Program: gdcm
Module: $RCSfile: gdcmDicomDir.cxx,v $
Language: C++
- Date: $Date: 2004/12/03 20:16:57 $
- Version: $Revision: 1.85 $
+ Date: $Date: 2005/01/19 08:57:14 $
+ Version: $Revision: 1.106 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <sys/types.h>
#ifdef _MSC_VER
-#define getcwd _getcwd
+# define getcwd _getcwd
#endif
-#if defined( _MSC_VER) || defined(__BORLANDC__)
- #include <direct.h>
+#if defined(_MSC_VER) || defined(__BORLANDC__)
+# include <direct.h>
#else
- #include <unistd.h>
+# include <unistd.h>
#endif
namespace gdcm
// Constructor / Destructor
/**
- * \ingroup DicomDir
* \brief Constructor : creates an empty DicomDir
*/
DicomDir::DicomDir()
* - false if user passed an already built DICOMDIR file
* and wants to use it
*/
-DicomDir::DicomDir(std::string const & fileName, bool parseDir ):
+DicomDir::DicomDir(std::string const &fileName, bool parseDir ):
Document( fileName )
{
- // Whatever user passed (a root directory or a DICOMDIR)
- // and whatever the value of parseDir was,
- // Document is already executed
+ // At this step, Document constructor is already executed,
+ // whatever user passed (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
{
- dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty");
+ if (!parseDir)
+ gdcmVerboseMacro( "Entry HT empty for file: "<<fileName);
- if ( fileName.size() == 1 && fileName[0] == '.' )
+ // Only if user passed a root directory
+ // ------------------------------------
+ if ( fileName == "." )
{
// user passed '.' as Name
// we get current directory name
{
MetaElems = NewMeta();
- dbg.Verbose(0, "DicomDir::DicomDir : Parse directory"
- " and create the DicomDir");
+ gdcmVerboseMacro( "Parse directory and create the DicomDir");
ParseDirectory();
}
else
{
/// \todo if parseDir == false, it should be tagged as an error
- // NON ! il suffit d'appeler ParseDirectory()
- // apres le constructeur
+ // NO ! user may just call ParseDirectory() *after* constructor
}
}
- else // Only if user passed a DICOMDIR
+ // Only if user passed a DICOMDIR
+ // ------------------------------
+ else
{
// Directory record sequence
- DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
+ DocEntry *e = GetDocEntry(0x0004, 0x1220);
if ( !e )
{
- dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record"
- " sequence (0x0004,0x1220)");
+ 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 ?
}
/**
* \brief Canonical Printer
*/
-void DicomDir::Print(std::ostream &os)
+void DicomDir::Print(std::ostream &os, std::string const & )
{
if( MetaElems )
{
cc != Patients.end();
++cc)
{
- (*cc)->SetPrintLevel( PrintLevel );
- (*cc)->Print( os );
+ (*cc)->SetPrintLevel(PrintLevel);
+ (*cc)->Print(os);
}
}
*/
bool DicomDir::IsReadable()
{
- if( !Document::IsReadable() )
+ if( Filetype == Unknown)
{
+ gdcmVerboseMacro( "Wrong filetype");
return false;
}
if( !MetaElems )
{
+ gdcmVerboseMacro( "Meta Elements missing in DicomDir");
return false;
}
if( Patients.size() <= 0 )
{
+ gdcmVerboseMacro( "NO Patient in DicomDir");
return false;
}
/**
- * \ingroup DicomDir
* \brief fills the whole structure, starting from a root Directory
*/
void DicomDir::ParseDirectory()
}
/**
- * \ingroup DicomDir
* \brief Set the start method to call when the parsing of the
* directory starts.
* @param method Method to call
* @param argDelete Argument
* \warning In python : the arg parameter isn't considered
*/
-void DicomDir::SetStartMethod( DicomDir::Method* method, void* arg,
- DicomDir::Method* argDelete )
+void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg,
+ DicomDir::Method *argDelete )
{
if( StartArg && StartMethodArgDelete )
{
}
/**
- * \ingroup DicomDir
* \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 )
+void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method )
{
StartMethodArgDelete = method;
}
/**
- * \ingroup DicomDir
* \brief Set the progress method to call when the parsing of the
* directory progress
* @param method Method to call
* @param argDelete Argument
* \warning In python : the arg parameter isn't considered
*/
-void DicomDir::SetProgressMethod( DicomDir::Method* method, void* arg,
- DicomDir::Method* argDelete )
+void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg,
+ DicomDir::Method *argDelete )
{
if( ProgressArg && ProgressMethodArgDelete )
{
}
/**
- * \ingroup DicomDir
* \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 )
+void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method )
{
ProgressMethodArgDelete = method;
}
/**
- * \ingroup DicomDir
* \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 )
+void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg,
+ DicomDir::Method *argDelete )
{
if( EndArg && EndMethodArgDelete )
{
}
/**
- * \ingroup DicomDir
* \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 )
+void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method )
{
EndMethodArgDelete = method;
}
/**
- * \ingroup 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 !
* @return false only when fail to open
*/
-bool DicomDir::WriteDicomDir(std::string const& fileName)
+bool DicomDir::WriteDicomDir(std::string const &fileName)
{
int i;
uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff };
uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff };
- std::ofstream* fp = new std::ofstream(fileName.c_str(),
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
std::ios::out | std::ios::binary);
if( !fp )
{
- dbg.Verbose(2, "Failed to open(write) File: ", fileName.c_str());
+ gdcmVerboseMacro("Failed to open(write) File: " << fileName.c_str());
return false;
}
// Protected
/**
- * \ingroup DicomDir
* \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 fileList(path,1); // gets recursively the file list
+ DirList dirList(path,1); // gets recursively the file list
unsigned int count = 0;
VectDocument list;
Header *header;
- for( DirList::iterator it = fileList.begin();
+ DirListType fileList = dirList.GetFilenames();
+
+ for( DirListType::iterator it = fileList.begin();
it != fileList.end();
++it )
{
break;
}
-std::cerr<<"File : "<<it->c_str()<<std::endl;
header = new Header( it->c_str() );
if( !header )
{
- dbg.Verbose( 1,
- "DicomDir::CreateDicomDirChainedList: "
- "failure in new Header ",
- it->c_str() );
+ gdcmVerboseMacro( "Failure in new Header " << it->c_str() );
continue;
}
{
// Add the file header to the chained list:
list.push_back(header);
- dbg.Verbose( 1,
- "DicomDir::CreateDicomDirChainedList: readable ",
- it->c_str() );
+ gdcmVerboseMacro( "Readable " << it->c_str() );
}
else
{
// sorts Patient/Study/Serie/
std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
- std::string tmp = fileList.GetDirName();
+ std::string tmp = dirList.GetDirName();
//for each Header of the chained list, add/update the Patient/Study/Serie/Image info
SetElements(tmp, list);
CallEndMethod();
- for(VectDocument::iterator it=list.begin();
- it!=list.end();
- ++it)
+ for(VectDocument::iterator itDoc=list.begin();
+ itDoc!=list.end();
+ ++itDoc)
{
- delete dynamic_cast<Header *>(*it);
+ delete dynamic_cast<Header *>(*itDoc);
}
}
/**
- * \ingroup DicomDir
* \brief adds *the* Meta to a partially created DICOMDIR
*/
cc != lastOneButSequence;
++cc)
{
- m->AddDocEntry( cc->second );
+ m->AddEntry( cc->second );
}
}
else // after root directory parsing
{
- ListDicomDirMetaElem const & elemList =
+ ListDicomDirMetaElem const &elemList =
Global::GetDicomDirElements()->GetDicomDirMetaElements();
m->FillObject(elemList);
}
/**
* \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR
*/
-DicomDirPatient * DicomDir::NewPatient()
+DicomDirPatient *DicomDir::NewPatient()
{
ListDicomDirPatientElem::const_iterator it;
uint16_t tmpGr,tmpEl;
{
tmpGr = it->Group;
tmpEl = it->Elem;
- dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl);
+ dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl);
entry = new ValEntry( 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() );
- }
- p->AddDocEntry( entry );
+ p->AddEntry( entry );
}
Patients.push_front( p );
* GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
* @param header Header of the current file
*/
-void DicomDir::SetElement(std::string const & path, DicomDirType type,
+void DicomDir::SetElement(std::string const &path, DicomDirType type,
Document *header)
{
ListDicomDirElem elemList; //FIXME this is going to be a by copy operation
si = new DicomDirImage();
if( !AddDicomDirImageToEnd(static_cast<DicomDirImage *>(si)) )
{
- dbg.Verbose(0,"DicomDir::SetElement:",
- "Add DicomDirImageToEnd failed");
+ gdcmVerboseMacro( "Add DicomDirImageToEnd failed");
}
break;
case GDCM_DICOMDIR_SERIE:
si = new DicomDirSerie();
if( !AddDicomDirSerieToEnd(static_cast<DicomDirSerie *>(si)) )
{
- dbg.Verbose(0,"DicomDir::SetElement:",
- "Add DicomDirSerieToEnd failed");
+ gdcmVerboseMacro( "Add DicomDirSerieToEnd failed");
}
break;
case GDCM_DICOMDIR_STUDY:
si = new DicomDirStudy();
if( !AddDicomDirStudyToEnd(static_cast<DicomDirStudy *>(si)) )
{
- dbg.Verbose(0,"DicomDir::SetElement:",
- "Add DicomDirStudyToEnd failed");
+ gdcmVerboseMacro( "Add DicomDirStudyToEnd failed");
}
break;
case GDCM_DICOMDIR_PATIENT:
si = new DicomDirPatient();
if( !AddDicomDirPatientToEnd(static_cast<DicomDirPatient *>(si)) )
{
- dbg.Verbose(0,"DicomDir::SetElement:",
- "Add DicomDirPatientToEnd failed");
+ gdcmVerboseMacro( "Add DicomDirPatientToEnd failed");
}
break;
case GDCM_DICOMDIR_META:
si = new DicomDirMeta();
if( MetaElems )
{
- dbg.Verbose(0,"DicomDir::SetElement:",
- "MetaElements already exist, they will be destroyed");
+ gdcmVerboseMacro( "MetaElements already exist, they will be destroyed");
delete MetaElems;
}
MetaElems = static_cast<DicomDirMeta *>(si);
{
tmpGr = it->Group;
tmpEl = it->Elem;
- dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl);
+ dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl);
entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
entry->SetOffset(0); // just to avoid further missprinting
- entry->SetLength(0); // just to avoid further missprinting
if( header )
{
// NULL when we Build Up (ex nihilo) a DICOMDIR
// or when we add the META elems
- val = header->GetEntryByNumber(tmpGr, tmpEl);
+ val = header->GetEntry(tmpGr, tmpEl);
}
else
{
{
if( header->GetFileName().substr(0, path.length()) != path )
{
- dbg.Verbose(0, "DicomDir::SetElement : the base path"
- " of file name is incorrect");
+ gdcmVerboseMacro( "The base path of file name is incorrect");
val = header->GetFileName();
}
else
}
else
{
- if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 )
+ if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
val = it->Value;
}
- // GDCM_UNFOUND or not !
-
entry->SetValue( val ); // troubles expected when vr=SQ ...
- if( dictEntry )
- {
- if( dictEntry->GetGroup() == 0xfffe )
- {
- entry->SetLength( entry->GetValue().length() ); // FIXME
- }
- else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" )
- {
- entry->SetLength(4);
- }
- else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" )
- {
- entry->SetLength(2);
- }
- else if( dictEntry->GetVR() == "SQ" )
- {
- entry->SetLength( 0xffffffff );
- }
- else
- {
- entry->SetLength( entry->GetValue().length() );
- }
- }
-
if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
{
std::cout << "GDCM_DICOMDIR_META ?!? should never print that"
//-----------------------------------------------------------------------------
/**
- * \ingroup DicomDir
* \brief CallProgressMethod
*/
void DicomDir::CallProgressMethod()
//-----------------------------------------------------------------------------
/**
- * \ingroup DicomDir
* \brief CallEndMethod
*/
void DicomDir::CallEndMethod()
//-----------------------------------------------------------------------------
// Private
/**
- * \ingroup DicomDir
* \brief create a 'DicomDir' from a DICOMDIR Header
*/
void DicomDir::CreateDicomDir()
// + loop to 1 -
// Directory record sequence
- DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
+ DocEntry *e = GetDocEntry(0x0004, 0x1220);
if ( !e )
{
- dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record"
- " sequence (0x0004,0x1220)");
+ gdcmVerboseMacro( "NO Directory record sequence (0x0004,0x1220)");
/// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ?
return;
}
- SeqEntry* s = dynamic_cast<SeqEntry*>(e);
+ SeqEntry *s = dynamic_cast<SeqEntry *>(e);
if ( !s )
{
- dbg.Verbose(0, "DicomDir::CreateDicomDir: no SeqEntry present");
+ gdcmVerboseMacro( "No SeqEntry present");
// useless : (0x0004,0x1220) IS a Sequence !
return;
}
- DicomDirType type; // = DicomDir::GDCM_DICOMDIR_META;
MetaElems = NewMeta();
ListSQItem listItems = s->GetSQItems();
- DocEntry * d;
+ DocEntry *d;
std::string v;
- SQItem * si;
+ SQItem *si;
for( ListSQItem::iterator i = listItems.begin();
i !=listItems.end(); ++i )
{
- d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type
- if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) )
+ d = (*i)->GetDocEntry(0x0004, 0x1430); // Directory Record Type
+ if ( ValEntry* valEntry = dynamic_cast<ValEntry *>(d) )
{
v = valEntry->GetValue();
}
else
{
- dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry.");
+ gdcmVerboseMacro( "Not a ValEntry.");
continue;
}
{
si = new DicomDirPatient();
AddDicomDirPatientToEnd( static_cast<DicomDirPatient *>(si) );
- type = DicomDir::GDCM_DICOMDIR_PATIENT;
}
else if( v == "STUDY " )
{
si = new DicomDirStudy();
AddDicomDirStudyToEnd( static_cast<DicomDirStudy *>(si) );
- type = DicomDir::GDCM_DICOMDIR_STUDY;
}
else if( v == "SERIES" )
{
si = new DicomDirSerie();
AddDicomDirSerieToEnd( static_cast<DicomDirSerie *>(si) );
- type = DicomDir::GDCM_DICOMDIR_SERIE;
}
else if( v == "IMAGE " )
{
si = new DicomDirImage();
AddDicomDirImageToEnd( static_cast<DicomDirImage *>(si) );
- type = DicomDir::GDCM_DICOMDIR_IMAGE;
}
else
{
}
/**
- * \ingroup DicomDir
* \brief Well ... there is only one occurence
*/
bool DicomDir::AddDicomDirMeta()
}
/**
- * \ingroup DicomDir
* \brief AddDicomDirPatientToEnd
- * @param s SQ Item to enqueue to the DicomPatient chained List
+ * @param dd SQ Item to enqueue to the DicomPatient chained List
*/
bool DicomDir::AddDicomDirPatientToEnd(DicomDirPatient *dd)
{
}
/**
- * \ingroup DicomDir
* \brief AddDicomDirStudyToEnd
- * @param s SQ Item to enqueue to the DicomDirStudy chained List
+ * @param dd SQ Item to enqueue to the DicomDirStudy chained List
*/
bool DicomDir::AddDicomDirStudyToEnd(DicomDirStudy *dd)
{
}
/**
- * \ingroup DicomDir
* \brief AddDicomDirSerieToEnd
- * @param s SQ Item to enqueue to the DicomDirSerie chained List
+ * @param dd SQ Item to enqueue to the DicomDirSerie chained List
*/
bool DicomDir::AddDicomDirSerieToEnd(DicomDirSerie *dd)
{
}
/**
- * \ingroup DicomDir
* \brief AddDicomDirImageToEnd
- * @param s SQ Item to enqueue to the DicomDirImage chained List
+ * @param dd SQ Item to enqueue to the DicomDirImage chained List
*/
bool DicomDir::AddDicomDirImageToEnd(DicomDirImage *dd)
{
}
/**
- * \ingroup DicomDir
* \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
it != list.end(); ++it )
{
// get the current file characteristics
- patCurName = (*it)->GetEntryByNumber(0x0010,0x0010);
- patCurID = (*it)->GetEntryByNumber(0x0010,0x0011);
- studCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000d);
- studCurID = (*it)->GetEntryByNumber(0x0020,0x0010);
- serCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000e);
- serCurID = (*it)->GetEntryByNumber(0x0020,0x0011);
+ patCurName = (*it)->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 )
{
}
/**
- * \ingroup DicomDir
- * \brief Move the content of the src SQItem to the dst SQItem
+ * \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(SQItem *dst,SQItem *src)
{
DocEntry *entry;
- src->Initialize();
- entry = src->GetNextEntry();
+ entry = src->GetFirstEntry();
while(entry)
{
src->RemoveEntryNoDestroy(entry);
dst->AddEntry(entry);
-
- src->Initialize();
entry = src->GetNextEntry();
}
}
/**
- * \ingroup DicomDir
* \brief compares two dgcmHeaders
*/
bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
{
return *header1 < *header2;
}
+
+
+/**
+ * \brief Get the first entry while visiting the DicomDirPatients
+ * \return The first DicomDirPatient if found, otherwhise NULL
+ */
+DicomDirPatient *DicomDir::GetFirstEntry()
+{
+ ItDicomDirPatient = Patients.begin();
+ if ( ItDicomDirPatient != Patients.end() )
+ return *ItDicomDirPatient;
+ 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::GetNextEntry()
+{
+ gdcmAssertMacro (ItDicomDirPatient != Patients.end());
+ {
+ ++ItDicomDirPatient;
+ if ( ItDicomDirPatient != Patients.end() )
+ return *ItDicomDirPatient;
+ }
+ return NULL;
+}
+
+
} // end namespace gdcm
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff