-// gdcmDicomDir.cxx
-//-----------------------------------------------------------------------------
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDicomDir.cxx,v $
+ Language: C++
+ Date: $Date: 2004/11/03 20:52:13 $
+ Version: $Revision: 1.77 $
+
+ 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.
+
+=========================================================================*/
+
#include "gdcmDicomDir.h"
-#include "gdcmStudy.h"
-#include "gdcmSerie.h"
-#include "gdcmImage.h"
+#include "gdcmDicomDirStudy.h"
+#include "gdcmDicomDirSerie.h"
+#include "gdcmDicomDirImage.h"
#include "gdcmDirList.h"
#include "gdcmUtil.h"
-
+#include "gdcmDebug.h"
+#include "gdcmGlobal.h"
+#include "gdcmHeader.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmSQItem.h"
+#include "gdcmValEntry.h"
+
+#include <fstream>
#include <string>
#include <algorithm>
-
#include <sys/types.h>
-#include <errno.h>
+
+#ifdef _MSC_VER
+ #include <direct.h>
+#else
+ #include <unistd.h>
+#endif
+namespace gdcm
+{
+
//-----------------------------------------------------------------------------
// For full DICOMDIR description, see:
// PS 3.3-2003, pages 731-750
//-----------------------------------------------------------------------------
// Constructor / Destructor
-/*
- * \ingroup gdcmDicomDir
- * \brief Constructor
- * @param Filename
- * @param exception_on_error
+
+/**
+ * \ingroup DicomDir
+ * \brief Constructor : creates an empty DicomDir
+ */
+DicomDir::DicomDir()
+ :Document( )
+{
+ Initialize(); // sets all private fields to NULL
+ std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ...
+ MetaElems = NewMeta();
+}
+
+/**
+ * \brief Constructor Parses recursively the directory and creates the DicomDir
+ * or uses an already built DICOMDIR, depending on 'parseDir' value.
+ * @param fileName name
+ * - of the root directory (parseDir = true)
+ * - of the DICOMDIR (parseDir = false)
+ * @param parseDir boolean
+ * - true if user passed an entry point
+ * and wants to explore recursively the directories
+ * - false if user passed an already built DICOMDIR file
+ * and wants to use it
*/
-gdcmDicomDir::gdcmDicomDir(const char *FileName, bool parseDir,
- bool exception_on_error):
- gdcmParser(FileName,exception_on_error,true)
+DicomDir::DicomDir(std::string const & fileName, bool parseDir ):
+ Document( fileName )
{
- metaElems=NULL;
+ // Whatever user passed (a root directory or a DICOMDIR)
+ // and whatever the value of parseDir was,
+ // Document is already executed
+ Initialize(); // sets all private fields to NULL
+
+ // if user passed a root directory, sure we didn't get anything
- if( GetListEntry().begin()==GetListEntry().end() )
+ if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse
{
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty");
+ dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty");
+
+ if ( fileName.size() == 1 && fileName[0] == '.' )
+ {
+ // 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)
+ if ( parseDir ) // user asked for a recursive parsing of a root directory
{
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir");
+ MetaElems = NewMeta();
+
+ dbg.Verbose(0, "DicomDir::DicomDir : Parse directory"
+ " and create the DicomDir");
ParseDirectory();
}
+ else
+ {
+ /// \todo if parseDir == false, it should be tagged as an error
+ // NON ! il suffit d'appeler ParseDirectory()
+ // apres le constructeur
+ }
}
- else
+ else // Only if user passed a DICOMDIR
+ {
+ // Directory record sequence
+ DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
+ if ( !e )
+ {
+ dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record"
+ " sequence (0x0004,0x1220)");
+ /// \todo FIXME : what do we do when the parsed file IS NOT a
+ /// DICOMDIR file ?
