Program: gdcm
Module: $RCSfile: gdcmDicomDir.cxx,v $
Language: C++
- Date: $Date: 2005/01/21 11:40:55 $
- Version: $Revision: 1.112 $
+ Date: $Date: 2005/07/07 16:37:40 $
+ Version: $Revision: 1.144 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
+//-----------------------------------------------------------------------------
+// For full DICOMDIR description, see:
+// PS 3.3-2003, pages 731-750
+//-----------------------------------------------------------------------------
#include "gdcmDicomDir.h"
#include "gdcmDicomDirStudy.h"
#include "gdcmDicomDirSerie.h"
#else
# include <unistd.h>
#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
+//
+// ----------------------
+// The current gdcm version only deals with :
+//
+// (Root directory Entity) PATIENT
+// PATIENT STUDY
+// STUDY SERIES
+// SERIES IMAGE
+// IMAGE /
+//
+// DicomDir::CreateDicomDir will have to be completed
+// Treelike structure management will have to be upgraded
+// ----------------------------------------------------------------------------
+
namespace gdcm
{
-
-//-----------------------------------------------------------------------------
-// For full DICOMDIR description, see:
-// PS 3.3-2003, pages 731-750
//-----------------------------------------------------------------------------
// Constructor / Destructor
-
/**
* \brief Constructor : creates an empty DicomDir
*/
DicomDir::DicomDir()
- :Document( )
+ :Document( )
{
Initialize(); // sets all private fields to NULL
NewMeta();
/**
* \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 use it
*/
DicomDir::DicomDir(std::string const &fileName, bool parseDir ):
- Document( fileName )
+ Document( )
{
// At this step, Document constructor is already executed,
- // whatever user passed (a root directory or a DICOMDIR)
+ // whatever user passed (either a root directory or a DICOMDIR)
// and whatever the value of parseDir was.
// (nothing is cheked in Document constructor, to avoid overhead)
- Initialize(); // sets all private fields to NULL
-
- // if user passed a root directory, sure we didn't get anything
- if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse
- {
- if (!parseDir)
- gdcmVerboseMacro( "Entry HT empty for file: "<<fileName);
-
- // Only if user passed a root directory
- // ------------------------------------
- if ( fileName == "." )
- {
- // user passed '.' as Name
- // we get current directory name
- char dummy[1000];
- getcwd(dummy, (size_t)1000);
- SetFileName( dummy ); // will be converted into a string
- }
-
- if ( parseDir ) // user asked for a recursive parsing of a root directory
- {
- NewMeta();
-
- gdcmVerboseMacro( "Parse directory and create the DicomDir");
- ParseDirectory();
- }
- else
- {
- /// \todo if parseDir == false, it should be tagged as an error
- // NO ! user may just call ParseDirectory() *after* constructor
- }
- }
- // Only if user passed a DICOMDIR
- // ------------------------------
- else
- {
- // Directory record sequence
- DocEntry *e = GetDocEntry(0x0004, 0x1220);
- if ( !e )
- {
- gdcmVerboseMacro( "NO 'Directory record sequence' (0x0004,0x1220)"
- << " in file " << fileName);
- /// \todo FIXME : what do we do when the parsed file IS NOT a
- /// DICOMDIR file ?
- }
- else
- CreateDicomDir();
- }
+ ParseDir = parseDir;
+ SetLoadMode (0x00000000); // concerns only dicom files
+ Load( fileName );
}
/**
SetProgressMethod(NULL);
SetEndMethod(NULL);
- for(ListDicomDirPatient::iterator cc = Patients.begin();
- cc!= Patients.end();
- ++cc)
- {
- delete *cc;
- }
+ ClearPatient();
if ( MetaElems )
{
delete MetaElems;
}
//-----------------------------------------------------------------------------
-// Print
+// Public
+
/**
- * \brief Canonical Printer
+ * \brief Loader. use SetLoadMode(), SetFileName() before !
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
*/
-void DicomDir::Print(std::ostream &os, std::string const & )
+bool DicomDir::Load( )
{
- if( MetaElems )
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
+
+ if (!ParseDir)
{
- MetaElems->SetPrintLevel(PrintLevel);
- MetaElems->Print(os);
- }
- for(ListDicomDirPatient::iterator cc = Patients.begin();
- cc != Patients.end();
- ++cc)
+ if ( ! this->Document::Load( ) )
+ return false;
+ }
+ return DoTheLoadingJob( );
+}
+
+/**
+ * \brief Loader. (DEPRECATED : 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.
+ */
+bool DicomDir::Load(std::string const &fileName )
+{
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
+
+ SetFileName( fileName );
+ if (!ParseDir)
{
- (*cc)->SetPrintLevel(PrintLevel);
- (*cc)->Print(os);
+ if ( ! this->Document::Load( ) )
+ return false;
}
+ return DoTheLoadingJob( );
+}
+
+/**
+ * \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.
+ */
+bool DicomDir::DoTheLoadingJob( )
+{
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
+
+ if (!ParseDir)
+ {
+ // Only if user passed a DICOMDIR
+ // ------------------------------
+ Fp = 0;
+ if ( !OpenFile() )
+ {
+ return false;
+ }
+ 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
+ {
+ // Only if user passed a root directory
+ // ------------------------------------
+ if ( GetFileName() == "." )
+ {
+ // user passed '.' as Name
+ // we get current directory name
+ char dummy[1000];
+ getcwd(dummy, (size_t)1000);
+ SetFileName( dummy ); // will be converted into a string
+ }
+ NewMeta();
+ gdcmWarningMacro( "Parse directory and create the DicomDir : "
+ << GetFileName() );
+ ParseDirectory();
+ }
+ return true;
}
-//-----------------------------------------------------------------------------
-// Public
/**
* \brief This predicate, based on hopefully reasonable heuristics,
* decides whether or not the current document was properly parsed
*/
bool DicomDir::IsReadable()
{
- if( Filetype == Unknown)
+ if ( Filetype == Unknown )
{
- gdcmVerboseMacro( "Wrong filetype");
+ gdcmWarningMacro( "Wrong filetype");
return false;
}
- if( !MetaElems )
+ if ( !MetaElems )
{
- gdcmVerboseMacro( "Meta Elements missing in DicomDir");
+ gdcmWarningMacro( "Meta Elements missing in DicomDir");
return false;
}
- if( Patients.size() <= 0 )
+ if ( Patients.size() <= 0 )
{
- gdcmVerboseMacro( "NO Patient in DicomDir");
+ gdcmWarningMacro( "NO Patient in DicomDir");
return false;
}
return true;
}
+/**
+ * \brief adds *the* Meta to a partially created DICOMDIR
+ */
+DicomDirMeta *DicomDir::NewMeta()
+{
+ if ( MetaElems )
+ delete MetaElems;
+
+ DocEntry *entry = GetFirstEntry();
+ if ( entry )
+ {
+ MetaElems = new DicomDirMeta(true); // true = empty
+
+ entry = GetFirstEntry();
+ while( entry )
+ {
+ if ( dynamic_cast<SeqEntry *>(entry) )
+ break;
+
+ RemoveEntryNoDestroy(entry);
+ MetaElems->AddEntry(entry);
+
+ entry = GetFirstEntry();
+ }
+ }
+ else // after root directory parsing
+ {
+ MetaElems = new DicomDirMeta(false); // false = not empty
+ }
+ MetaElems->SetSQItemNumber(0); // To avoid further missprinting
+ return MetaElems;
+}
+
+/**
+ * \brief adds a new Patient (with the basic elements) to a partially created
+ * DICOMDIR
+ */
+DicomDirPatient *DicomDir::NewPatient()
+{
+ DicomDirPatient *p = new DicomDirPatient();
+ AddPatientToEnd( p );
+ return p;
+}
+
+/**
+ * \brief Remove all Patients
+ */
+void DicomDir::ClearPatient()
+{
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc!= Patients.end();
+ ++cc)
+ {
+ delete *cc;
+ }
+ Patients.clear();
+}
+
+/**
+ * \brief Get the first entry while visiting the DicomDirPatients
+ * \return The first DicomDirPatient if found, otherwhise NULL
+ */
+DicomDirPatient *DicomDir::GetFirstPatient()
+{
+ ItPatient = Patients.begin();
+ if ( ItPatient != Patients.end() )
+ return *ItPatient;
+ return NULL;
+}
+
+/**
+ * \brief Get the next entry while visiting the DicomDirPatients
+ * \note : meaningfull only if GetFirstEntry already called
+ * \return The next DicomDirPatient if found, otherwhise NULL
+ */
+DicomDirPatient *DicomDir::GetNextPatient()
+{
+ gdcmAssertMacro (ItPatient != Patients.end());
+
+ ++ItPatient;
+ if ( ItPatient != Patients.end() )
+ return *ItPatient;
+ return NULL;
+}
+
/**
* \brief fills the whole structure, starting from a root Directory
*/
void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg,
DicomDir::Method *argDelete )
{
- if( StartArg && StartMethodArgDelete )
+ if ( StartArg && StartMethodArgDelete )
{
StartMethodArgDelete( StartArg );
}
StartMethodArgDelete = argDelete;
}
-/**
- * \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 DicomDir::SetStartMethodArgDelete( DicomDir::Method *method )
-{
- StartMethodArgDelete = method;
-}
/**
* \brief Set the progress method to call when the parsing of the
void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg,
DicomDir::Method *argDelete )
{
- if( ProgressArg && ProgressMethodArgDelete )
+ if ( ProgressArg && ProgressMethodArgDelete )
{
ProgressMethodArgDelete( ProgressArg );
}
ProgressMethodArgDelete = argDelete;
}
-/**
- * \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 DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method )
-{
- ProgressMethodArgDelete = method;
-}
-
/**
* \brief Set the end method to call when the parsing of the directory ends
* @param method Method to call
void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg,
DicomDir::Method *argDelete )
{
- if( EndArg && EndMethodArgDelete )
+ if ( EndArg && EndMethodArgDelete )
{
EndMethodArgDelete( EndArg );
}
/**
* \brief Set the method to delete the argument
- * The argument is destroyed when the method is changed or when
- * the class is destroyed
+ * 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 DicomDir::SetEndMethodArgDelete( DicomDir::Method *method )
+void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method )
{
- EndMethodArgDelete = method;
+ StartMethodArgDelete = method;
}
/**
- * \brief Get the first entry while visiting the DicomDirPatients
- * \return The first DicomDirPatient if found, otherwhise NULL
- */
-DicomDirPatient *DicomDir::GetFirstPatient()
+ * \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 DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method )
{
- ItPatient = Patients.begin();
- if ( ItPatient != Patients.end() )
- return *ItPatient;
- return NULL;
+ ProgressMethodArgDelete = method;
}
/**
- * \brief Get the next entry while visiting the DicomDirPatients
- * \note : meaningfull only if GetFirstEntry already called
- * \return The next DicomDirPatient if found, otherwhise NULL
+ * \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
*/
-DicomDirPatient *DicomDir::GetNextPatient()
+void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method )
{
- gdcmAssertMacro (ItPatient != Patients.end());
- {
- ++ItPatient;
- if ( ItPatient != Patients.end() )
- return *ItPatient;
- }
- return NULL;
+ EndMethodArgDelete = method;
}
/**
* \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
*/
std::ofstream *fp = new std::ofstream(fileName.c_str(),
std::ios::out | std::ios::binary);
- if( !fp )
+ if ( !fp )
{
- gdcmVerboseMacro("Failed to open(write) File: " << fileName.c_str());
+ gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
return false;
}
char filePreamble[128];
memset(filePreamble, 0, 128);
- fp->write(filePreamble, 128); //FIXME
+ fp->write(filePreamble, 128);
binary_write( *fp, "DICM");
DicomDirMeta *ptrMeta = GetMeta();
return true;
}
-//-----------------------------------------------------------------------------
-// Protected
-
-/**
- * \brief create a Document-like chained list from a root Directory
- * @param path entry point of the tree-like structure
- */
-void DicomDir::CreateDicomDirChainedList(std::string const & path)
-{
- CallStartMethod();
- DirList dirList(path,1); // gets recursively the file list
- unsigned int count = 0;
- VectDocument list;
- File *header;
-
- DirListType fileList = dirList.GetFilenames();
-
- for( DirListType::iterator it = fileList.begin();
- it != fileList.end();
- ++it )
- {
- Progress = (float)(count+1)/(float)fileList.size();
- CallProgressMethod();
- if( Abort )
- {
- break;
- }
-
- header = new File( it->c_str() );
- if( !header )
- {
- gdcmVerboseMacro( "Failure in new gdcm::File " << it->c_str() );
- continue;
- }
-
- if( header->IsReadable() )
- {
- // Add the file to the chained list:
- list.push_back(header);
- gdcmVerboseMacro( "Readable " << it->c_str() );
- }
- else
- {
- delete header;
- }
- count++;
- }
- // sorts Patient/Study/Serie/
- 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();
-
- for(VectDocument::iterator itDoc=list.begin();
- itDoc!=list.end();
- ++itDoc)
- {
- delete dynamic_cast<File *>(*itDoc);
- }
-}
-
/**
- * \brief adds *the* Meta to a partially created DICOMDIR
+ * \brief Anonymize a DICOMDIR
+ * @return true
*/
-
-DicomDirMeta * DicomDir::NewMeta()
+
+bool DicomDir::AnonymizeDicomDir()
{
- if( MetaElems )
- delete MetaElems;
-
-
- if ( TagHT.begin() != TagHT.end() ) // after Document Parsing
- {
- MetaElems = new DicomDirMeta(true);
-
- TagDocEntryHT::iterator lastOneButSequence = TagHT.end();
- lastOneButSequence --;
- // ALL the 'out of Sequence' Tags belong to Meta Elems
- // (we skip 0004|1220 [Directory record sequence] )
- for ( TagDocEntryHT::iterator cc = TagHT.begin();
- cc != lastOneButSequence;
+ ValEntry *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)
- {
- MetaElems->AddEntry( cc->second );
- }
- }
- else // after root directory parsing
- {
- MetaElems = new DicomDirMeta(false);
- }
- MetaElems->SetSQItemNumber(0); // To avoid further missprinting
- return MetaElems;
-}
-
-/**
- * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR
- */
-DicomDirPatient *DicomDir::NewPatient()
-{
- DicomDirPatient *p = new DicomDirPatient();
- AddPatientToEnd( p );
- return p;
-}
-
-/**
- * \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
- */
-void DicomDir::SetElement(std::string const &path, DicomDirType type,
- Document *header)
-{
- ListDicomDirElem elemList; //FIXME this is going to be a by copy operation
- ListDicomDirElem::const_iterator it;
- uint16_t tmpGr, tmpEl;
- DictEntry *dictEntry;
- ValEntry *entry;
- std::string val;
- SQItem *si;
-
- switch( type )
{
- case GDCM_DICOMDIR_IMAGE:
- elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
- si = new DicomDirImage(true);
- if( !AddImageToEnd(static_cast<DicomDirImage *>(si)) )
- {
- delete si;
- gdcmErrorMacro( "Add ImageToEnd failed");
- }
- break;
- case GDCM_DICOMDIR_SERIE:
- elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
- si = new DicomDirSerie(true);
- if( !AddSerieToEnd(static_cast<DicomDirSerie *>(si)) )
- {
- delete si;
- gdcmErrorMacro( "Add SerieToEnd failed");
- }
- break;
- case GDCM_DICOMDIR_STUDY:
- elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
- si = new DicomDirStudy(true);
- if( !AddStudyToEnd(static_cast<DicomDirStudy *>(si)) )
- {
- delete si;
- gdcmErrorMacro( "Add StudyToEnd failed");
- }
- break;
- case GDCM_DICOMDIR_PATIENT:
- elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
- si = new DicomDirPatient(true);
- if( !AddPatientToEnd(static_cast<DicomDirPatient *>(si)) )
- {
- delete si;
- gdcmErrorMacro( "Add PatientToEnd failed");
- }
- break;
- case GDCM_DICOMDIR_META:
- elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
- si = new DicomDirMeta(true);
- if( MetaElems )
- {
- delete MetaElems;
- gdcmErrorMacro( "MetaElements already exist, they will be destroyed");
- }
- MetaElems = static_cast<DicomDirMeta *>(si);
- break;
- default:
- return;
- }
- // 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
- // for all the relevant elements found in their own spot of the DicomDir.dic
- // FIXME : troubles found when it's a SeqEntry
-
- for( it = elemList.begin(); it != elemList.end(); ++it)
- {
- tmpGr = it->Group;
- tmpEl = it->Elem;
- dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl);
-
- entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
-
- entry->SetOffset(0); // just to avoid further missprinting
-
- if( header )
+ s << i;
+ v = (*cc)->GetValEntry(0x0010, 0x0010) ; // Patient's Name
+ if (v)
{
- // NULL when we Build Up (ex nihilo) a DICOMDIR
- // or when we add the META elems
- val = header->GetEntry(tmpGr, tmpEl);
+ v->SetValue(s.str());
}
- else
+
+ v = (*cc)->GetValEntry(0x0010, 0x0020) ; // Patient ID
+ if (v)
{
- val = GDCM_UNFOUND;
+ v->SetValue(" ");
}
- if( val == GDCM_UNFOUND)
+ v = (*cc)->GetValEntry(0x0010, 0x0030) ; // Patient's BirthDate
+ if (v)
{
- if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID
- {
- // force to the *end* File Name
- val = Util::GetName( path );
- }
- else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image
- {
- if( header->GetFileName().substr(0, path.length()) != path )
- {
- gdcmVerboseMacro( "The base path of file name is incorrect");
- val = header->GetFileName();
- }
- else
- {
- val = &(header->GetFileName().c_str()[path.length()]);
- }
- }
- else
- {
- val = it->Value;
- }
+ v->SetValue(" ");
}
- else
+ s << "";
+ i++;
+ }
+ return true;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief create a Document-like chained list from a root Directory
+ * @param path entry point of the tree-like structure
+ */
+void DicomDir::CreateDicomDirChainedList(std::string const &path)
+{
+ CallStartMethod();
+ DirList dirList(path,1); // gets recursively the file list
+ unsigned int count = 0;
+ VectDocument list;
+ File *f;
+
+ DirListType fileList = dirList.GetFilenames();
+
+ for( DirListType::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
+ {
+ Progress = (float)(count+1)/(float)fileList.size();
+ CallProgressMethod();
+ if ( Abort )
{
- if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
- val = it->Value;
+ break;
}
- entry->SetValue( val ); // troubles expected when vr=SQ ...
+ f = new File( );
+ f->SetLoadMode(LoadMode); // we allow user not to load Sequences...
+ f->Load( it->c_str() );
- if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
+// if ( !f )
+// {
+// gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() );
+// continue;
+// }
+
+ if ( f->IsReadable() )
{
- gdcmVerboseMacro("GDCM_DICOMDIR_META ?!? should never print that");
- }
- si->AddEntry(entry);
+ // Add the file to the chained list:
+ list.push_back(f);
+ gdcmWarningMacro( "Readable " << it->c_str() );
+ }
+ else
+ {
+ delete f;
+ }
+ count++;
+ }
+ // sorts Patient/Study/Serie/
+ 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();
+
+ for(VectDocument::iterator itDoc=list.begin();
+ itDoc!=list.end();
+ ++itDoc)
+ {
+ delete dynamic_cast<File *>(*itDoc);
}
}
-//-----------------------------------------------------------------------------
/**
* \brief CallStartMethod
*/
{
Progress = 0.0f;
Abort = false;
- if( StartMethod )
+ if ( StartMethod )
{
StartMethod( StartArg );
}
}
-//-----------------------------------------------------------------------------
/**
* \brief CallProgressMethod
*/
void DicomDir::CallProgressMethod()
{
- if( ProgressMethod )
+ if ( ProgressMethod )
{
ProgressMethod( ProgressArg );
}
}
-//-----------------------------------------------------------------------------
/**
* \brief CallEndMethod
*/
void DicomDir::CallEndMethod()
{
Progress = 1.0f;
- if( EndMethod )
+ if ( EndMethod )
{
EndMethod( EndArg );
}
}
/**
- * \brief create a 'DicomDir' from a DICOMDIR Header
+ * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header
*/
void DicomDir::CreateDicomDir()
{
- // The list is parsed.
+ // The SeqEntries of "Directory Record Sequence" are parsed.
// When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
// 1 - we save the beginning iterator
// 2 - we continue to parse
DocEntry *e = GetDocEntry(0x0004, 0x1220);
if ( !e )
{
- gdcmVerboseMacro( "NO Directory record sequence (0x0004,0x1220)");
- /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ?
+ gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found");
return;
}
SeqEntry *s = dynamic_cast<SeqEntry *>(e);
if ( !s )
{
- gdcmVerboseMacro( "No SeqEntry present");
- // useless : (0x0004,0x1220) IS a Sequence !
+ gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?");
return;
}
NewMeta();
-
- //ListSQItem listItems = s->GetSQItems();
DocEntry *d;
std::string v;
}
else
{
- gdcmVerboseMacro( "Not a ValEntry.");
+ gdcmWarningMacro( "(0004,1430) not a ValEntry ?!?");
continue;
}
- if( v == "PATIENT " )
+ // A decent DICOMDIR has much more images than series,
+ // more series than studies, and so on.
+ // This is the right order to preform the tests
+
+ if ( v == "IMAGE " )
{
- si = new DicomDirPatient(true);
- if( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
+ si = new DicomDirImage(true);
+ if ( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
{
delete si;
si = NULL;
- gdcmErrorMacro( "Add PatientToEnd failed");
+ gdcmErrorMacro( "Add AddImageToEnd failed");
}
}
- else if( v == "STUDY " )
+ else if ( v == "SERIES" )
{
- si = new DicomDirStudy(true);
- if( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
+ si = new DicomDirSerie(true);
+ if ( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
{
delete si;
si = NULL;
- gdcmErrorMacro( "Add AddStudyToEnd failed");
+ gdcmErrorMacro( "Add AddSerieToEnd failed");
}
}
- else if( v == "SERIES" )
+ else if ( v == "STUDY " )
{
- si = new DicomDirSerie(true);
- if( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
+ si = new DicomDirStudy(true);
+ if ( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
{
delete si;
si = NULL;
- gdcmErrorMacro( "Add AddSerieToEnd failed");
+ gdcmErrorMacro( "Add AddStudyToEnd failed");
}
}
- else if( v == "IMAGE " )
+ else if ( v == "PATIENT " )
{
- si = new DicomDirImage(true);
- if( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
+ si = new DicomDirPatient(true);
+ if ( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
{
delete si;
si = NULL;
- gdcmErrorMacro( "Add AddImageToEnd failed");
+ gdcmErrorMacro( "Add PatientToEnd failed");
}
}
else
{
- // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
- // neither an 'IMAGE' SQItem. Skip to next item.
- continue;
+ // 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 SQItem was found : "
+ << v);
+
+ // FIXME : deal with other item types !
+ tmpSI=s->GetNextSQItem(); // To avoid infinite loop
+ continue;
}
-
- if( si )
+ if ( si )
MoveSQItem(si,tmpSI);
tmpSI=s->GetNextSQItem();
}
- TagHT.clear();
+ ClearEntry();
}
/**
*/
bool DicomDir::AddStudyToEnd(DicomDirStudy *dd)
{
- if( Patients.size() > 0 )
+ if ( Patients.size() > 0 )
{
ListDicomDirPatient::iterator itp = Patients.end();
itp--;
*/
bool DicomDir::AddSerieToEnd(DicomDirSerie *dd)
{
- if( Patients.size() > 0 )
+ if ( Patients.size() > 0 )
{
ListDicomDirPatient::iterator itp = Patients.end();
itp--;
DicomDirStudy *study = (*itp)->GetLastStudy();
- if( study )
+ if ( study )
{
study->AddSerie(dd);
return true;
}
-/* if( (*itp)->GetDicomDirStudies().size() > 0 )
- {
- ListDicomDirStudy::const_iterator itst =
- (*itp)->GetDicomDirStudies().end();
- itst--;
- (*itst)->AddSerie(dd);
- return true;
- }*/
}
return false;
}
*/
bool DicomDir::AddImageToEnd(DicomDirImage *dd)
{
- if( Patients.size() > 0 )
+ if ( Patients.size() > 0 )
{
ListDicomDirPatient::iterator itp = Patients.end();
itp--;
DicomDirStudy *study = (*itp)->GetLastStudy();
- if( study )
+ if ( study )
{
DicomDirSerie *serie = study->GetLastSerie();
- if( serie )
+ if ( serie )
{
serie->AddImage(dd);
return true;
}
}
-/* if( (*itp)->GetDicomDirStudies().size() > 0 )
- {
- ListDicomDirStudy::const_iterator itst =
- (*itp)->GetDicomDirStudies().end();
- itst--;
-
- if( (*itst)->GetDicomDirSeries().size() > 0 )
- {
- ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end();
- its--;
- (*its)->AddImage(dd);
- return true;
- }
- }*/
}
return false;
}
/**
- * \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 DicomDir::SetElements(std::string const & path, VectDocument const &list)
+void DicomDir::SetElements(std::string const &path, VectDocument const &list)
{
- TagHT.clear();
- Patients.clear();
+ ClearEntry();
+ ClearPatient();
std::string patPrevName = "", patPrevID = "";
std::string studPrevInstanceUID = "", studPrevID = "";
bool first = true;
for( VectDocument::const_iterator it = list.begin();
- it != list.end(); ++it )
+ it != list.end();
+ ++it )
{
// get the current file characteristics
- patCurName = (*it)->GetEntry(0x0010,0x0010);
- patCurID = (*it)->GetEntry(0x0010,0x0011);
- studCurInstanceUID = (*it)->GetEntry(0x0020,0x000d);
- studCurID = (*it)->GetEntry(0x0020,0x0010);
- serCurInstanceUID = (*it)->GetEntry(0x0020,0x000e);
- serCurID = (*it)->GetEntry(0x0020,0x0011);
-
- if( patCurName != patPrevName || patCurID != patPrevID || first )
+ patCurName = (*it)->GetEntryValue(0x0010,0x0010);
+ patCurID = (*it)->GetEntryValue(0x0010,0x0011);
+ studCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000d);
+ studCurID = (*it)->GetEntryValue(0x0020,0x0010);
+ serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e);
+ serCurID = (*it)->GetEntryValue(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
+ // 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
+ // if new Serie, deal with 'SERIE' Elements
+ if ( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID
|| first )
{
SetElement(path, GDCM_DICOMDIR_SERIE, *it);
- first = true;
}
// Always Deal with 'IMAGE' Elements
}
}
+/**
+ * \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
+ */
+void DicomDir::SetElement(std::string const &path, DicomDirType type,
+ Document *header)
+{
+ ListDicomDirElem elemList;
+ ListDicomDirElem::const_iterator it;
+ uint16_t tmpGr, tmpEl;
+ DictEntry *dictEntry;
+ ValEntry *entry;
+ std::string val;
+ SQItem *si;
+
+ switch( type )
+ {
+ case GDCM_DICOMDIR_IMAGE:
+ elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
+ si = new DicomDirImage(true);
+ if ( !AddImageToEnd(static_cast<DicomDirImage *>(si)) )
+ {
+ delete si;
+ gdcmErrorMacro( "Add ImageToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_SERIE:
+ elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
+ si = new DicomDirSerie(true);
+ if ( !AddSerieToEnd(static_cast<DicomDirSerie *>(si)) )
+ {
+ delete si;
+ gdcmErrorMacro( "Add SerieToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_STUDY:
+ elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
+ si = new DicomDirStudy(true);
+ if ( !AddStudyToEnd(static_cast<DicomDirStudy *>(si)) )
+ {
+ delete si;
+ gdcmErrorMacro( "Add StudyToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_PATIENT:
+ elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
+ si = new DicomDirPatient(true);
+ if ( !AddPatientToEnd(static_cast<DicomDirPatient *>(si)) )
+ {
+ delete si;
+ gdcmErrorMacro( "Add PatientToEnd failed");
+ }
+ break;
+ case GDCM_DICOMDIR_META:
+ elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
+ si = new DicomDirMeta(true);
+ if ( MetaElems )
+ {
+ delete MetaElems;
+ gdcmErrorMacro( "MetaElements already exist, they will be destroyed");
+ }
+ MetaElems = static_cast<DicomDirMeta *>(si);
+ break;
+ default:
+ return;
+ }
+ // 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
+
+ // FIXME : troubles found when it's a SeqEntry
+
+ // 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;
+ dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl);
+
+ entry = new ValEntry( 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->GetEntryValue(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 = Util::GetName( path );
+ }
+ else if ( tmpGr == 0x0004 && tmpEl == 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
+ {
+ val = &(header->GetFileName().c_str()[path.length()]);
+ }
+ }
+ else
+ {
+ val = it->Value;
+ }
+ }
+ else
+ {
+ if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
+ val = it->Value;
+ }
+
+ entry->SetValue( val ); // troubles expected when vr=SQ ...
+
+ if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
+ {
+ gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that");
+ }
+ si->AddEntry(entry);
+ }
+}
+
/**
* \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(SQItem *dst,SQItem *src)
+void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src)
{
DocEntry *entry;
}
/**
- * \brief compares two dgcmHeaders
+ * \brief compares two files
*/
bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
{
return *header1 < *header2;
}
-} // end namespace gdcm
+//-----------------------------------------------------------------------------
+// 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);
+ }
+ 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