \brief CallEndMethod
+ * \brief AddStudyToEnd
+ * @param dd SQ Item to enqueue to the DicomDirStudy chained List
*/
-void gdcmDicomDir::CallEndMethod(void)
+bool DicomDir::AddStudyToEnd(DicomDirStudy *dd)
{
- progress=1.0f;
- if(endMethod)
- endMethod(endArg);
+ if ( Patients.size() > 0 )
+ {
+ ListDicomDirPatient::iterator itp = Patients.end();
+ itp--;
+ (*itp)->AddStudy(dd);
+ return true;
+ }
+ return false;
}
-//-----------------------------------------------------------------------------
-// Private
/**
- * \ingroup gdcmDicomDir
- * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader
+ * \brief AddSerieToEnd
+ * @param dd SQ Item to enqueue to the DicomDirSerie chained List
*/
-void gdcmDicomDir::CreateDicomDir()
+bool DicomDir::AddSerieToEnd(DicomDirSerie *dd)
{
- // 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;
-
- gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); // Directory record sequence
- if (e==NULL) {
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record sequence (0x0004,0x1220)"
- );
- // FIXME : what to do when the parsed file IS NOT a DICOMDIR file ?
- return;
- }
-
- gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT);
-
- gdcmSeqEntry *s = (gdcmSeqEntry *)e; // FIXME : It is allowed ???
- ListSQItem listItems = s->GetSQItems();
-
- gdcmDocEntry * d;
- for(ListSQItem::iterator i=listItems.begin(); i !=listItems.end();++i)
- {
- d=(*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type
- std::string v=((gdcmValEntry *)d)->GetValue();
-
- if(v=="PATIENT ")
- {
- 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;
- }
+ if ( Patients.size() > 0 )
+ {
+ ListDicomDirPatient::iterator itp = Patients.end();
+ itp--;
- else if(v=="IMAGE ")
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
{
- AddDicomDirImageToEnd(*i);
- // AddObjectToEnd(type,*i);
- type=gdcmDicomDir::GDCM_DICOMDIR_IMAGE;
+ study->AddSerie(dd);
+ return true;
}
-
- else
- continue ; // It was 'non PATIENT', 'non STUDY', 'non SERIE', 'non IMAGE' SQItem
- }
-}
-/**
- * \ingroup gdcmDicomDir
- * \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
- */
-
-// now useless ?
-
-/*void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,gdcmSQItem *s)
-{
- if(s==NULL) // ??
- return;
-
- switch(type)
- {
- 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_DICOMDIR_SERIE:
- AddDicomDirSerieToEnd(s);
- break;
- case gdcmDicomDir::GDCM_DICOMDIR_IMAGE:
- AddDicomDirImageToEnd(s);
- break;
- case gdcmDicomDir::GDCM_DICOMDIR_NONE:
- AddDicomDirImageToEnd(s); //FIXME
- break;
}
-}
-
-*/
-
-/**
- * \ingroup gdcmDicomDir
- * \brief Well ... there is only one occurence
-*/
-void gdcmDicomDir::AddDicomDirMeta()
-{
- if(metaElems)
- delete metaElems;
- metaElems = new gdcmDicomDirMeta(&tagHT);
+ return false;
}
/**
- * \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 AddDicomDirStudyToEnd
- * @param s SQ Item to enqueue to the DicomDirStudy chained List
+ * \brief AddVisitToEnd
+ * @param dd SQ Item to enqueue to the DicomDirVisit chained List
*/
- void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s)
+bool DicomDir::AddVisitToEnd(DicomDirVisit *dd)
{
- if(patients.size()>0)
+ if ( Patients.size() > 0 )
{
- ListDicomDirPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(s, &tagHT));
+
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
+ {
+ study->AddVisit(dd);
+ return true;
+ }
}
+ return false;
}
/**
- * \ingroup gdcmDicomDir
- * \brief AddDicomDirSerieToEnd
- * @param s SQ Item to enqueue to the DicomDirSerie chained List
+ * \brief AddImageToEnd
+ * @param dd SQ Item to enqueue to the DicomDirImage chained List
*/
-void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s)
+bool DicomDir::AddImageToEnd(DicomDirImage *dd)
{
- if(patients.size()>0)
+ if ( Patients.size() > 0 )
{
- ListDicomDirPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- if((*itp)->GetDicomDirStudies().size()>0)
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
{
- ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end();
- itst--;
- (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &tagHT));
+ DicomDirSerie *serie = study->GetLastSerie();
+ if ( serie )
+ {
+ serie->AddImage(dd);
+ return true;
+ }
}
}
+ return false;
}
/**
- * \ingroup gdcmDicomDir
- * \brief AddDicomDirImageToEnd
- * @param s SQ Item to enqueue to the DicomDirImage chained List
+ * \brief AddPrivateToEnd
+ * @param dd SQ Item to enqueue to the DicomDirPrivate chained List
+ * (checked for SIEMENS 'CSA non image')
*/
- void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s)
+bool DicomDir::AddPrivateToEnd(DicomDirPrivate *dd)
{
- if(patients.size()>0)
+ if ( Patients.size() > 0 )
{
- ListDicomDirPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- if((*itp)->GetDicomDirStudies().size()>0)
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
{
- ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end();
- itst--;
-
- if((*itst)->GetDicomDirSeries().size()>0)
+ DicomDirSerie *serie = study->GetLastSerie();
+ if ( serie )
{
- ListDicomDirSerie::iterator its=(*itst)->GetDicomDirSeries().end();
- its--;