+ }
CreateDicomDir();
+ }
}
-/*
- * \ingroup gdcmDicomDir
+/**
* \brief Canonical destructor
*/
-gdcmDicomDir::~gdcmDicomDir()
+DicomDir::~DicomDir()
{
- if(metaElems)
- delete metaElems;
-
- for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ SetStartMethod(NULL);
+ SetProgressMethod(NULL);
+ SetEndMethod(NULL);
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc!= Patients.end();
+ ++cc)
{
delete *cc;
}
+ if ( MetaElems )
+ {
+ delete MetaElems;
+ }
}
//-----------------------------------------------------------------------------
// Print
-/*
- * \ingroup gdcmDicomDir
+/**
* \brief Canonical Printer
*/
-void gdcmDicomDir::Print(std::ostream &os)
+void DicomDir::Print(std::ostream &os)
{
- if(metaElems)
+ if( MetaElems )
{
- metaElems->SetPrintLevel(printLevel);
- metaElems->Print(os);
- }
-
- for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ MetaElems->SetPrintLevel(PrintLevel);
+ MetaElems->Print(os);
+ }
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc != Patients.end();
+ ++cc)
{
- (*cc)->SetPrintLevel(printLevel);
- (*cc)->Print(os);
+ (*cc)->SetPrintLevel( PrintLevel );
+ (*cc)->Print( os );
}
}
//-----------------------------------------------------------------------------
// Public
/**
- * \ingroup gdcmDicomDir
- * \brief writes on disc a DICOMDIR
- * \ warning does NOT add the missing elements in the header :
- * it's up to the user doing it !
- * @param fileName file to be written to
- * @return false only when fail to open
+ * \brief This predicate, based on hopefully reasonable heuristics,
+ * decides whether or not the current header was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable DicomDir.
+ * @return true when Document is the one of a reasonable DicomDir,
+ * false otherwise.
*/
-bool gdcmDicomDir::Write(std::string fileName)
+bool DicomDir::IsReadable()
{
- FILE * fp1;
-
- fp1=fopen(fileName.c_str(),"wb");
- if(fp1==NULL)
+ if( !Document::IsReadable() )
{
- printf("Failed to open(write) File [%s] \n",fileName.c_str());
- return(false);
+ return false;
+ }
+ if( !MetaElems )
+ {
+ return false;
+ }
+ if( Patients.size() <= 0 )
+ {
+ return false;
}
- char * filePreamble;
- filePreamble=(char*)calloc(128,1);
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
- free(filePreamble);
-
- WriteEntries(fp1,DICOMDIR);
+ return true;
+}
- fclose(fp1);
+/**
+ * \brief Sets all fields to NULL
+ */
- return true;
+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;
+
+ MetaElems = 0;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief fills whole the structure
+
+/**
+ * \ingroup DicomDir
+ * \brief fills the whole structure, starting from a root Directory
*/
-void gdcmDicomDir::ParseDirectory(void)
+void DicomDir::ParseDirectory()
{
- NewDicomDir(GetPath());
+ CreateDicomDirChainedList( GetFileName() );
CreateDicomDir();
}
-//-----------------------------------------------------------------------------
-// Protected
-/*
- * \ingroup gdcmDicomDir
- * \brief create a gdcmDicomDir from a root Directory
- * @param path entry point of the stree-like structure
+/**
+ * \ingroup DicomDir
+ * \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::NewDicomDir(std::string path)
+void DicomDir::SetStartMethod(Method* method, void* arg,
+ Method* argDelete )
{
- gdcmDirList fileList(path,1);
- ListHeader list;
- gdcmHeader *header;
+ if( StartArg && StartMethodArgDelete )
+ {
+ StartMethodArgDelete( StartArg );
+ }
- listEntries.clear();
- patients.clear();
+ StartMethod = method;
+ StartArg = arg;
+ StartMethodArgDelete = argDelete;
+}
- for(gdcmDirList::iterator it=fileList.begin();
- it!=fileList.end(); ++it)
+/**
+ * \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(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 arg Argument to pass to the method
+ * @param argDelete Argument
+ * \warning In python : the arg parameter isn't considered
+ */
+void DicomDir::SetProgressMethod(Method* method, void* arg,
+ Method* argDelete )
+{
+ if( ProgressArg && ProgressMethodArgDelete )
{
- header=new gdcmHeader(it->c_str());
- if(header->IsReadable())
- list.push_back(header);
- else
- delete header;
+ ProgressMethodArgDelete( ProgressArg );
}
- std::sort(list.begin(),list.end(),gdcmDicomDir::HeaderLessThan);
-
- std::string tmp=fileList.GetDirName();
- SetElements(tmp,list);
+ ProgressMethod = method;
+ ProgressArg = arg;
+ ProgressMethodArgDelete = argDelete;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief Get the DicomDir path
- * @param
+/**
+ * \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
*/
-std::string gdcmDicomDir::GetPath(void)
+void DicomDir::SetProgressMethodArgDelete(Method* method)
{
- std::string path=GetFileName();
+ ProgressMethodArgDelete = method;
+}
- int pos1=path.rfind("/");
- int pos2=path.rfind("\\");
- if(pos1>pos2)
- path.resize(pos1);
- else
- path.resize(pos2);
+/**
+ * \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(Method* method, void* arg,
+ Method* argDelete )
+{
+ if( EndArg && EndMethodArgDelete )
+ {
+ EndMethodArgDelete( EndArg );
+ }
- return(path);
+ EndMethod = method;
+ EndArg = arg;
+ EndMethodArgDelete = argDelete;
}
-//-----------------------------------------------------------------------------
-// Private
-/*
- * \ingroup gdcmDicomDir
- * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader
+/**
+ * \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 gdcmDicomDir::CreateDicomDir()
+void DicomDir::SetEndMethodArgDelete(Method* method)
{
- // The list is parsed. When a tag 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 -
+ 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 !
+ * \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 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::ios::out | std::ios::binary);
+ if( !fp )
+ {
+ dbg.Verbose(2, "Failed to open(write) File: ", fileName.c_str());
+ return false;
+ }
+
+ char filePreamble[128];
+ memset(filePreamble, 0, 128);
+ fp->write(filePreamble, 128); //FIXME
+ binary_write( *fp, "DICM");
+
+ DicomDirMeta *ptrMeta = GetDicomDirMeta();
+ ptrMeta->Write(fp, ExplicitVR);
+
+ // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
+ for(i=0;i<4;++i)
+ {
+ binary_write(*fp, sq[i]);
+ }
+
+ for(ListDicomDirPatient::iterator cc = Patients.begin();
+ cc != Patients.end();
+ ++cc )
+ {
+ (*cc)->Write( fp, ExplicitVR );
+ }
+
+ // force writing Sequence Delimitation Item
+ for(i=0;i<4;++i)
+ {
+ binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
+ }
- gdcmDicomDirType type=gdcmDicomDir::GDCM_META;
- ListTag::iterator begin;
- ListTag::iterator end;
+ fp->close();
+ return true;
+}
+
+//-----------------------------------------------------------------------------
+// Protected
- begin=listEntries.begin();
- end=begin;
- for(ListTag::iterator i=end;i !=listEntries.end();++i)
+/**
+ * \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
+ unsigned int count = 0;
+ VectDocument list;
+ Header *header;
+
+ TagHT.clear();
+ Patients.clear();
+
+ for( DirList::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
{
- std::string v=(*i)->GetValue();
- if(v=="PATIENT ")
+ Progress = (float)(count+1)/(float)fileList.size();
+ CallProgressMethod();
+ if( Abort )
{
- end=i;
- AddObjectToEnd(type,begin,end);
+ break;
+ }
- type=gdcmDicomDir::GDCM_PATIENT;
- begin=end;
- }
+ header = new Header( it->c_str() );
+ if( !header )
+ {
+ dbg.Verbose( 1,
+ "DicomDir::CreateDicomDirChainedList: "
+ "failure in new Header ",
+ it->c_str() );
+ }
+
+ if( header->IsReadable() )
+ {
+ // Add the file header to the chained list:
+ list.push_back(header);
+ dbg.Verbose( 1,
+ "DicomDir::CreateDicomDirChainedList: readable ",
+ it->c_str() );
+
+ }
+ else
+ {
+ delete header;
+ }
+ count++;
+ }
+ // sorts Patient/Study/Serie/
+ std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
+
+ std::string tmp = fileList.GetDirName();
+ //for each Header of the chained list, add/update the Patient/Study/Serie/Image info
+ SetElements(tmp, list);
+ CallEndMethod();
+}
- if(v=="STUDY ")
+/**
+ * \ingroup DicomDir
+ * \brief adds *the* Meta to a partially created DICOMDIR
+ */
+
+DicomDirMeta * DicomDir::NewMeta()
+{
+ DicomDirMeta *m = new DicomDirMeta( &TagHT );
+
+ if ( TagHT.begin() != TagHT.end() ) // after Document Parsing
+ {
+ 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;
+ ++cc)
{
- end=i;
- AddObjectToEnd(type,begin,end);
+ m->AddDocEntry( cc->second );
+ }
+ }
+ else // after root directory parsing
+ {
+ ListDicomDirMetaElem const & elemList =
+ Global::GetDicomDirElements()->GetDicomDirMetaElements();
+ m->FillObject(elemList);
+ }
+ m->SetSQItemNumber(0); // To avoid further missprinting
+ return m;
+}
- type=gdcmDicomDir::GDCM_STUDY;
- begin=end;
+/**
+ * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR
+ */
+DicomDirPatient * DicomDir::NewPatient()
+{
+ ListDicomDirPatientElem::const_iterator it;
+ uint16_t tmpGr,tmpEl;
+ DictEntry *dictEntry;
+ ValEntry *entry;
+
+ ListDicomDirPatientElem const & elemList =
+ Global::GetDicomDirElements()->GetDicomDirPatientElements();
+ SQItem *s = new SQItem(0);
+
+ // for all the DicomDirPatient Elements
+ for( it = elemList.begin(); it != elemList.end(); ++it )
+ {
+ tmpGr = it->Group;
+ tmpEl = it->Elem;
+ dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl);
+ entry = new 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() );
}
+ s->AddDocEntry( entry );
+ }
+
+ DicomDirPatient *p = new DicomDirPatient(s, &TagHT);
+ Patients.push_front( p );
- if(v=="SERIES")
+ 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 = new SQItem(0); // all the items will be at level 1
+ switch( type )
+ {
+ case GDCM_DICOMDIR_IMAGE:
+ elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
+ break;
+
+ case GDCM_DICOMDIR_SERIE:
+ elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
+ break;
+
+ case GDCM_DICOMDIR_STUDY:
+ elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
+ break;
+
+ case GDCM_DICOMDIR_PATIENT:
+ elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
+ break;
+
+ case GDCM_DICOMDIR_META:
+ elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
+ 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()->GetDictEntryByNumber(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);
+ }
+ else
{
- end=i;
- AddObjectToEnd(type,begin,end);
+ val = GDCM_UNFOUND;
+ }
- type=gdcmDicomDir::GDCM_SERIE;
- begin=end;
+ 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 )
+ {
+ dbg.Verbose(0, "DicomDir::SetElement : the base path"
+ " of file name is incorrect");
+ val = header->GetFileName();
+ }
+ else
+ {
+ val = &(header->GetFileName().c_str()[path.length()]);
+ }
+ }
+ else
+ {
+ val = it->Value;
+ }
+ }
+ else
+ {
+ if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 )
+ val = it->Value;
}
- if(v=="IMAGE ")
+ // GDCM_UNFOUND or not !
+
+ entry->SetValue( val ); // troubles expected when vr=SQ ...
+
+ if( dictEntry )
{
- end=i;
- AddObjectToEnd(type,begin,end);
+ 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() );
+ }
+ }
- type=gdcmDicomDir::GDCM_IMAGE;
- begin=end;
+ if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
+ {
+ std::cout << "GDCM_DICOMDIR_META ?!? should never print that"
+ << std::endl;
}
+ si->AddEntry(entry);
+ }
+ switch( type )
+ {
+ case GDCM_DICOMDIR_IMAGE:
+ AddDicomDirImageToEnd(si);
+ break;
+
+ case GDCM_DICOMDIR_SERIE:
+ AddDicomDirSerieToEnd(si);
+ break;
+
+ case GDCM_DICOMDIR_STUDY:
+ AddDicomDirStudyToEnd(si);
+ break;
+
+ case GDCM_DICOMDIR_PATIENT:
+ AddDicomDirPatientToEnd(si);
+ break;
+
+ default:
+ return;
+ }
+ //int count=1; // find a trick to increment
+ //s->AddEntry(si, count); // Seg Faults
+
+}
+
+//-----------------------------------------------------------------------------
+/**
+ * \brief CallStartMethod
+ */
+void DicomDir::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ if( StartMethod )
+ {
+ StartMethod( StartArg );
}
+}
- if(begin!=end)
+//-----------------------------------------------------------------------------
+/**
+ * \ingroup DicomDir
+ * \brief CallProgressMethod
+ */
+void DicomDir::CallProgressMethod()
+{
+ if( ProgressMethod )
{
- end=GetListEntry().end();
- AddObjectToEnd(type,begin,end);
+ ProgressMethod( ProgressArg );
}
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param type
- * @param begin
- * @param end
+
+//-----------------------------------------------------------------------------
+/**
+ * \ingroup DicomDir
+ * \brief CallEndMethod
*/
-void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end)
+void DicomDir::CallEndMethod()
{
- if(begin==end)
+ Progress = 1.0f;
+ if( EndMethod )
+ {
+ EndMethod( EndArg );
+ }
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \ingroup DicomDir
+ * \brief create a 'DicomDir' from a DICOMDIR Header
+ */
+void DicomDir::CreateDicomDir()
+{
+ // 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 -
+
+ // Directory record sequence
+ DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
+ if ( !e )
+ {
+ dbg.Verbose(0, "DicomDir::DicomDir : 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);
+ if ( !s )
+ {
+ dbg.Verbose(0, "DicomDir::CreateDicomDir: no SeqEntry present");
+ // useless : (0x0004,0x1220) IS a Sequence !
return;
+ }
+
+ DicomDirType type = DicomDir::GDCM_DICOMDIR_META;
+ MetaElems = NewMeta();
- switch(type)
+ ListSQItem listItems = s->GetSQItems();
+
+ DocEntry * d;
+ std::string v;
+ for( ListSQItem::iterator i = listItems.begin();
+ i !=listItems.end(); ++i )
{
- case gdcmDicomDir::GDCM_META:
- AddMetaToEnd(begin,end);
- break;
- case gdcmDicomDir::GDCM_PATIENT:
- AddPatientToEnd(begin,end);
- break;
- case gdcmDicomDir::GDCM_STUDY:
- AddStudyToEnd(begin,end);
- break;
- case gdcmDicomDir::GDCM_SERIE:
- AddSerieToEnd(begin,end);
- break;
- case gdcmDicomDir::GDCM_IMAGE:
- AddImageToEnd(begin,end);
- break;
+ d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type
+ if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) )
+ {
+ v = valEntry->GetValue();
+ }
+ else
+ {
+ dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry.");
+ continue;
+ }
+
+ if( v == "PATIENT " )
+ {
+ AddDicomDirPatientToEnd( *i );
+ type = DicomDir::GDCM_DICOMDIR_PATIENT;
+ }
+ else if( v == "STUDY " )
+ {
+ AddDicomDirStudyToEnd( *i );
+ type = DicomDir::GDCM_DICOMDIR_STUDY;
+ }
+ else if( v == "SERIES" )
+ {
+ AddDicomDirSerieToEnd( *i );
+ type = DicomDir::GDCM_DICOMDIR_SERIE;
+ }
+ else if( v == "IMAGE " )
+ {
+ AddDicomDirImageToEnd( *i );
+ type = DicomDir::GDCM_DICOMDIR_IMAGE;
+ }
+ else
+ {
+ // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
+ // neither an 'IMAGE' SQItem. Skip to next item.
+ continue;
+ }
}
}
-/*
- * \ingroup gdcmDicomDir
- * \brief Well ... Not realy to end, there is only one occurence
- * @param begin
- * @param end
-*/
-void gdcmDicomDir::AddMetaToEnd(ListTag::iterator begin,ListTag::iterator end)
+/**
+ * \ingroup DicomDir
+ * \brief Well ... there is only one occurence
+ */
+void DicomDir::AddDicomDirMeta()
{
- if(metaElems)
- delete metaElems;
- metaElems = new gdcmMeta(begin,end);
+ if( MetaElems )
+ {
+ delete MetaElems;
+ }
+ MetaElems = new DicomDirMeta( &TagHT );
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
-*/
-void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end)
+/**
+ * \ingroup DicomDir
+ * \brief AddDicomDirPatientToEnd
+ * @param s SQ Item to enqueue to the DicomPatient chained List
+ */
+void DicomDir::AddDicomDirPatientToEnd(SQItem *s)
{
- patients.push_back(new gdcmPatient(begin,end));
+ Patients.push_back(new DicomDirPatient(s, &TagHT));
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
+/**
+ * \ingroup DicomDir
+ * \brief AddDicomDirStudyToEnd
+ * @param s SQ Item to enqueue to the DicomDirStudy chained List
*/
- void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end)
+ void DicomDir::AddDicomDirStudyToEnd(SQItem *s)
{
- if(patients.size()>0)
+ if( Patients.size() > 0 )
{
- ListPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- (*itp)->AddStudy(new gdcmStudy(begin,end));
+ (*itp)->AddDicomDirStudy(new DicomDirStudy(s, &TagHT));
}
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
+
+/**
+ * \ingroup DicomDir
+ * \brief AddDicomDirSerieToEnd
+ * @param s SQ Item to enqueue to the DicomDirSerie chained List
*/
-void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end)
+void DicomDir::AddDicomDirSerieToEnd(SQItem *s)
{
- if(patients.size()>0)
+ if( Patients.size() > 0 )
{
- ListPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- if((*itp)->GetStudies().size()>0)
+ if( (*itp)->GetDicomDirStudies().size() > 0 )
{
- ListStudy::iterator itst=(*itp)->GetStudies().end();
+ ListDicomDirStudy::const_iterator itst =
+ (*itp)->GetDicomDirStudies().end();
itst--;
- (*itst)->AddSerie(new gdcmSerie(begin,end));
+ (*itst)->AddDicomDirSerie(new DicomDirSerie(s, &TagHT));
}
}
}
-/*
- * \ingroup gdcmDicomDir
- * @param begin
- * @param end
- * @param
+/**
+ * \ingroup DicomDir
+ * \brief AddDicomDirImageToEnd
+ * @param s SQ Item to enqueue to the DicomDirImage chained List
*/
- void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end)
+ void DicomDir::AddDicomDirImageToEnd(SQItem *s)
{
- if(patients.size()>0)
+ if( Patients.size() > 0 )
{
- ListPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- if((*itp)->GetStudies().size()>0)
+ if( (*itp)->GetDicomDirStudies().size() > 0 )
{
- ListStudy::iterator itst=(*itp)->GetStudies().end();
+ ListDicomDirStudy::const_iterator itst =
+ (*itp)->GetDicomDirStudies().end();
itst--;
- if((*itst)->GetSeries().size()>0)
+ if( (*itst)->GetDicomDirSeries().size() > 0 )
{
- ListSerie::iterator its=(*itst)->GetSeries().end();
+ ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end();
its--;
- (*its)->AddImage(new gdcmImage(begin,end));
+ (*its)->AddDicomDirImage(new DicomDirImage(s, &TagHT));
}
}
}
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param path
- * @param list
+/**
+ * \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
*/
-void gdcmDicomDir::SetElements(std::string &path,ListHeader &list)
+void DicomDir::SetElements(std::string const & path, VectDocument const &list)
{
- std::string patPrevName="", patPrevID="";
- std::string studPrevInstanceUID="", studPrevID="";
- std::string serPrevInstanceUID="", serPrevID="";
+ std::string patPrevName = "", patPrevID = "";
+ std::string studPrevInstanceUID = "", studPrevID = "";
+ std::string serPrevInstanceUID = "", serPrevID = "";
- std::string patCurName, patCurID;
+ std::string patCurName, patCurID;
std::string studCurInstanceUID, studCurID;
- std::string serCurInstanceUID, serCurID;
+ std::string serCurInstanceUID, serCurID;
- SetElement(path,GDCM_NONE,NULL);
-
- ListTag::iterator debPat=listEntries.begin();
- for(ListHeader::iterator it=list.begin();it!=list.end();++it)
+ 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_PATIENT,*it);
+ 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_STUDY,*it);
+ if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID )
+ {
+ SetElement(path, GDCM_DICOMDIR_STUDY, *it);
+ }
// if new Serie Deal with 'SERIE' Elements
- if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID)
- SetElement(path,GDCM_SERIE,*it);
+ if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID )
+ {
+ SetElement(path, GDCM_DICOMDIR_SERIE, *it);
+ }
// Always Deal with 'IMAGE' Elements
- SetElement(path,GDCM_IMAGE,*it);
-
- patPrevName=patCurName;
- patPrevID=patCurID;
- studPrevInstanceUID=studCurInstanceUID;
- studPrevID=studCurID;
- serPrevInstanceUID=serCurInstanceUID;
- serPrevID=serCurID;
+ SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
+
+ patPrevName = patCurName;
+ patPrevID = patCurID;
+ studPrevInstanceUID = studCurInstanceUID;
+ studPrevID = studCurID;
+ serPrevInstanceUID = serCurInstanceUID;
+ serPrevID = serCurID;
}
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param path
- * @param type
- * @param header
+/**
+ * \ingroup DicomDir
+ * \brief compares two dgcmHeaders
*/
-void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header)
-{
- std::list<gdcmElement> elemList;
- std::list<gdcmElement>::iterator it;
- guint16 tmpGr, tmpEl;
- gdcmDictEntry *dictEntry;
- gdcmHeaderEntry *entry;
- std::string val;
-
- switch(type)
- {
- case GDCM_PATIENT:
- elemList=gdcmGlobal::GetDicomDirElements()->GetPatientElements();
- break;
- case GDCM_STUDY:
- elemList=gdcmGlobal::GetDicomDirElements()->GetStudyElements();
- break;
- case GDCM_SERIE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetSerieElements();
- break;
- case GDCM_IMAGE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetImageElements();
- break;
- case GDCM_NONE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetMetaElements();
- break;
- default:
- return;
- }
-
- for(it=elemList.begin();it!=elemList.end();++it)
- {
- tmpGr=it->group;
- tmpEl=it->elem;
-
- dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl);
- entry=new gdcmHeaderEntry(dictEntry);
- entry->SetOffset(0); // just to avoid missprinting
-
- if(header)
- val=header->GetEntryByNumber(tmpGr,tmpEl);
- else
- val=GDCM_UNFOUND;
-
- if(val==GDCM_UNFOUND)
- {
- if((tmpGr==0x0004) &&(tmpEl==0x1130) )
- {
- // TODO force the *end* File Name(remove path)
- val=path;
- }
- else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image
- {
- if(header->GetFileName().substr(0,path.length())!=path)
- {
- dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path of file name is incorrect");
- val=header->GetFileName();
- }
- else
- val=&(header->GetFileName()[path.length()]);
- }
- else
- {
- val=it->value;
- }
- }
- entry->SetValue(val);
-
- if(dictEntry)
- {
- if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") )
- {
- entry->SetLength(4);
- }
- else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") )
- {
- entry->SetLength(2);
- }
- else if(dictEntry->GetVR()=="SQ")
- {
- entry->SetLength(0xffffffff);
- }
- else
- {
- entry->SetLength(entry->GetValue().length());
- }
- }
-
- listEntries.push_back(entry);
- }
-}
-
-bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2)
+bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
{
- return(*header1<*header2);
+ return *header1 < *header2;
}
+} // end namespace gdcm
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff