X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=4949504a1bfcfab68a2bc5fae0e9cf8642a4ef98;hb=16c512e7912f1b96087f4ad5bece2b20fe7ca6ea;hp=f382906c22bd0e36dc7537f04dc84a3c95ffe838;hpb=6c514fed47b5884b2025e43e9a6f6ee413a6fd5e;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index f382906c..4949504a 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2005/11/04 15:46:03 $ - Version: $Revision: 1.169 $ + Date: $Date: 2006/04/13 08:05:52 $ + Version: $Revision: 1.188 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -37,6 +37,7 @@ #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmDataEntry.h" +#include "gdcmCommandManager.h" #include #include @@ -52,6 +53,11 @@ #else # include #endif + +#if defined(__BORLANDC__) + #include // for memset +#endif + // ---------------------------------------------------------------------------- // Note for future developpers // ---------------------------------------------------------------------------- @@ -117,22 +123,47 @@ namespace gdcm * \brief Constructor : creates an empty DicomDir */ DicomDir::DicomDir() - :Document( ) { Initialize(); // sets all private fields to NULL ParseDir = false; NewMeta(); } +#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 (LD_ALL); // concerns only dicom files + SetFileName( fileName ); + Load( ); +} +#endif + /** * \brief Canonical destructor */ DicomDir::~DicomDir() { - SetStartMethod(NULL,NULL,NULL); - SetProgressMethod(NULL,NULL,NULL); - SetEndMethod(NULL,NULL,NULL); - ClearPatient(); if ( MetaElems ) { @@ -158,30 +189,26 @@ bool DicomDir::Load( ) } return DoTheLoadingJob( ); } - #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, +/** + * \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 + * @deprecated use SetFileName(n) + Load() instead */ bool DicomDir::Load(std::string const &fileName ) { - SetFileName(fileName); - return Load(); -} + // We should clean out anything that already exists. + Initialize(); // sets all private fields to NULL -/// DEPRECATED : use SetDirectoryName(dname) instead -/* * - * \brief Loader. (DEPRECATED : kept not to break the API) - * @param paseDir Parse Dir - * @deprecated use SetDirectoryName(dname) instead - */ -void DicomDir::SetParseDir(bool parseDir) -{ - ParseDir = parseDir; + SetFileName( fileName ); + if (!ParseDir) + { + if ( ! this->Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); } #endif @@ -232,13 +259,13 @@ bool DicomDir::DoTheLoadingJob( ) char buf[2048]; const char *cwd = getcwd(buf, 2048); if( cwd ) - { - SetFileName( cwd ); // will be converted into a string - } + { + SetFileName( buf ); // will be converted into a string + } else - { - gdcmErrorMacro( "Path was too long to fit on 2048 bytes" ); - } + { + gdcmErrorMacro( "Path was too long to fit on 2048 bytes" ); + } } NewMeta(); gdcmDebugMacro( "Parse directory and create the DicomDir : " @@ -371,117 +398,6 @@ void DicomDir::ParseDirectory() CreateDicomDir(); } -void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg ) -{ - SetStartMethod(method,arg,NULL); -} - -void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg ) -{ - SetProgressMethod(method,arg,NULL); -} - -void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg ) -{ - SetEndMethod(method,arg,NULL); -} - -/** - * \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 : @@ -493,8 +409,8 @@ void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) bool DicomDir::Write(std::string const &fileName) { int i; - uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; - uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; + uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0x0000, 0x0000 }; std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); @@ -513,7 +429,7 @@ bool DicomDir::Write(std::string const &fileName) ptrMeta->WriteContent(fp, ExplicitVR); // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta - for(i=0;i<4;++i) + for(i=0;i<6;++i) { binary_write(*fp, sq[i]); } @@ -528,7 +444,7 @@ bool DicomDir::Write(std::string const &fileName) // force writing Sequence Delimitation Item for(i=0;i<4;++i) { - binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff + binary_write(*fp, sqt[i]); // fffe e0dd 0000 0000 } fp->close(); @@ -576,6 +492,33 @@ bool DicomDir::Anonymize() return true; } +/** + * \brief Copies all the attributes from an other DocEntrySet + * @param set entry to copy from + * @remarks The contained DocEntries are not copied, only referenced + */ +void DicomDir::Copy(DocEntrySet *set) +{ + // Remove all previous childs + ClearPatient(); + + Document::Copy(set); + + DicomDir *dd = dynamic_cast(set); + if( dd ) + { + if(MetaElems) + MetaElems->Unregister(); + MetaElems = dd->MetaElems; + if(MetaElems) + MetaElems->Register(); + + Patients = dd->Patients; + for(ItPatient = Patients.begin();ItPatient != Patients.end();++ItPatient) + (*ItPatient)->Register(); + } +} + //----------------------------------------------------------------------------- // Protected /** @@ -591,12 +534,12 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) File *f; DirListType fileList = dirList.GetFilenames(); - + unsigned int nbFile = fileList.size(); for( DirListType::iterator it = fileList.begin(); it != fileList.end(); ++it ) { - Progress = (float)(count+1)/(float)fileList.size(); + Progress = (float)(count+1)/(float)nbFile; CallProgressMethod(); if ( Abort ) { @@ -637,41 +580,6 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) } } -/** - * \brief CallStartMethod - */ -void DicomDir::CallStartMethod() -{ - Progress = 0.0f; - Abort = false; - if ( StartMethod ) - { - StartMethod( StartArg ); - } -} - -/** - * \brief CallProgressMethod - */ -void DicomDir::CallProgressMethod() -{ - if ( ProgressMethod ) - { - ProgressMethod( ProgressArg ); - } -} - -/** - * \brief CallEndMethod - */ -void DicomDir::CallEndMethod() -{ - Progress = 1.0f; - if ( EndMethod ) - { - EndMethod( EndArg ); - } -} //----------------------------------------------------------------------------- // Private @@ -680,16 +588,6 @@ void DicomDir::CallEndMethod() */ 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; @@ -747,7 +645,7 @@ void DicomDir::CreateDicomDir() // 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 + // This is the right order to perform the tests if ( v == "IMAGE " ) { @@ -812,7 +710,7 @@ void DicomDir::CreateDicomDir() continue; } if ( si ) - si->MoveObject(tmpSI); // New code : Copies the List + si->Copy(tmpSI); tmpSI=s->GetNextSQItem(); } @@ -991,7 +889,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, ListDicomDirElem elemList; ListDicomDirElem::const_iterator it; uint16_t tmpGr, tmpEl; - DictEntry *dictEntry; + //DictEntry *dictEntry; DataEntry *entry; std::string val; SQItem *si; @@ -1047,6 +945,9 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, default: return; } + + // FIXME : troubles found when it's a SeqEntry + // removed all the seems-to-be-useless stuff about Referenced Image Sequence // to avoid further troubles // imageElem 0008 1140 "" // Referenced Image Sequence @@ -1055,23 +956,23 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, // 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 - + std::string referencedVal; // 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; - dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl); - - entry = DataEntry::New( dictEntry ); + //dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl); + //entry = DataEntry::New( dictEntry ); + + entry = DataEntry::New(tmpGr, tmpEl, GDCM_VRUNKNOWN); /// \todo : modify dicomelements file, to store VR entry->SetOffset(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->GetEntryString(tmpGr, tmpEl); + val = header->GetEntryString(tmpGr, tmpEl); } else { @@ -1080,33 +981,87 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, if ( val == GDCM_UNFOUND) { - if ( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID + if ( tmpGr == 0x0004 ) // never present in File ! { - // force to the *end* File Name - val = Util::GetName( path ); - } - else if ( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image - { - if ( header->GetFileName().substr(0, path.length()) != path ) - { - gdcmWarningMacro( "The base path of file name is incorrect"); - val = header->GetFileName(); - } - else + switch (tmpEl) { - val = &(header->GetFileName().c_str()[path.length()+1]); - } + case 0x1130: // File-set ID + // force to the *end* File Name + val = Util::GetName( path ); + break; + + case 0x1500: // Only used for image + if ( header->GetFileName().substr(0, path.length()) != path ) + { + gdcmWarningMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); + } + else + { + // avoid the first '/' in File name ! + if ( header->GetFileName().c_str()[path.length()] + == GDCM_FILESEPARATOR ) + val = &(header->GetFileName().c_str()[path.length()+1]); + else + val = &(header->GetFileName().c_str()[path.length()]); + } + break; + + case 0x1510: // Referenced SOP Class UID in File + referencedVal = header->GetEntryString(0x0008, 0x0016); + // FIXME : probabely something to check + val = referencedVal; + break; + + case 0x1511: // Referenced SOP Instance UID in File + referencedVal = header->GetEntryString(0x0008, 0x0018); + // FIXME : probabely something to check + val = referencedVal; + break; + + case 0x1512: // Referenced Transfer Syntax UID in File + referencedVal = header->GetEntryString(0x0002, 0x0010); + // FIXME : probabely something to check + val = referencedVal; + break; + + default : + val = it->Value; + } } else { - val = it->Value; - } + // If the entry is not found in the Header, don't write its 'value' in the DICOMDIR ! + entry->Delete(); + continue; + } } else { if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) + { val = it->Value; + // Don't polute the DICOMDIR with empty fields + if (val == "") + { + entry->Delete(); + continue; + } + } + } + +/* FIX later the pb of creating the 'Implementation Version Name'! + + if (val == GDCM_UNFOUND) + val = ""; + + if ( tmpGr == 0x0002 && tmpEl == 0x0013) + { + // 'Implementation Version Name' + std::string val = "GDCM "; + val += Util::GetVersion(); } +*/ entry->SetString( val ); // troubles expected when vr=SQ ... @@ -1114,6 +1069,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, { gdcmDebugMacro("GDCM_DICOMDIR_META ?!? should never print that"); } + si->AddEntry(entry); entry->Delete(); } @@ -1125,15 +1081,16 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, * @param dst destination SQItem * @param src source SQItem */ -void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src) +void DicomDir::MoveSQItem(DocEntrySet *dst, DocEntrySet *src) { DocEntry *entry; - +// todo : rewrite the whole stuff, without using RemoveEntry an AddEntry, +// to save time entry = src->GetFirstEntry(); while(entry) { + dst->AddEntry(entry); // use it, *before* removing it! src->RemoveEntry(entry); - dst->AddEntry(entry); // we destroyed -> the current iterator is not longer valid entry = src->GetFirstEntry(); }