X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=e920abfe2464db1cd6dba1299aec3e3bfa574962;hb=8bf45262260369e9f9f773c5793acb4924639cc1;hp=cd1ab61b5968db25ea628216e06f927fe5fb389f;hpb=cc3e689024eb9b36d9d8db4f977fd04512282a48;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index cd1ab61b..e920abfe 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,651 +1,956 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- -#include "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.h" -#include "gdcmDirList.h" -#include "gdcmUtil.h" +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2004/09/23 10:47:10 $ + Version: $Revision: 1.68 $ + + 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.htm 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 - +#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 + #include +#else + #include +#endif + +#include "gdcmDicomDir.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" +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -/* + +/** * \ingroup gdcmDicomDir - * \brief - * @param Filename - * @param exception_on_error + * \brief Constructor : creates an empty gdcmDicomDir */ -gdcmDicomDir::gdcmDicomDir(const char *FileName, - bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) +gdcmDicomDir::gdcmDicomDir() + :gdcmDocument( ) +{ + 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(std::string const & fileName, bool parseDir ): + gdcmDocument( fileName ) { - if( GetListEntry().begin()==GetListEntry().end() ) + // Whatever user passed (a root directory or a DICOMDIR) + // and whatever the value of parseDir was, + // gdcmDocument is already executed + Initialize(); // sets all private fields to NULL + + // if user passed a root directory, sure we didn't get anything + + if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); + + if ( fileName.size() == 1 && fileName[0] == '.' ) + { + // user passed '.' as Name + // we get current directory name + char* dummy = new char[1000]; + getcwd(dummy, (size_t)1000); + SetFileName( dummy ); // will be converted into a string + delete[] dummy; // no longer needed + } - std::string path=FileName; - std::string file; + if ( parseDir ) // user asked for a recursive parsing of a root directory + { + metaElems = NewMeta(); - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory" + " and create the DicomDir"); + ParseDirectory(); + } else - path.resize(pos2); - NewDicomDir(path); + { + /// \todo if parseDir == false, it should be tagged as an error + // NON ! il suffit d'appeler ParseDirectory() + // apres le constructeur + } + } + else // Only if user passed a DICOMDIR + { + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME : what do we do when the parsed file IS NOT a + /// DICOMDIR file ? + } + CreateDicomDir(); } - - CreateDicomDir(); -} - -/* - * \ingroup gdcmDicomDir - * \brief - * @param exception_on_error - */ -gdcmDicomDir::gdcmDicomDir(ListTag *l, - bool exception_on_error): - gdcmParser(exception_on_error ) -{ - listEntries=*l; - CreateDicomDir(); } -/* - * \ingroup gdcmDicomDir +/** * \brief Canonical destructor */ gdcmDicomDir::~gdcmDicomDir() { - 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 +/** + * \brief Canonical Printer + */ void gdcmDicomDir::Print(std::ostream &os) { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + if(metaElems) { - (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + metaElems->SetPrintLevel(PrintLevel); + metaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = patients.begin(); + cc != patients.end(); + ++cc) + { + (*cc)->SetPrintLevel( PrintLevel ); + (*cc)->Print( os ); } } //----------------------------------------------------------------------------- // Public +/** + * \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 gdcmDocument is the one of a reasonable DicomDir, + * false otherwise. + */ +bool gdcmDicomDir::IsReadable() +{ + if( !gdcmDocument::IsReadable() ) + { + return false; + } + if( !metaElems ) + { + return false; + } + if( patients.size() <= 0 ) + { + return false; + } + + return true; +} + +/** + * \brief Sets all fields to NULL + */ + +void gdcmDicomDir::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 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 fills the whole structure, starting from a root Directory + */ +void gdcmDicomDir::ParseDirectory() +{ + CreateDicomDirChainedList( GetFileName() ); + CreateDicomDir(); +} + +/** + * \ingroup gdcmDicomDir + * \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::SetStartMethod(gdcmMethod *method, void *arg, + gdcmMethod *argDelete ) +{ + if( startArg && startMethodArgDelete ) + { + startMethodArgDelete( startArg ); + } + + startMethod = method; + startArg = arg; + startMethodArgDelete = argDelete; +} + +/** + * \ingroup gdcmDicomDir + * \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::SetStartMethodArgDelete(gdcmMethod *method) +{ + startMethodArgDelete = method; +} + +/** + * \ingroup gdcmDicomDir + * \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 gdcmDicomDir::SetProgressMethod(gdcmMethod *method, void *arg, + gdcmMethod *argDelete ) +{ + if( progressArg && progressMethodArgDelete ) + { + progressMethodArgDelete( progressArg ); + } + + progressMethod = method; + progressArg = arg; + progressMethodArgDelete = argDelete; +} + +/** + * \ingroup gdcmDicomDir + * \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 gdcmDicomDir::SetProgressMethodArgDelete(gdcmMethod *method) { - FILE * fp1; + progressMethodArgDelete = method; +} - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) +/** + * \ingroup gdcmDicomDir + * \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 gdcmDicomDir::SetEndMethod(gdcmMethod *method, void *arg, + gdcmMethod *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; +} + +/** + * \ingroup gdcmDicomDir + * \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::SetEndMethodArgDelete(gdcmMethod *method) +{ + endMethodArgDelete = method; +} - WriteEntries(fp1,DICOMDIR); +/** + * \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 ! + * \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 gdcmDicomDir::WriteDicomDir(std::string const & fileName) +{ + uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; + + FILE * fp = fopen(fileName.c_str(), "wb"); + if( !fp ) + { + printf("Failed to open(write) File [%s] \n", fileName.c_str()); + return false; + } - fclose(fp1); + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble,128,1,fp); + fwrite("DICM",4,1,fp); + delete[] filePreamble; + + gdcmDicomDirMeta *ptrMeta = GetDicomDirMeta(); + ptrMeta->Write(fp, gdcmExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within gdcmDicomDirMeta + fwrite(&sq[0],8,1,fp); // 0004 1220 ffff ffff + + for(ListDicomDirPatient::iterator cc = patients.begin();cc!=patients.end();++cc) + { + (*cc)->Write( fp, gdcmExplicitVR ); + } + + // force writing Sequence Delimitation Item + fwrite(&sqt[0],8,1,fp); // fffe e0dd ffff ffff + fclose( fp ); return true; } //----------------------------------------------------------------------------- // Protected -/* + +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief create a gdcmDocument-like chained list from a root Directory + * @param path entry point of the tree-like structure */ -void gdcmDicomDir::NewDicomDir(std::string path) +void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) { - gdcmDirList fileList(path,1); - ListHeader list; + CallStartMethod(); + gdcmDirList fileList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; gdcmHeader *header; - listEntries.clear(); + TagHT.clear(); + patients.clear(); - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) + for( gdcmDirList::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 gdcmHeader( it->c_str() ); + if( !header ) + { + dbg.Verbose( 1, + "gdcmDicomDir::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, + "gdcmDicomDir::CreateDicomDirChainedList: readable ", + it->c_str() ); + + } + else + { + delete header; + } + count++; + } + // sorts Patient/Study/Serie/ + std::sort(list.begin(), list.end(), gdcmDicomDir::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(); +} + +/** + * \ingroup gdcmDicomDir + * \brief adds *the* Meta to a partially created DICOMDIR + */ + +gdcmDicomDirMeta * gdcmDicomDir::NewMeta() +{ + gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &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) + { + m->AddDocEntry( cc->second ); + } + } + else // after root directory parsing + { + std::list elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + m->FillObject(elemList); + } + m->SetSQItemNumber(0); // To avoid further missprinting + return m; +} + +/** + * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + */ +gdcmDicomDirPatient * gdcmDicomDir::NewPatient() +{ + std::list::iterator it; + uint16_t tmpGr,tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + + std::list elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + gdcmSQItem *s = new gdcmSQItem(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 gdcmValEntry( 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 ); + } + + gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &TagHT); + patients.push_front( p ); + + return p; +} + +/** + * \brief adds to the HTable + * the gdcmEntries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type gdcmDicomDirObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header gdcmHeader of the current file + */ +void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, + gdcmDocument *header) +{ + std::list elemList; + std::list::iterator it; + uint16_t tmpGr, tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + std::string val; + gdcmSQItem *si = new gdcmSQItem(0); // all the items will be at level 1 + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + break; + + case GDCM_DICOMDIR_SERIE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + break; + + case GDCM_DICOMDIR_STUDY: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); + break; + + case GDCM_DICOMDIR_PATIENT: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + break; + + case GDCM_DICOMDIR_META: + elemList = gdcmGlobal::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 gdcmValEntry( 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 + val = GDCM_UNFOUND; + + if( val == GDCM_UNFOUND) + { + if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID + { + // force to the *end* File Name + val = GetName( 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().c_str()[path.length()]); + } + else + val = it->value; + } else - delete header; + { + if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) + val = it->value; + } + + // GDCM_UNFOUND or not ! + + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if( dictEntry ) + { + if( dictEntry->GetGroup() == 0xfffe ) + { + entry->SetLength( entry->GetValue().length() ); // FIXME + } + else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) + { + entry->SetLength(4); + } + else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" ) + { + entry->SetLength(2); + } + else if( dictEntry->GetVR() == "SQ" ) + { + entry->SetLength( 0xffffffff ); + } + else + { + entry->SetLength( entry->GetValue().length() ); + } + } + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + std::cout << "GDCM_DICOMDIR_META ?!? should never print that" + << 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 gdcmDicomDir::CallStartMethod() +{ + progress = 0.0f; + abort = false; + if( startMethod ) + { + startMethod( startArg ); + } +} + +/** + * \ingroup gdcmDicomDir + * \brief CallProgressMethod + */ +void gdcmDicomDir::CallProgressMethod() +{ + if( progressMethod ) + { + progressMethod( progressArg ); } +} - SetElements(path,list); +/** + * \ingroup gdcmDicomDir + * \brief CallEndMethod + */ +void gdcmDicomDir::CallEndMethod() +{ + progress = 1.0f; + if( endMethod ) + { + endMethod( endArg ); + } } //----------------------------------------------------------------------------- // Private -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader */ void gdcmDicomDir::CreateDicomDir() { - // The list is parsed. When a tag is found : + // 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 - - gdcmDicomDirType type=gdcmDicomDir::GDCM_NONE; - ListTag::iterator begin; - ListTag::iterator end; - - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=listEntries.begin();i !=listEntries.end();++i) + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) { - // std::cout << std::hex <<(*i)->GetGroup() << - // " " <<(*i)->GetElement() << endl; - - std::string v=(*i)->GetValue(); - if(v=="PATIENT ") - { - // std::cout<<"PATIENT"<(e); + if ( !s ) + { + dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); + // useless : (0x0004,0x1220) IS a Sequence ! + return; + } - type=gdcmDicomDir::GDCM_PATIENT; - begin=end; - } + gdcmDicomDirType type = gdcmDicomDir::GDCM_DICOMDIR_META; + metaElems = NewMeta(); - if(v=="STUDY ") + ListSQItem listItems = s->GetSQItems(); + + gdcmDocEntry * d; + std::string v; + for( ListSQItem::iterator i = listItems.begin(); + i !=listItems.end(); ++i ) + { + d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type + if ( gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(d) ) { - // std::cout<<"STUDY"<GetValue(); } - - if(v=="SERIES") + else { - // std::cout<<"SERIES"<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 gdcmDicomDirStudy(s, &TagHT)); } } -/* + +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirSerieToEnd + * @param s SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *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::iterator itst=(*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddSerie(new gdcmSerie(begin,end)); + (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &TagHT)); } } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirImageToEnd + * @param s SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *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::iterator itst = (*itp)->GetDicomDirStudies().end(); itst--; - if((*itst)->GetSeries().size()>0) + if( (*itst)->GetDicomDirSeries().size() > 0 ) { - ListSerie::iterator its=(*itst)->GetSeries().end(); + ListDicomDirSerie::iterator its = (*itst)->GetDicomDirSeries().end(); its--; - (*its)->AddImage(new gdcmImage(begin,end)); + (*its)->AddDicomDirImage(new gdcmDicomDirImage(s, &TagHT)); } } } } -/* +/** * \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 gdcmDicomDir::SetElements(std::string &path, VectDocument &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; - - SetElement(path,GDCM_NONE,NULL); + std::string serCurInstanceUID, serCurID; - ListTag::iterator debPat=listEntries.begin(); - for(ListHeader::iterator it=list.begin();it!=list.end();++it) + for( VectDocument::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)->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) + if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID ) { - SetElement(path,GDCM_SERIE,*it); - } + 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 + * \brief compares two dgcmHeaders */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) +bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1, gdcmDocument *header2) { - ELEMENTS *elemList; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; - std::string val; - - switch(type) - { - 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; - } - - 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()); - } - } - - listEntries.push_back(entry); - } + return *header1 < *header2; } //-----------------------------------------------------------------------------