X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=34f7025cf1dace136fe11e7a72a75abd66847923;hb=8670efa6c3fc51c51fe71c2f62af2297a19b07e2;hp=cd1ab61b5968db25ea628216e06f927fe5fb389f;hpb=cc3e689024eb9b36d9d8db4f977fd04512282a48;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index cd1ab61b..34f7025c 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,651 +1,987 @@ -// gdcmDicomDir.cxx +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2005/02/01 10:34:59 $ + Version: $Revision: 1.124 $ + + 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 "gdcmDicomDirStudy.h" +#include "gdcmDicomDirSerie.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 #include - +#include #include -#include -//----------------------------------------------------------------------------- -class ELEMENTS -{ -public : - ELEMENTS(unsigned short int _group,unsigned short int _elem,std::string _value) - {group=_group;elem=_elem;value=_value;} - - unsigned short int group; - unsigned short int elem; - std::string value; -}; - -ELEMENTS metaElem[]={ - //Meta Group Length : to be computed later - ELEMENTS(0x0002,0x0000,"12345"), - //File Meta Information Version - ELEMENTS(0x0002,0x0001,"\2\0\0\0"), - //Media Stored SOP Class UID i.e. : 'Media Storage Directory Storage' - ELEMENTS(0x0002,0x0002,"1.2.840.10008.1.3.10"), - //Media Stored SOP Instance UID : may be forged later - ELEMENTS(0x0002,0x0003,""), - //Transfer Syntax UID i.e. : Explicit VR - Little Endian - ELEMENTS(0x0002,0x0010,"1.2.840.10008.1.2.1"), - //Implementation Class UID : may be forged later - ELEMENTS(0x0002,0x0012,""), - //Implementation Version Name - ELEMENTS(0x0002,0x0013,"gdcmLib"), - //File-set ID : - ELEMENTS(0x0004,0x1130,""), - //Offset of the first dir of root dir entity : to be computed later - ELEMENTS(0x0004,0x1200,"0"), - //Offset of the last dir of root dir entity : to be computed later - ELEMENTS(0x0004,0x1202,"0"), - //File-set consistency flag - ELEMENTS(0x0004,0x1212,"0"), - //Directory record sequence : *length* to be set later - ELEMENTS(0x0004,0x1220,"0"), - ELEMENTS(0xffff,0xffff,"") -} ; - -ELEMENTS patientElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"PATIENT "), // don't remove trailing space ! - - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Patient's Name - ELEMENTS(0x0010,0x0010,""), - // Patient ID - ELEMENTS(0x0010,0x0020,""), - // Patient's Birthdate - ELEMENTS(0x0010,0x0030,""), - // Patient's Sex - ELEMENTS(0x0010,0x0040,""), - ELEMENTS(0xffff,0xffff,"") - }; - -ELEMENTS studyElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"STUDY "), // don't remove trailing space ! - - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Study Date - ELEMENTS(0x0008,0x0020,""), - // Study Time - ELEMENTS(0x0008,0x0030,""), - // Accession Number - ELEMENTS(0x0008,0x0050,""), - // Study Description - ELEMENTS(0x0008,0x1030,""), - // Study Instance UID : may be forged later - ELEMENTS(0x0020,0x000d,""), - // Study ID : may be forged later - ELEMENTS(0x0020,0x0010,""), - ELEMENTS(0xffff,0xffff,"") -}; - - -ELEMENTS serieElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"SERIES"), // don't add trailing space ! - - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Series Date - ELEMENTS(0x0008,0x0021,""), - // Series Time - ELEMENTS(0x0008,0x0031,""), - // Modality - ELEMENTS(0x0008,0x0060,""), - // Institution Name : may be forged later - ELEMENTS(0x0008,0x0080,""), - // Institution Address : may be forged later - ELEMENTS(0x0008,0x0081,""), - // Series Description : may be forged later - ELEMENTS(0x0008,0x103e,""), - // Series Instance UID : may be forged later - ELEMENTS(0x0020,0x000e,""), - // Series Number : may be forged later - ELEMENTS(0x0020,0x0011,"0"), - ELEMENTS(0xffff,0xffff,"") -}; - -ELEMENTS imageElem[]={ - ELEMENTS(0xfffe,0xe000,"0"), - // Offset of next directory record : to be computed later - ELEMENTS(0x0004,0x1400,"0"), - // Record in use flag : 65535(?) - ELEMENTS(0x0004,0x1410,"65535"), - // Offset of referenced lower-level dir entity : to be computed later - ELEMENTS(0x0004,0x1420,"0"), - // Directory Record Type - ELEMENTS(0x0004,0x1430,"IMAGE "), // don't remove trailing space ! - - // Referenced File ID : to be set later(relative File Name) - ELEMENTS(0x0004,0x1500,""), - // Referenced SOP Class UID in File : may be forged later - ELEMENTS(0x0004,0x1510,""), - // Referenced SOP Class UID in File : may be forged later - ELEMENTS(0x0004,0x1511,""), - // Referenced Transfer Syntax in File - ELEMENTS(0x0004,0x1512,""), - // Specific Character Set - ELEMENTS(0x0008,0x0005,"ISO_IR 100"), - // Image Type - ELEMENTS(0x0008,0x0008,""), - // SOP Class UID : to be set/forged later - ELEMENTS(0x0008,0x0016,""), - // SOP Instance UID : to be set/forged later - ELEMENTS(0x0008,0x0018,""), - // Content Date - ELEMENTS(0x0008,0x0023,""), - // Content Time - ELEMENTS(0x0008,0x0033,""), - // Referenced Image Sequence : to be set/forged later - ELEMENTS(0x0008,0x1040,""), - ELEMENTS(0xfffe,0xe000,"0"), - // Referenced SOP Class UID : to be set/forged later - ELEMENTS(0x0008,0x1150,""), - // Referenced SOP Instance UID : to be set/forged later - ELEMENTS(0x0008,0x1155,""), - // Image Number - ELEMENTS(0x0020,0x0013,"0"), - // Image Position Patient - ELEMENTS(0x0020,0x0032,"0"), - // Image Orientation(Patient) - ELEMENTS(0x0020,0x0037,"0"), - // Frame of Reference UID - ELEMENTS(0x0020,0x0052,"0"), - // Rows - ELEMENTS(0x0028,0x0010,"0"), - // Columns - ELEMENTS(0x0028,0x0011,"0"), - // Pixel Spacing - ELEMENTS(0x0028,0x0030,"0"), - // Calibration Image - ELEMENTS(0x0050,0x0004,"0"), - ELEMENTS(0xffff,0xffff,"") -}; +#ifdef _MSC_VER +# define getcwd _getcwd +#endif + +#if defined(_MSC_VER) || defined(__BORLANDC__) +# include +#else +# include +#endif +namespace gdcm +{ //----------------------------------------------------------------------------- // Constructor / Destructor -/* - * \ingroup gdcmDicomDir - * \brief - * @param Filename - * @param exception_on_error +/** + * \brief Constructor : creates an empty DicomDir */ -gdcmDicomDir::gdcmDicomDir(const char *FileName, - bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) +DicomDir::DicomDir() + :Document( ) { - if( GetListEntry().begin()==GetListEntry().end() ) + Initialize(); // sets all private fields to NULL + NewMeta(); +} + +/** + * \brief Constructor Parses recursively the directory and creates the DicomDir + * or uses an already built DICOMDIR, depending on 'parseDir' value. + * @param fileName name + * - 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 + */ +DicomDir::DicomDir(std::string const &fileName, bool parseDir ): + Document( fileName ) +{ + // 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 ( GetFirstEntry() == 0 ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); + if (!parseDir) + gdcmVerboseMacro( "Entry HT empty for file: "<pos2) - path.resize(pos1); + if ( parseDir ) // user asked for a recursive parsing of a root directory + { + NewMeta(); + + gdcmVerboseMacro( "Parse directory and create the DicomDir"); + ParseDirectory(); + } else - path.resize(pos2); - NewDicomDir(path); + { + /// \todo if parseDir == false, it should be tagged as an error + // NO ! user may just call ParseDirectory() *after* constructor + } } + // Only if user passed a DICOMDIR + // ------------------------------ + else + { + // Directory record sequence + DocEntry *e = GetDocEntry(0x0004, 0x1220); + if ( !e ) + { + gdcmVerboseMacro( "NO 'Directory record sequence' (0x0004,0x1220)" + << " in file " << fileName); + /// \todo FIXME : what do we do when the parsed file IS NOT a + /// DICOMDIR file ? + } + else + CreateDicomDir(); + } +} - CreateDicomDir(); +/** + * \brief Canonical destructor + */ +DicomDir::~DicomDir() +{ + SetStartMethod(NULL); + SetProgressMethod(NULL); + SetEndMethod(NULL); + + ClearPatient(); + if ( MetaElems ) + { + delete MetaElems; + } } -/* - * \ingroup gdcmDicomDir - * \brief - * @param exception_on_error +//----------------------------------------------------------------------------- +// Public +/** + * \brief This predicate, based on hopefully reasonable heuristics, + * 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 Document is the one of a reasonable DicomDir, + * false otherwise. */ -gdcmDicomDir::gdcmDicomDir(ListTag *l, - bool exception_on_error): - gdcmParser(exception_on_error ) -{ - listEntries=*l; +bool DicomDir::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; + } + + return true; +} + +/** + * \brief fills the whole structure, starting from a root Directory + */ +void DicomDir::ParseDirectory() +{ + CreateDicomDirChainedList( GetFileName() ); CreateDicomDir(); } -/* - * \ingroup gdcmDicomDir - * \brief Canonical destructor +/** + * \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 */ -gdcmDicomDir::~gdcmDicomDir() +void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + if( StartArg && StartMethodArgDelete ) { - delete *cc; + StartMethodArgDelete( StartArg ); } + + StartMethod = method; + StartArg = arg; + StartMethodArgDelete = argDelete; } -//----------------------------------------------------------------------------- -// Print -void gdcmDicomDir::Print(std::ostream &os) +/** + * \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 ) { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + StartMethodArgDelete = method; +} + +/** + * \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 ) { - (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + ProgressMethodArgDelete( ProgressArg ); } + + ProgressMethod = method; + ProgressArg = arg; + ProgressMethodArgDelete = argDelete; } -//----------------------------------------------------------------------------- -// 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 + * \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 */ -bool gdcmDicomDir::Write(std::string fileName) +void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method ) { - FILE * fp1; + ProgressMethodArgDelete = method; +} - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) +/** + * \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 ) { - printf("Failed to open(write) File [%s] \n",fileName.c_str()); - return(false); + EndMethodArgDelete( EndArg ); } - char * filePreamble; - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - free(filePreamble); + 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::SetEndMethodArgDelete( DicomDir::Method *method ) +{ + EndMethodArgDelete = method; +} + +/** + * \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; +} - WriteEntries(fp1,DICOMDIR); +/** + * \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 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 ) + { + gdcmVerboseMacro("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 = 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) + { + binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff + } - fclose(fp1); + fp->close(); + delete fp; return true; } //----------------------------------------------------------------------------- // Protected -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \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) { - gdcmDirList fileList(path,1); - ListHeader list; - gdcmHeader *header; + CallStartMethod(); + DirList dirList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; + File *header; - listEntries.clear(); + DirListType fileList = dirList.GetFilenames(); - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) + for( DirListType::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) { -// std::cout<<*it<c_str()); - if(header->IsReadable()) + Progress = (float)(count+1)/(float)fileList.size(); + CallProgressMethod(); + if( Abort ) + { + break; + } + + header = new File( it->c_str() ); + if( !header ) + { + gdcmVerboseMacro( "Failure in new gdcm::File " << it->c_str() ); + continue; + } + + if( header->IsReadable() ) + { + // Add the file to the chained list: list.push_back(header); - else - delete header; + gdcmVerboseMacro( "Readable " << it->c_str() ); + } + else + { + delete header; + } + count++; + } + // sorts Patient/Study/Serie/ + std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); + + std::string tmp = dirList.GetDirName(); + //for each File of the chained list, add/update the Patient/Study/Serie/Image info + SetElements(tmp, list); + CallEndMethod(); + + for(VectDocument::iterator itDoc=list.begin(); + itDoc!=list.end(); + ++itDoc) + { + delete dynamic_cast(*itDoc); } +} + +/** + * \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); + + entry = GetFirstEntry(); + while( entry ) + { + if( dynamic_cast(entry) ) + break; - SetElements(path,list); + RemoveEntryNoDestroy(entry); + MetaElems->AddEntry(entry); + + entry = GetFirstEntry(); + } + } + else // after root directory parsing + { + MetaElems = new DicomDirMeta(false); + } + MetaElems->SetSQItemNumber(0); // To avoid further missprinting + return MetaElems; } -//----------------------------------------------------------------------------- -// Private -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief adds a new Patient (with the basic elements) to a partially created + * DICOMDIR */ -void gdcmDicomDir::CreateDicomDir() +DicomDirPatient *DicomDir::NewPatient() { - // 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 - + DicomDirPatient *p = new DicomDirPatient(); + AddPatientToEnd( p ); + return p; +} - gdcmDicomDirType type=gdcmDicomDir::GDCM_NONE; - ListTag::iterator begin; - ListTag::iterator end; +/** + * \brief Remove all Patients + */ +void DicomDir::ClearPatient() +{ + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) + { + delete *cc; + } + Patients.clear(); +} - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=listEntries.begin();i !=listEntries.end();++i) +/** + * \brief adds to the HTable + * the Entries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header Header of the current file + */ +void DicomDir::SetElement(std::string const &path, DicomDirType type, + Document *header) +{ + ListDicomDirElem elemList; //FIXME this is going to be a by copy operation + ListDicomDirElem::const_iterator it; + uint16_t tmpGr, tmpEl; + DictEntry *dictEntry; + ValEntry *entry; + std::string val; + SQItem *si; + + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = new DicomDirImage(true); + if( !AddImageToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add ImageToEnd failed"); + } + break; + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = new DicomDirSerie(true); + if( !AddSerieToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add SerieToEnd failed"); + } + break; + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = new DicomDirStudy(true); + if( !AddStudyToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add StudyToEnd failed"); + } + break; + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = new DicomDirPatient(true); + if( !AddPatientToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add PatientToEnd failed"); + } + break; + case GDCM_DICOMDIR_META: + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + si = new DicomDirMeta(true); + if( MetaElems ) + { + delete MetaElems; + gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); + } + MetaElems = static_cast(si); + break; + default: + return; + } + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + // for all the relevant elements found in their own spot of the DicomDir.dic + // FIXME : troubles found when it's a SeqEntry + + for( it = elemList.begin(); it != elemList.end(); ++it) { - // std::cout << std::hex <<(*i)->GetGroup() << - // " " <<(*i)->GetElement() << endl; + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl); - std::string v=(*i)->GetValue(); - if(v=="PATIENT ") - { - // std::cout<<"PATIENT"<SetOffset(0); // just to avoid further missprinting - if(v=="STUDY ") + if( header ) { - // std::cout<<"STUDY"<GetEntryValue(tmpGr, tmpEl); } - - if(v=="SERIES") + else { - // std::cout<<"SERIES"<GetFileName().substr(0, path.length()) != path ) + { + gdcmVerboseMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); + } + else + { + val = &(header->GetFileName().c_str()[path.length()]); + } + } + else + { + val = it->Value; + } + } + else { - // std::cout<<"IMAGE"<GetEntryLength(tmpGr,tmpEl) == 0 ) + val = it->Value; + } + + entry->SetValue( val ); // troubles expected when vr=SQ ... - type=gdcmDicomDir::GDCM_IMAGE; - begin=end; + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + gdcmVerboseMacro("GDCM_DICOMDIR_META ?!? should never print that"); } + si->AddEntry(entry); } +} - end=GetListEntry().end(); - AddObjectToEnd(type,begin,end); +/** + * \brief CallStartMethod + */ +void DicomDir::CallStartMethod() +{ + Progress = 0.0f; + Abort = false; + if( StartMethod ) + { + StartMethod( StartArg ); + } +} + +/** + * \brief CallProgressMethod + */ +void DicomDir::CallProgressMethod() +{ + if( ProgressMethod ) + { + ProgressMethod( ProgressArg ); + } } -/* - * \ingroup gdcmDicomDir - * \brief - * @param + +/** + * \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 +/** + * \brief Sets all fields to NULL + */ +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 = NULL; +} + +/** + * \brief create a 'DicomDir' from a DICOMDIR Header + */ +void DicomDir::CreateDicomDir() +{ + // 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 - + + // Directory record sequence + DocEntry *e = GetDocEntry(0x0004, 0x1220); + if ( !e ) + { + gdcmVerboseMacro( "No Directory Record Sequence (0004,1220) found"); + /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? + return; + } + + SeqEntry *s = dynamic_cast(e); + if ( !s ) + { + gdcmVerboseMacro( "Element (0004,1220) is not a Sequence ?!?"); return; + } - switch(type) + NewMeta(); + + DocEntry *d; + std::string v; + SQItem *si; + + SQItem *tmpSI=s->GetFirstSQItem(); + while(tmpSI) { - 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 = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast(d) ) + { + v = valEntry->GetValue(); + } + else + { + gdcmVerboseMacro( "Not a ValEntry."); + continue; + } + + if( v == "PATIENT " ) + { + si = new DicomDirPatient(true); + if( !AddPatientToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add PatientToEnd failed"); + } + } + else if( v == "STUDY " ) + { + si = new DicomDirStudy(true); + if( !AddStudyToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddStudyToEnd failed"); + } + } + else if( v == "SERIES" ) + { + si = new DicomDirSerie(true); + if( !AddSerieToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddSerieToEnd failed"); + } + } + else if( v == "IMAGE " ) + { + si = new DicomDirImage(true); + if( !AddImageToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddImageToEnd failed"); + } + } + else + { + // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // neither an 'IMAGE' SQItem. Skip to next item. + continue; + } + if( si ) + MoveSQItem(si,tmpSI); + + tmpSI=s->GetNextSQItem(); } + ClearEntry(); } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief AddPatientToEnd + * @param dd SQ Item to enqueue to the DicomPatient chained List */ -void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) { - patients.push_back(new gdcmPatient(begin,end)); + Patients.push_back(dd); + return true; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief AddStudyToEnd + * @param dd SQ Item to enqueue to the DicomDirStudy chained List */ - void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddStudyToEnd(DicomDirStudy *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)); + (*itp)->AddStudy(dd); + return true; } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param + +/** + * \brief AddSerieToEnd + * @param dd SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddSerieToEnd(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--; - 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->AddSerie(dd); + return true; } } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @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 +/** + * \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); + // get the current file characteristics + 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) - SetElement(path,GDCM_STUDY,*it); + if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID + || first ) + { + SetElement(path, GDCM_DICOMDIR_STUDY, *it); + first = true; + } // if new Serie Deal with 'SERIE' Elements - if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID) + if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID + || first ) { - SetElement(path,GDCM_SERIE,*it); - } + SetElement(path, GDCM_DICOMDIR_SERIE, *it); + first = true; + } // 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 +/** + * \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 gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) +void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src) { - ELEMENTS *elemList; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; - std::string val; + DocEntry *entry; - switch(type) + entry = src->GetFirstEntry(); + while(entry) { - case GDCM_PATIENT: - elemList=patientElem; - break; - case GDCM_STUDY: - elemList=studyElem; - break; - case GDCM_SERIE: - elemList=serieElem; - break; - case GDCM_IMAGE: - elemList=imageElem; - break; - case GDCM_NONE: - elemList=metaElem; - break; - default: - return; + src->RemoveEntryNoDestroy(entry); + dst->AddEntry(entry); + // we destroyed -> the current iterator is not longer valid + entry = src->GetFirstEntry(); } +} - for(int i=0;;i++) - { - tmpGr=elemList[i].group; - tmpEl=elemList[i].elem; - if(tmpGr==0xffff) - break; - - 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=elemList[i].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()); - } - } +/** + * \brief compares two files + */ +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) +{ + return *header1 < *header2; +} - listEntries.push_back(entry); - } +//----------------------------------------------------------------------------- +// Print +/** + * \brief Canonical Printer + * @param os ostream we want to print in + * @param indent Indentation string to be prepended during printing + */ +void DicomDir::Print(std::ostream &os, std::string const & ) +{ + if( MetaElems ) + { + MetaElems->SetPrintLevel(PrintLevel); + MetaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc) + { + (*cc)->SetPrintLevel(PrintLevel); + (*cc)->Print(os); + } } //----------------------------------------------------------------------------- +} // end namespace gdcm