- (*its)->AddDicomDirImage(new gdcmDicomDirImage(s, &tagHT));
+ serie->AddPrivate(dd);
+ return true;
}
}
}
+ return false;
}
/**
- * \ingroup gdcmDicomDir
- * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info
+ * \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, VectDocument &list)
+void DicomDir::SetElements(std::string const &path, VectDocument const &list)
{
- std::string patPrevName="", patPrevID="";
- std::string studPrevInstanceUID="", studPrevID="";
- std::string serPrevInstanceUID="", serPrevID="";
+ ClearEntry();
+ ClearPatient();
+
+ 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);
-
- for(VectDocument::iterator it=list.begin();it!=list.end();++it)
+ bool first = true;
+ for( VectDocument::const_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);
+ patCurName = (*it)->GetEntryString(0x0010,0x0010);
+ patCurID = (*it)->GetEntryString(0x0010,0x0011);
+ studCurInstanceUID = (*it)->GetEntryString(0x0020,0x000d);
+ studCurID = (*it)->GetEntryString(0x0020,0x0010);
+ serCurInstanceUID = (*it)->GetEntryString(0x0020,0x000e);
+ serCurID = (*it)->GetEntryString(0x0020,0x0011);
+
+ if ( patCurName != patPrevName || patCurID != patPrevID || first )
+ {
+ SetElement(path, GDCM_DICOMDIR_PATIENT, *it);
+ first = true;
+ }
+
+ // if new Study, deal with 'STUDY' Elements
+ if ( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID
+ || first )
+ {
+ SetElement(path, GDCM_DICOMDIR_STUDY, *it);
+ first = true;
+ }
+
+ // if new Serie, deal with 'SERIE' Elements
+ if ( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID
+ || first )
+ {
+ 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;
+ SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
+
+ patPrevName = patCurName;
+ patPrevID = patCurID;
+ studPrevInstanceUID = studCurInstanceUID;
+ studPrevID = studCurID;
+ serPrevInstanceUID = serCurInstanceUID;
+ serPrevID = serCurID;
+ first = false;
}
}
/**
- * \ingroup gdcmDicomDir
- * \brief compares two dgcmHeaders
+ * \brief adds to the HTable
+ * the Entries (Dicom Elements) corresponding to the given type
+ * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE
+ * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT,
+ * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
+ * @param header Header of the current file
*/
-bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1,gdcmDocument *header2)
+void DicomDir::SetElement(std::string const &path, DicomDirType type,
+ Document *header)
{
- return(*header1<*header2);
+ ListDicomDirElem elemList;
+ ListDicomDirElem::const_iterator it;
+ uint16_t tmpGr, tmpEl;
+ //DictEntry *dictEntry;
+ DataEntry *entry;
+ std::string val;
+ SQItem *si;
+ switch( type )
+ {
+ case GDCM_DICOMDIR_IMAGE:
+ elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
+ si = DicomDirImage::New(true);
+ if ( !AddImageToEnd(static_cast<DicomDirImage *>(si)) )
+ {
+ si->Delete();
+ gdcmErrorMacro( "Add ImageToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_SERIE:
+ elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
+ si = DicomDirSerie::New(true);
+ if ( !AddSerieToEnd(static_cast<DicomDirSerie *>(si)) )
+ {
+ si->Delete();
+ gdcmErrorMacro( "Add SerieToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_STUDY:
+ elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
+ si = DicomDirStudy::New(true);
+ if ( !AddStudyToEnd(static_cast<DicomDirStudy *>(si)) )
+ {
+ si->Delete();
+ gdcmErrorMacro( "Add StudyToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_PATIENT:
+ elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
+ si = DicomDirPatient::New(true);
+ if ( !AddPatientToEnd(static_cast<DicomDirPatient *>(si)) )
+ {
+ si->Delete();
+ gdcmErrorMacro( "Add PatientToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_META: // never used ?!? --> Done within DoTheLoadingJob
+ if ( MetaElems )
+ {
+ MetaElems->Delete();
+ gdcmErrorMacro( "MetaElements already exist, they will be destroyed");
+ }
+ elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
+ MetaElems = DicomDirMeta::New(true);
+ si = MetaElems;
+ break;
+ default:
+ return;
+ }
+
+ // FIXME : troubles found when it's a SeqEntry
+
+ // removed all the seems-to-be-useless stuff about Referenced Image Sequence
+ // to avoid further troubles
+ // imageElem 0008 1140 "" // Referenced Image Sequence
+ // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later
+ // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later
+ // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later
+ // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later
+
+ std::string referencedVal;
+ // for all the relevant elements found in their own spot of the DicomDir.dic
+ for( it = elemList.begin(); it != elemList.end(); ++it)
+ {
+ tmpGr = it->Group;
+ tmpEl = it->Elem;
+
+ entry = DataEntry::New(tmpGr, tmpEl, it->VR); // dicomelements file was modified, to store VR
+ 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->GetEntryString(tmpGr, tmpEl);
+ }
+ else
+ {
+ val = GDCM_UNFOUND;
+ }
+
+ if ( val == GDCM_UNFOUND)
+ {
+ if ( tmpGr == 0x0004 ) // never present in File !
+ {
+ switch (tmpEl)
+ {
+ case 0x1130: // File-set ID
+ // force to the *end* File Name
+ val = Util::GetName( path );
+ break;
+
+ case 0x1500: // Only used for image
+ if ( header->GetFileName().substr(0, path.length()) != path )
+ {
+ gdcmWarningMacro( "The base path of file name is incorrect");
+ val = header->GetFileName();
+ }
+ else
+ {
+ // avoid the first '/' in File name !
+ if ( header->GetFileName().c_str()[path.length()]
+ == GDCM_FILESEPARATOR )
+ val = &(header->GetFileName().c_str()[path.length()+1]);
+ else
+ val = &(header->GetFileName().c_str()[path.length()]);
+ }
+ break;
+
+ case 0x1510: // Referenced SOP Class UID in File
+ referencedVal = header->GetEntryString(0x0008, 0x0016);
+ // FIXME : probabely something to check
+ val = referencedVal;
+ break;
+
+ case 0x1511: // Referenced SOP Instance UID in File
+ referencedVal = header->GetEntryString(0x0008, 0x0018);
+ // FIXME : probabely something to check
+ val = referencedVal;
+ break;
+
+ case 0x1512: // Referenced Transfer Syntax UID in File
+ referencedVal = header->GetEntryString(0x0002, 0x0010);
+ // FIXME : probabely something to check
+ val = referencedVal;
+ break;
+
+ default :
+ val = it->Value;
+ }
+ }
+ else
+ {
+ // If the entry is not found in the Header, don't write its 'value' in the DICOMDIR !
+ entry->Delete();
+ continue;
+ }
+ }
+ else
+ {
+ if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
+ {
+ val = it->Value;
+ // Don't polute the DICOMDIR with empty fields
+ if (val == "")
+ {
+ entry->Delete();
+ continue;
+ }
+ }
+ }
+
+/* FIX later the pb of creating the 'Implementation Version Name'!
+
+ if (val == GDCM_UNFOUND)
+ val = "";
+
+ if ( tmpGr == 0x0002 && tmpEl == 0x0013)
+ {
+ // 'Implementation Version Name'
+ std::string val = "GDCM ";
+ val += Util::GetVersion();
+ }
+*/
+
+ entry->SetString( val ); // troubles expected when vr=SQ ...
+
+ if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
+ {
+ gdcmDebugMacro("GDCM_DICOMDIR_META ?!? should never print that");
+ }
+
+ si->AddEntry(entry);
+ entry->Delete();
+ }
}
/**
- * \ingroup gdcmDicomDir
- * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR
+ * \brief Move the content of the source SQItem to the destination SQItem
+ * Only DocEntry's are moved
+ * @param dst destination SQItem
+ * @param src source SQItem
*/
+void DicomDir::MoveSQItem(DocEntrySet *dst, DocEntrySet *src)
+{
+ DocEntry *entry;
+// todo : rewrite the whole stuff, without using RemoveEntry an AddEntry,
+// to save time
+ entry = src->GetFirstEntry();
+ while(entry)
+ {
+ dst->AddEntry(entry); // use it, *before* removing it!
+ src->RemoveEntry(entry);
+ // we destroyed -> the current iterator is not longer valid
+ entry = src->GetFirstEntry();
+ }
+}
-void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() {
-
-// FIXME : to go on compiling
+/**
+ * \brief compares two files
+ */
+bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
+{
+ return *header1 < *header2;
+}
-// 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.
- }
+//-----------------------------------------------------------------------------
+// Print
+/**
+ * \brief Canonical Printer
+ * @param os ostream we want to print in
+ * @param indent Indentation string to be prepended during printing
+ */
+void DicomDir::Print(std::ostream &os, std::string const & )
+{
+ if ( MetaElems )
+ {
+ MetaElems->SetPrintLevel(PrintLevel);
+ MetaElems->Print(os);
}
- //bool res=SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps.
- SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps.
- return;
- */
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc != Patients.end();
+ ++cc)
+ {
+ (*cc)->SetPrintLevel(PrintLevel);
+ (*cc)->Print(os);
+ }
}
//-----------------------------------------------------------------------------
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff