-// gdcmDicomDir.cxx
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDicomDir.cxx,v $
+ Language: C++
+ Date: $Date: 2005/08/29 09:41:22 $
+ Version: $Revision: 1.154 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+//-----------------------------------------------------------------------------
+// For full DICOMDIR description, see:
+// PS 3.3-2003, pages 731-750
//-----------------------------------------------------------------------------
#include "gdcmDicomDir.h"
-#include "gdcmStudy.h"
-#include "gdcmSerie.h"
-#include "gdcmImage.h"
+#include "gdcmDicomDirObject.h"
+#include "gdcmDicomDirStudy.h"
+#include "gdcmDicomDirSerie.h"
+#include "gdcmDicomDirVisit.h"
+#include "gdcmDicomDirImage.h"
+#include "gdcmDicomDirPatient.h"
+#include "gdcmDicomDirMeta.h"
+#include "gdcmDicomDirElement.h"
#include "gdcmDirList.h"
#include "gdcmUtil.h"
-
+#include "gdcmDebug.h"
+#include "gdcmGlobal.h"
+#include "gdcmFile.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmSQItem.h"
+#include "gdcmValEntry.h"
+
+#include <fstream>
#include <string>
#include <algorithm>
-
#include <sys/types.h>
-#include <errno.h>
-//-----------------------------------------------------------------------------
-// For full DICOMDIR description, see:
-// PS 3.3-2003, pages 731-750
+#ifdef _MSC_VER
+# define getcwd _getcwd
+#endif
+
+#if defined(_MSC_VER) || defined(__BORLANDC__)
+# include <direct.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
+// STUDY VISIT
+// SERIES IMAGE
+// IMAGE /
+//
+// DicomDir::CreateDicomDir will have to be completed
+// Treelike structure management will have to be upgraded
+// ----------------------------------------------------------------------------
+
+namespace gdcm
+{
//-----------------------------------------------------------------------------
// Constructor / Destructor
-/*
- * \ingroup gdcmDicomDir
- * \brief Constructor
- * @param Filename
- * @param exception_on_error
+/**
+ * \brief Constructor : creates an empty DicomDir
*/
-gdcmDicomDir::gdcmDicomDir(const char *FileName, bool parseDir,
- bool exception_on_error):
- gdcmParser(FileName,exception_on_error,true)
+DicomDir::DicomDir()
+ :Document( )
{
- startMethod=NULL;
- progressMethod=NULL;
- endMethod=NULL;
- startArg=NULL;
- progressArg=NULL;
- endArg=NULL;
+ Initialize(); // sets all private fields to NULL
+ ParseDir = false;
+ NewMeta();
+}
- progress=NULL;
- abort=false;
+#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 cheked in Document constructor, to avoid overhead)
+
+ ParseDir = parseDir;
+ SetLoadMode (0x00000000); // concerns only dicom files
+ SetFileName( fileName );
+ Load( );
+}
+#endif
- metaElems=NULL;
+/**
+ * \brief Canonical destructor
+ */
+DicomDir::~DicomDir()
+{
+ SetStartMethod(NULL);
+ SetProgressMethod(NULL);
+ SetEndMethod(NULL);
- if( GetListEntry().begin()==GetListEntry().end() )
+ ClearPatient();
+ if ( MetaElems )
{
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty");
+ delete MetaElems;
+ }
+}
- if(parseDir)
- {
- dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir");
- ParseDirectory();
- }
+//-----------------------------------------------------------------------------
+// Public
+
+/**
+ * \brief Loader. use SetFileName(fn)
+ * or SetLoadMode(lm) + SetDirectoryName(dn) before !
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool DicomDir::Load( )
+{
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
+
+ if (!ParseDir)
+ {
+ if ( ! this->Document::Load( ) )
+ return false;
}
- else
- CreateDicomDir();
+ return DoTheLoadingJob( );
}
-/*
- * \ingroup gdcmDicomDir
- * \brief Canonical destructor
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Loader. (DEPRECATED : kept not to break the API)
+ * @param fileName file to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ * @deprecated use SetFileName(n) + Load() instead
*/
-gdcmDicomDir::~gdcmDicomDir()
+bool DicomDir::Load(std::string const &fileName )
{
- if(metaElems)
- delete metaElems;
-
- for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
+
+ SetFileName( fileName );
+ if (!ParseDir)
{
- delete *cc;
+ if ( ! this->Document::Load( ) )
+ return false;
}
+ return DoTheLoadingJob( );
}
-//-----------------------------------------------------------------------------
-// Print
-/*
- * \ingroup gdcmDicomDir
- * \brief Canonical Printer
+/// DEPRECATED : use SetDirectoryName(dname) instead
+void DicomDir::SetParseDir(bool parseDir)
+{
+ ParseDir = parseDir;
+}
+#endif
+
+/**
+ * \brief Does the Loading Job (internal use only)
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
*/
-void gdcmDicomDir::Print(std::ostream &os)
+bool DicomDir::DoTheLoadingJob( )
{
- if(metaElems)
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
+
+ if (!ParseDir)
{
- metaElems->SetPrintLevel(printLevel);
- metaElems->Print(os);
+ // 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();
}
-
- for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc)
+ else
{
- (*cc)->SetPrintLevel(printLevel);
- (*cc)->Print(os);
+ // Only if user passed a root directory
+ // ------------------------------------
+ if ( GetFileName() == "." )
+ {
+ // user passed '.' as Name
+ // we get current directory name
+ char 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
-/*
- * \ingroup gdcmDicomDir
+/**
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmParser was properly parsed
+ * decides whether or not the current document was properly parsed
* and contains the mandatory information for being considered as
* a well formed and usable DicomDir.
- * @return true when gdcmParser is the one of a reasonable DicomDir,
+ * @return true when Document is the one of a reasonable DicomDir,
* false otherwise.
*/
-bool gdcmDicomDir::IsReadable(void)
+bool DicomDir::IsReadable()
{
- if(!gdcmParser::IsReadable())
- return(false);
- if(!metaElems)
- return(false);
- if(patients.size()<=0)
- return(false);
+ if ( Filetype == Unknown )
+ {
+ gdcmWarningMacro( "Wrong filetype");
+ return false;
+ }
+ if ( !MetaElems )
+ {
+ gdcmWarningMacro( "Meta Elements missing in DicomDir");
+ return false;
+ }
+ if ( Patients.size() <= 0 )
+ {
+ gdcmWarningMacro( "NO Patient in DicomDir");
+ return false;
+ }
- return(true);
+ return true;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief fills whole the structure
+/**
+ * \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 gdcmDicomDir::ParseDirectory(void)
+void DicomDir::ParseDirectory()
{
- NewDicomDir(GetPath());
+ CreateDicomDirChainedList( GetFileName() );
CreateDicomDir();
}
/**
- * \ingroup gdcmDicomDir
- * \brief writes on disc a 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 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 :
* it's up to the user doing it !
* @param fileName file to be written to
* @return false only when fail to open
*/
-bool gdcmDicomDir::Write(std::string fileName)
-{
- FILE * fp1;
+
+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 )
+ {
+ gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
+ return false;
+ }
- fp1=fopen(fileName.c_str(),"wb");
- if(fp1==NULL)
+ char filePreamble[128];
+ memset(filePreamble, 0, 128);
+ fp->write(filePreamble, 128);
+ binary_write( *fp, "DICM");
+
+ DicomDirMeta *ptrMeta = GetMeta();
+ ptrMeta->WriteContent(fp, ExplicitVR);
+
+ // 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)->WriteContent( fp, ExplicitVR );
+ }
+
+ // force writing Sequence Delimitation Item
+ for(i=0;i<4;++i)
{
- printf("Failed to open(write) File [%s] \n",fileName.c_str());
- return(false);
+ binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
}
- char * filePreamble;
- filePreamble=(char*)calloc(128,1);
- fwrite(filePreamble,128,1,fp1);
- fwrite("DICM",4,1,fp1);
- free(filePreamble);
+ fp->close();
+ delete fp;
- WriteEntries(fp1,DICOMDIR);
+ return true;
+}
- fclose(fp1);
+/**
+ * \brief Anonymize a DICOMDIR
+ * @return true
+ */
+
+bool DicomDir::AnonymizeDicomDir()
+{
+ 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)
+ {
+ s << i;
+ v = (*cc)->GetValEntry(0x0010, 0x0010) ; // Patient's Name
+ if (v)
+ {
+ v->SetValue(s.str());
+ }
+ v = (*cc)->GetValEntry(0x0010, 0x0020) ; // Patient ID
+ if (v)
+ {
+ v->SetValue(" ");
+ }
+
+ v = (*cc)->GetValEntry(0x0010, 0x0030) ; // Patient's BirthDate
+ if (v)
+ {
+ v->SetValue(" ");
+ }
+ s << "";
+ i++;
+ }
return true;
}
//-----------------------------------------------------------------------------
// Protected
-/*
- * \ingroup gdcmDicomDir
- * \brief create a gdcmDicomDir from a root Directory
- * @param path entry point of the stree-like structure
+/**
+ * \brief create a Document-like chained list from a root Directory
+ * @param path entry point of the tree-like structure
*/
-void gdcmDicomDir::NewDicomDir(std::string path)
+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;
- gdcmDirList fileList(path,1);
- unsigned int count=0;
- ListHeader list;
- gdcmHeader *header;
+ DirListType fileList = dirList.GetFilenames();
- listEntries.clear();
- patients.clear();
-
- for(gdcmDirList::iterator it=fileList.begin();
- it!=fileList.end(); ++it)
+ for( DirListType::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
{
- progress=(float)(count+1)/(float)fileList.size();
+ Progress = (float)(count+1)/(float)fileList.size();
CallProgressMethod();
- if(abort)
+ if ( Abort )
+ {
break;
+ }
- header=new gdcmHeader(it->c_str());
- if(header->IsReadable())
- list.push_back(header);
- else
- delete header;
-
- count++;
+ f = new File( );
+ f->SetLoadMode(LoadMode); // we allow user not to load Sequences, or Shadow
+ // groups, or ......
+ f->SetFileName( it->c_str() );
+ /*int res = */f->Load( );
+
+// if ( !f )
+// {
+// gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() );
+// continue;
+// }
+
+ if ( f->IsReadable() )
+ {
+ // Add the file to the chained list:
+ list.push_back(f);
+ gdcmWarningMacro( "Readable " << it->c_str() );
+ }
+ else
+ {
+ delete f;
+ }
+ count++;
}
-
- std::sort(list.begin(),list.end(),gdcmDicomDir::HeaderLessThan);
-
- std::string tmp=fileList.GetDirName();
- SetElements(tmp,list);
-
+ // 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);
+ }
}
-/*
- * \ingroup gdcmDicomDir
- * \brief Get the DicomDir path
- * @param
+/**
+ * \brief CallStartMethod
*/
-std::string gdcmDicomDir::GetPath(void)
+void DicomDir::CallStartMethod()
{
- std::string path=GetFileName();
-
- int pos1=path.rfind("/");
- int pos2=path.rfind("\\");
- if(pos1>pos2)
- path.resize(pos1);
- else
- path.resize(pos2);
-
- return(path);
+ Progress = 0.0f;
+ Abort = false;
+ if ( StartMethod )
+ {
+ StartMethod( StartArg );
+ }
}
-void gdcmDicomDir::CallStartMethod(void)
+/**
+ * \brief CallProgressMethod
+ */
+void DicomDir::CallProgressMethod()
{
- progress=0.0f;
- abort=false;
- if(startMethod)
- startMethod(startArg);
+ if ( ProgressMethod )
+ {
+ ProgressMethod( ProgressArg );
+ }
}
-void gdcmDicomDir::CallProgressMethod(void)
+/**
+ * \brief CallEndMethod
+ */
+void DicomDir::CallEndMethod()
{
- if(progressMethod)
- progressMethod(progressArg);
+ Progress = 1.0f;
+ if ( EndMethod )
+ {
+ EndMethod( EndArg );
+ }
}
-void gdcmDicomDir::CallEndMethod(void)
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \brief Sets all fields to NULL
+ */
+void DicomDir::Initialize()
{
- progress=1.0f;
- if(endMethod)
- endMethod(endArg);
+ StartMethod = NULL;
+ ProgressMethod = NULL;
+ EndMethod = NULL;
+ StartMethodArgDelete = NULL;
+ ProgressMethodArgDelete = NULL;
+ EndMethodArgDelete = NULL;
+ StartArg = NULL;
+ ProgressArg = NULL;
+ EndArg = NULL;
+
+ Progress = 0.0;
+ Abort = false;
+
+ MetaElems = NULL;
}
-//-----------------------------------------------------------------------------
-// Private
-/*
- * \ingroup gdcmDicomDir
- * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader
+/**
+ * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header
*/
-void gdcmDicomDir::CreateDicomDir()
+void DicomDir::CreateDicomDir()
{
- // The list is parsed. When a tag is found :
+ // 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
// 3 - we find an other tag
// + we create the object for the precedent tag
// + loop to 1 -
- gdcmDicomDirType type=gdcmDicomDir::GDCM_META;
- ListTag::iterator begin;
- ListTag::iterator end;
+ // Directory record sequence
+ DocEntry *e = GetDocEntry(0x0004, 0x1220);
+ if ( !e )
+ {
+ gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found");
+ return;
+ }
+
+ SeqEntry *s = dynamic_cast<SeqEntry *>(e);
+ if ( !s )
+ {
+ gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?");
+ return;
+ }
- begin=listEntries.begin();
- end=begin;
- for(ListTag::iterator i=end;i !=listEntries.end();++i)
+ NewMeta();
+
+ DocEntry *d;
+ std::string v;
+ SQItem *si;
+
+ SQItem *tmpSI=s->GetFirstSQItem();
+ while(tmpSI)
{
- std::string v=(*i)->GetValue();
- if(v=="PATIENT ")
+ d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type
+ if ( ValEntry* valEntry = dynamic_cast<ValEntry *>(d) )
{
- end=i;
- AddObjectToEnd(type,begin,end);
+ v = valEntry->GetValue();
+ }
+ else
+ {
+ gdcmWarningMacro( "(0004,1430) not a ValEntry ?!?");
+ continue;
+ }
- type=gdcmDicomDir::GDCM_PATIENT;
- begin=end;
- }
+ // 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=="STUDY ")
+ if ( v == "IMAGE " )
{
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_STUDY;
- begin=end;
+ si = new DicomDirImage(true);
+ if ( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
+ {
+ delete si;
+ si = NULL;
+ gdcmErrorMacro( "Add AddImageToEnd failed");
+ }
}
-
- if(v=="SERIES")
+ else if ( v == "SERIES" )
{
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_SERIE;
- begin=end;
+ si = new DicomDirSerie(true);
+ if ( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
+ {
+ delete si;
+ si = NULL;
+ gdcmErrorMacro( "Add AddSerieToEnd failed");
+ }
}
-
- if(v=="IMAGE ")
+ else if ( v == "VISIT " )
{
- end=i;
- AddObjectToEnd(type,begin,end);
-
- type=gdcmDicomDir::GDCM_IMAGE;
- begin=end;
+ si = new DicomDirVisit(true);
+ if ( !AddVisitToEnd( static_cast<DicomDirVisit *>(si)) )
+ {
+ delete si;
+ si = NULL;
+ gdcmErrorMacro( "Add AddVisitToEnd failed");
+ }
}
- }
-
- end=GetListEntry().end();
- if(begin!=end)
- AddObjectToEnd(type,begin,end);
-}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param type
- * @param begin
- * @param end
- */
-void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end)
-{
- if(begin==end)
- return;
+ else if ( v == "STUDY " )
+ {
+ si = new DicomDirStudy(true);
+ if ( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
+ {
+ delete si;
+ si = NULL;
+ gdcmErrorMacro( "Add AddStudyToEnd failed");
+ }
+ }
+ else if ( v == "PATIENT " )
+ {
+ si = new DicomDirPatient(true);
+ if ( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
+ {
+ delete si;
+ si = NULL;
+ gdcmErrorMacro( "Add PatientToEnd failed");
+ }
+ }
+ else
+ {
+ // It was neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
+ // nor an 'IMAGE' SQItem. Skip to next item.
+ gdcmWarningMacro( " -------------------------------------------"
+ << "a non PATIENT/STUDY/SERIE/IMAGE SQItem was found : "
+ << v);
+
+ // FIXME : deal with other item types !
+ tmpSI=s->GetNextSQItem(); // To avoid infinite loop
+ continue;
+ }
+ if ( si )
+ //MoveSQItem(si,tmpSI); // Old code : Copies each Entry
+ // -and then removes the source-
+ si->MoveObject(tmpSI); // New code : Copies the List
- switch(type)
- {
- 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;
+ tmpSI=s->GetNextSQItem();
}
+ ClearEntry();
}
-/*
- * \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)
+/**
+ * \brief AddPatientToEnd
+ * @param dd SQ Item to enqueue to the DicomPatient chained List
+ */
+bool DicomDir::AddPatientToEnd(DicomDirPatient *dd)
{
- if(metaElems)
- delete metaElems;
- metaElems = new gdcmMeta(begin,end);
+ Patients.push_back(dd);
+ return true;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
-*/
-void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end)
+/**
+ * \brief AddStudyToEnd
+ * @param dd SQ Item to enqueue to the DicomDirStudy chained List
+ */
+bool DicomDir::AddStudyToEnd(DicomDirStudy *dd)
{
- patients.push_back(new gdcmPatient(begin,end));
+ if ( Patients.size() > 0 )
+ {
+ ListDicomDirPatient::iterator itp = Patients.end();
+ itp--;
+ (*itp)->AddStudy(dd);
+ return true;
+ }
+ return false;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
+/**
+ * \brief AddSerieToEnd
+ * @param dd SQ Item to enqueue to the DicomDirSerie chained List
*/
- void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end)
+bool DicomDir::AddSerieToEnd(DicomDirSerie *dd)
{
- 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));
+
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
+ {
+ study->AddSerie(dd);
+ return true;
+ }
}
+ return false;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param begin
- * @param end
+
+/**
+ * \brief AddVisitToEnd
+ * @param dd SQ Item to enqueue to the DicomDirVisit chained List
*/
-void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end)
+bool DicomDir::AddVisitToEnd(DicomDirVisit *dd)
{
- if(patients.size()>0)
+ if ( Patients.size() > 0 )
{
- ListPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- if((*itp)->GetStudies().size()>0)
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
{
- ListStudy::iterator itst=(*itp)->GetStudies().end();
- itst--;
- (*itst)->AddSerie(new gdcmSerie(begin,end));
+ study->AddVisit(dd);
+ return true;
}
}
+ return false;
}
-
-/*
- * \ingroup gdcmDicomDir
- * @param begin
- * @param end
- * @param
+/**
+ * \brief AddImageToEnd
+ * @param dd SQ Item to enqueue to the DicomDirImage chained List
*/
- void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end)
+bool DicomDir::AddImageToEnd(DicomDirImage *dd)
{
- if(patients.size()>0)
+ if ( Patients.size() > 0 )
{
- ListPatient::iterator itp=patients.end();
+ ListDicomDirPatient::iterator itp = Patients.end();
itp--;
- if((*itp)->GetStudies().size()>0)
+ DicomDirStudy *study = (*itp)->GetLastStudy();
+ if ( study )
{
- ListStudy::iterator itst=(*itp)->GetStudies().end();
- itst--;
-
- if((*itst)->GetSeries().size()>0)
+ DicomDirSerie *serie = study->GetLastSerie();
+ if ( serie )
{
- ListSerie::iterator its=(*itst)->GetSeries().end();
- its--;
- (*its)->AddImage(new gdcmImage(begin,end));
+ serie->AddImage(dd);
+ return true;
}
}
}
+ return false;
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param path
- * @param list
+/**
+ * \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="";
+ ClearEntry();
+ ClearPatient();
- std::string patCurName, patCurID;
- std::string studCurInstanceUID, studCurID;
- std::string serCurInstanceUID, serCurID;
+ std::string patPrevName = "", patPrevID = "";
+ std::string studPrevInstanceUID = "", studPrevID = "";
+ std::string serPrevInstanceUID = "", serPrevID = "";
- SetElement(path,GDCM_NONE,NULL);
+ std::string patCurName, patCurID;
+ std::string studCurInstanceUID, studCurID;
+ std::string serCurInstanceUID, serCurID;
- ListTag::iterator debPat=listEntries.begin();
- for(ListHeader::iterator it=list.begin();it!=list.end();++it)
+ bool first = true;
+ for( VectDocument::const_iterator it = list.begin();
+ it != list.end();
+ ++it )
{
// get the current file characteristics
- patCurName=(*it)->GetEntryByNumber(0x0010,0x0010);
- patCurID=(*it)->GetEntryByNumber(0x0010,0x0011);
- studCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000d);
- studCurID=(*it)->GetEntryByNumber(0x0020,0x0010);
- serCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000e);
- serCurID=(*it)->GetEntryByNumber(0x0020,0x0011);
-
- if(patCurName!=patPrevName || patCurID!=patPrevID)
- SetElement(path,GDCM_PATIENT,*it);
-
- // if new Study Deal with 'STUDY' Elements
- if(studCurInstanceUID!=studPrevInstanceUID || studCurID!=studPrevID)
- SetElement(path,GDCM_STUDY,*it);
-
- // if new Serie Deal with 'SERIE' Elements
- if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID)
- SetElement(path,GDCM_SERIE,*it);
+ 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
+ || first )
+ {
+ SetElement(path, GDCM_DICOMDIR_STUDY, *it);
+ first = true;
+ }
+
+ // if new Serie, deal with 'SERIE' Elements
+ if ( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID
+ || first )
+ {
+ SetElement(path, GDCM_DICOMDIR_SERIE, *it);
+ }
// Always Deal with 'IMAGE' Elements
- SetElement(path,GDCM_IMAGE,*it);
-
- patPrevName=patCurName;
- patPrevID=patCurID;
- studPrevInstanceUID=studCurInstanceUID;
- studPrevID=studCurID;
- serPrevInstanceUID=serCurInstanceUID;
- serPrevID=serCurID;
+ SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
+
+ patPrevName = patCurName;
+ patPrevID = patCurID;
+ studPrevInstanceUID = studCurInstanceUID;
+ studPrevID = studCurID;
+ serPrevInstanceUID = serCurInstanceUID;
+ serPrevID = serCurID;
+ first = false;
}
}
-/*
- * \ingroup gdcmDicomDir
- * \brief
- * @param path
- * @param type
- * @param header
+/**
+ * \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 gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header)
+void DicomDir::SetElement(std::string const &path, DicomDirType type,
+ Document *header)
{
- std::list<gdcmElement> elemList;
- std::list<gdcmElement>::iterator it;
- guint16 tmpGr, tmpEl;
- gdcmDictEntry *dictEntry;
- gdcmHeaderEntry *entry;
+ ListDicomDirElem elemList;
+ ListDicomDirElem::const_iterator it;
+ uint16_t tmpGr, tmpEl;
+ DictEntry *dictEntry;
+ ValEntry *entry;
std::string val;
+ SQItem *si;
- switch(type)
+ switch( type )
{
- case GDCM_PATIENT:
- elemList=gdcmGlobal::GetDicomDirElements()->GetPatientElements();
+ 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_STUDY:
- elemList=gdcmGlobal::GetDicomDirElements()->GetStudyElements();
+ 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_SERIE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetSerieElements();
+ 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_IMAGE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetImageElements();
+ 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_NONE:
- elemList=gdcmGlobal::GetDicomDirElements()->GetMetaElements();
+ 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;
}
-
- for(it=elemList.begin();it!=elemList.end();++it)
+ // 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;
+ tmpGr = it->Group;
+ tmpEl = it->Elem;
+ dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl);
+
+ entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
- dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl);
- entry=new gdcmHeaderEntry(dictEntry);
- entry->SetOffset(0); // just to avoid missprinting
+ entry->SetOffset(0); // just to avoid further missprinting
- if(header)
- val=header->GetEntryByNumber(tmpGr,tmpEl);
+ 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;
+ {
+ val = GDCM_UNFOUND;
+ }
- if(val==GDCM_UNFOUND)
+ if ( val == GDCM_UNFOUND)
{
- if((tmpGr==0x0004) &&(tmpEl==0x1130) )
+ if ( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID
{
- // TODO force the *end* File Name(remove path)
- val=path;
+ // force to the *end* File Name
+ val = Util::GetName( path );
}
- else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image
+ else if ( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image
{
- if(header->GetFileName().substr(0,path.length())!=path)
+ if ( header->GetFileName().substr(0, path.length()) != path )
{
- dbg.Verbose(0, "gdcmDicomDir::SetElement : 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()[path.length()]);
+ {
+ val = &(header->GetFileName().c_str()[path.length()]);
+ }
}
else
{
- val=it->value;
+ val = it->Value;
}
}
- entry->SetValue(val);
+ else
+ {
+ if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
+ val = it->Value;
+ }
+
+ entry->SetValue( val ); // troubles expected when vr=SQ ...
- if(dictEntry)
+ if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
{
- 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());
- }
+ 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(DocEntrySet *dst,DocEntrySet *src)
+{
+ DocEntry *entry;
+
+ entry = src->GetFirstEntry();
+ while(entry)
+ {
+ src->RemoveEntryNoDestroy(entry);
+ dst->AddEntry(entry);
+ // we destroyed -> the current iterator is not longer valid
+ entry = src->GetFirstEntry();
+ }
+}
- listEntries.push_back(entry);
- }
+/**
+ * \brief compares two files
+ */
+bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
+{
+ return *header1 < *header2;
}
-bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2)
+//-----------------------------------------------------------------------------
+// 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 & )
{
- return(*header1<*header2);
+ 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