Program: gdcm
Module: $RCSfile: gdcmDicomDir.cxx,v $
Language: C++
- Date: $Date: 2005/11/06 01:38:02 $
- Version: $Revision: 1.171 $
+ Date: $Date: 2010/04/09 15:23:40 $
+ Version: $Revision: 1.198 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmDicomDirSerie.h"
#include "gdcmDicomDirVisit.h"
#include "gdcmDicomDirImage.h"
+#include "gdcmDicomDirPrivate.h"
#include "gdcmDicomDirPatient.h"
#include "gdcmDicomDirMeta.h"
#include "gdcmDicomDirElement.h"
#include "gdcmSeqEntry.h"
#include "gdcmSQItem.h"
#include "gdcmDataEntry.h"
+#include "gdcmCommandManager.h"
#include <fstream>
#include <string>
#else
# include <unistd.h>
#endif
+
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
+
// ----------------------------------------------------------------------------
// Note for future developpers
// ----------------------------------------------------------------------------
// 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 :
//
// Treelike structure management will have to be upgraded
// ----------------------------------------------------------------------------
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
//-----------------------------------------------------------------------------
// Constructor / Destructor
* \brief Constructor : creates an empty DicomDir
*/
DicomDir::DicomDir()
- :Document( )
{
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
+ * - 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
+ * @deprecated use : new DicomDir() + [ SetLoadMode(lm) + ] SetDirectoryName(name)
+ * or : new DicomDir() + SetFileName(name)
+ */
+ /*
+DicomDir::DicomDir(std::string const &fileName, bool parseDir ):
+ Document( )
+{
+ // 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
+
/**
* \brief Canonical destructor
*/
DicomDir::~DicomDir()
{
- SetStartMethod(NULL,NULL,NULL);
- SetProgressMethod(NULL,NULL,NULL);
- SetEndMethod(NULL,NULL,NULL);
-
ClearPatient();
if ( MetaElems )
{
}
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,
+//#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
+ * @deprecated use SetFileName(n) + Load() instead
*/
+ /*
bool DicomDir::Load(std::string const &fileName )
{
- SetFileName(fileName);
- return Load();
-}
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
-/// DEPRECATED : use SetDirectoryName(dname) instead
-/* *
- * \brief Loader. (DEPRECATED : kept not to break the API)
- * @param paseDir Parse Dir
- * @deprecated use SetDirectoryName(dname) instead
- */
-void DicomDir::SetParseDir(bool parseDir)
-{
- ParseDir = parseDir;
+ SetFileName( fileName );
+ if (!ParseDir)
+ {
+ if ( ! this->Document::Load( ) )
+ return false;
+ }
+ return DoTheLoadingJob( );
}
-#endif
+*/
+//#endif
/**
* \brief Does the Loading Job (internal use only)
return false;
}
else
+ {
CreateDicomDir();
+ }
}
else
{
char buf[2048];
const char *cwd = getcwd(buf, 2048);
if( cwd )
- {
- SetFileName( buf ); // will be converted into a string
- }
+ {
+ SetFileName( buf ); // will be converted into a string
+ }
else
- {
- gdcmErrorMacro( "Path was too long to fit on 2048 bytes" );
- }
+ {
+ gdcmErrorMacro( "Path was too long to fit on 2048 bytes" );
+ }
}
NewMeta();
gdcmDebugMacro( "Parse directory and create the DicomDir : "
DicomDirMeta *DicomDir::NewMeta()
{
if ( MetaElems )
+ {
MetaElems->Delete();
-
+ }
DocEntry *entry = GetFirstEntry();
if ( entry )
{
CreateDicomDir();
}
-void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg )
-{
- SetStartMethod(method,arg,NULL);
-}
-
-void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg )
-{
- SetProgressMethod(method,arg,NULL);
-}
-
-void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg )
-{
- SetEndMethod(method,arg,NULL);
-}
-
-/**
- * \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 DicomDir::SetStartMethod( DicomDir::Method *method, void *arg,
- DicomDir::Method *argDelete )
-{
- if ( StartArg && StartMethodArgDelete )
- {
- StartMethodArgDelete( StartArg );
- }
-
- StartMethod = method;
- StartArg = arg;
- StartMethodArgDelete = argDelete;
-}
-
-
-/**
- * \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 DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg,
- DicomDir::Method *argDelete )
-{
- if ( ProgressArg && ProgressMethodArgDelete )
- {
- ProgressMethodArgDelete( ProgressArg );
- }
-
- ProgressMethod = method;
- ProgressArg = arg;
- ProgressMethodArgDelete = argDelete;
-}
-
-/**
- * \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 DicomDir::SetEndMethod( DicomDir::Method *method, void *arg,
- DicomDir::Method *argDelete )
-{
- if ( EndArg && EndMethodArgDelete )
- {
- EndMethodArgDelete( EndArg );
- }
-
- EndMethod = method;
- EndArg = arg;
- EndMethodArgDelete = 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 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 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::SetEndMethodArgDelete( DicomDir::Method *method )
-{
- EndMethodArgDelete = method;
-}
-
/**
* \brief writes on disc a DICOMDIR
* \ warning does NOT add the missing elements in the header :
{
int i;
uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff };
- uint16_t sqt[4]= { 0xfffe, 0xe0dd, 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 )
+ if ( !fp )
{
gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
return false;
binary_write( *fp, "DICM");
DicomDirMeta *ptrMeta = GetMeta();
- ptrMeta->WriteContent(fp, ExplicitVR);
+ ptrMeta->WriteContent(fp, ExplicitVR, true, false);
// force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
for(i=0;i<6;++i)
cc != Patients.end();
++cc )
{
- (*cc)->WriteContent( fp, ExplicitVR );
+ (*cc)->WriteContent( fp, ExplicitVR, false, true );
}
// force writing Sequence Delimitation Item
for(i=0;i<4;++i)
{
- binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
+ binary_write(*fp, sqt[i]); // fffe e0dd 0000 0000
}
fp->close();
return true;
}
+/**
+ * \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();
+
+ 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
/**
File *f;
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 )
{
}
}
-/**
- * \brief CallStartMethod
- */
-void DicomDir::CallStartMethod()
-{
- Progress = 0.0f;
- Abort = false;
- if ( StartMethod )
- {
- StartMethod( StartArg );
- }
-}
-
-/**
- * \brief CallProgressMethod
- */
-void DicomDir::CallProgressMethod()
-{
- if ( ProgressMethod )
- {
- ProgressMethod( ProgressArg );
- }
-}
-
-/**
- * \brief CallEndMethod
- */
-void DicomDir::CallEndMethod()
-{
- Progress = 1.0f;
- if ( EndMethod )
- {
- EndMethod( EndArg );
- }
-}
//-----------------------------------------------------------------------------
// Private
*/
void DicomDir::Initialize()
{
- StartMethod = NULL;
- ProgressMethod = NULL;
- EndMethod = NULL;
- StartMethodArgDelete = NULL;
- ProgressMethodArgDelete = NULL;
- EndMethodArgDelete = NULL;
- StartArg = NULL;
- ProgressArg = NULL;
- EndArg = NULL;
-
Progress = 0.0;
Abort = false;
{
// 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
// 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
+ // This is the right order to perform the tests
if ( v == "IMAGE " )
{
- si = DicomDirImage::New(true);
+ si = DicomDirImage::New(true); // true = empty
if ( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
{
si->Delete();
}
else if ( v == "SERIES" )
{
- si = DicomDirSerie::New(true);
+ si = DicomDirSerie::New(true); // true = empty
if ( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
{
si->Delete();
}
else if ( v == "VISIT " )
{
- si = DicomDirVisit::New(true);
+ si = DicomDirVisit::New(true); // true = empty
if ( !AddVisitToEnd( static_cast<DicomDirVisit *>(si)) )
{
si->Delete();
}
else if ( v == "STUDY " )
{
- si = DicomDirStudy::New(true);
+ si = DicomDirStudy::New(true); // true = empty
if ( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
{
si->Delete();
}
else if ( v == "PATIENT " )
{
- si = DicomDirPatient::New(true);
+ si = DicomDirPatient::New(true); // true = empty
if ( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
{
si->Delete();
gdcmErrorMacro( "Add PatientToEnd failed");
}
}
+ /// \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)) )
+ {
+ 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.
- gdcmDebugMacro( " -------------------------------------------"
- << "a non PATIENT/STUDY/SERIE/IMAGE SQItem was found : "
+ gdcmWarningMacro( " -------------------------------------------"
+ << "a non PATIENT/STUDY/SERIE/IMAGE /VISIT/PRIVATE SQItem was found : "
<< v);
// FIXME : deal with other item types !
continue;
}
if ( si )
- si->MoveObject(tmpSI); // New code : Copies the List
+ si->Copy(tmpSI);
tmpSI=s->GetNextSQItem();
}
return false;
}
+/**
+ * \brief AddPrivateToEnd
+ * @param dd SQ Item to enqueue to the DicomDirPrivate chained List
+ * (checked for SIEMENS 'CSA non image')
+ */
+bool DicomDir::AddPrivateToEnd(DicomDirPrivate *dd)
+{
+ if ( Patients.size() > 0 )
+ {
+ ListDicomDirPatient::iterator itp = Patients.end();
+ itp--;
+
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
+ {
+ DicomDirSerie *serie = study->GetLastSerie();
+ if ( serie )
+ {
+ serie->AddPrivate(dd);
+ return true;
+ }
+ }
+ }
+ return false;
+}
+
/**
* \brief for each Header of the chained list,
* add/update the Patient/Study/Serie/Image info
{
// get the current file characteristics
patCurName = (*it)->GetEntryString(0x0010,0x0010);
+ if (patCurName == "") // to prevent further troubles when wild anonymization was performed
+ patCurName = "gdcm^Patient";
patCurID = (*it)->GetEntryString(0x0010,0x0011);
studCurInstanceUID = (*it)->GetEntryString(0x0020,0x000d);
studCurID = (*it)->GetEntryString(0x0020,0x0010);
ListDicomDirElem elemList;
ListDicomDirElem::const_iterator it;
uint16_t tmpGr, tmpEl;
- DictEntry *dictEntry;
+ //DictEntry *dictEntry;
DataEntry *entry;
std::string val;
SQItem *si;
-
switch( type )
{
case GDCM_DICOMDIR_IMAGE:
gdcmErrorMacro( "Add PatientToEnd failed");
}
break;
- case GDCM_DICOMDIR_META:
+ case GDCM_DICOMDIR_META: // never used ?!? --> Done within DoTheLoadingJob
if ( MetaElems )
{
MetaElems->Delete();
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
{
tmpGr = it->Group;
tmpEl = it->Elem;
- dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl);
-
- entry = DataEntry::New( dictEntry );
+
+ 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);
+ val = header->GetEntryString(tmpGr, tmpEl);
}
else
{
}
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 0x1130: // File-set ID
+ // force to the *end* File Name
+ val = Util::GetName( path );
+ break;
- case 0x1500: // Only used for image
+ 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();
+ {
+ gdcmWarningMacro( "The base path of file name is incorrect");
+ val = header->GetFileName();
}
else
- {
- val = &(header->GetFileName().c_str()[path.length()+1]);
+ {
+ // 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;
+ break;
- case 0x1510: // Referenced SOP Class UID in File
- referencedVal = header->GetEntryString(0x0008, 0x0016);
- // FIXME : probabely something to check
- val = referencedVal;
- 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 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;
+ 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;
- }
+ 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 = "";
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();
}
* @param dst destination SQItem
* @param src source SQItem
*/
-void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src)
+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);
- dst->AddEntry(entry);
// we destroyed -> the current iterator is not longer valid
entry = src->GetFirstEntry();
}
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