X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FSplitIntoDirectories.cxx;h=abcfbe75c18877f16da89cde16d99ce83750d474;hb=e7a642c06e4cdcfdbaf024090754283ccc564408;hp=1e453a19976959428c18a1454d5acf48354d5ad7;hpb=f6ebb61b9b3fa1a6ae9a380ff918efe08b6788c4;p=gdcm.git diff --git a/Example/SplitIntoDirectories.cxx b/Example/SplitIntoDirectories.cxx index 1e453a19..abcfbe75 100755 --- a/Example/SplitIntoDirectories.cxx +++ b/Example/SplitIntoDirectories.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: SplitIntoDirectories.cxx,v $ Language: C++ - Date: $Date: 2007/09/26 08:14:27 $ - Version: $Revision: 1.1 $ + Date: $Date: 2009/05/28 15:44:34 $ + Version: $Revision: 1.5 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -29,16 +29,16 @@ #include /** - * \brief + * \brief * - explores recursively the given directory * - keeps the requested series * - orders the gdcm-readable found Files * according to their Patient/Study/Serie/Image characteristics - */ + */ typedef std::map SortedFiles; -int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { START_USAGE(usage) " \n SplitIntoDirectories :\n ", @@ -46,7 +46,7 @@ int main(int argc, char *argv[]) " - keeps the requested series / drops the unrequested series ", " - orders the gdcm-readable found Files according to their ", " (0x0010, 0x0010) Patient's Name ", - " (0x0020, 0x000d) Study Instance UID ", + " (0x0020, 0x000d) Study Instance UID ", " (0x0020, 0x000e) Series Instance UID ", " - fills a tree-like structure of directories as : ", " - Patient ", @@ -60,7 +60,7 @@ int main(int argc, char *argv[]) " dirout=outputDirectoryName ", " { [keep= list of seriesNumber to process] ", " | [drop= list of seriesNumber to ignore] } ", - " [listonly] ", + " [listonly] [skel] [seriedescr] ", " [noshadowseq][noshadow][noseq] [verbose] [debug] ", " ", " dirout : will be created if doesn't exist ", @@ -69,7 +69,10 @@ int main(int argc, char *argv[]) " drop : if user wants to ignore a limited number of series ", " he gives the list of 'SeriesNumber' (tag 0020|0011) ", " SeriesNumber are short enough to be human readable ", - " e.g : 1030,1035,1043 ", + " e.g : 1030,1035,1043 ", + " seriedescr : SerieDescription+SerieNumber use for directory name ", + " (instead of SeriesInstanceUID) ", + " skel : name skeleton eg : patName_1.nema -> skel=patName_ ", " noshadowseq: user doesn't want to load Private Sequences ", " noshadow : user doesn't want to load Private groups (odd number) ", " noseq : user doesn't want to load Sequences ", @@ -78,17 +81,24 @@ int main(int argc, char *argv[]) FINISH_USAGE + // VERY IMPORTANT : + // Respect this order while creating 'UserFileIdentifier' + // (mind the order of the 'AddSeriesDetail' !) + enum Index { IND_PatientName, IND_StudyInstanceUID, - IND_SerieInstanceUID + IND_SerieInstanceUID, + IND_SerieDescription, + IND_SerieNumber, + IND_FileName }; std::cout << "... inside " << argv[0] << std::endl; // ----- Initialize Arguments Manager ------ - + GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv); if (argc == 1 || am->ArgMgrDefined("usage")) @@ -98,16 +108,16 @@ int main(int argc, char *argv[]) return 0; } - const char *dirNamein; - dirNamein = am->ArgMgrGetString("dirin","."); + const char *dirNamein; + dirNamein = am->ArgMgrGetString("dirin","."); const char *dirNameout; - dirNameout = am->ArgMgrGetString("dirout","."); + dirNameout = am->ArgMgrGetString("dirout","."); int loadMode = GDCM_NAME_SPACE::LD_ALL; if ( am->ArgMgrDefined("noshadowseq") ) loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ; - else + else { if ( am->ArgMgrDefined("noshadow") ) loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW; @@ -118,31 +128,33 @@ int main(int argc, char *argv[]) if (am->ArgMgrDefined("debug")) GDCM_NAME_SPACE::Debug::DebugOn(); - bool verbose = ( 0 != am->ArgMgrDefined("verbose") ); - bool listonly = ( 0 != am->ArgMgrDefined("listonly") ); - + bool verbose = ( 0 != am->ArgMgrDefined("verbose") ); + bool listonly = ( 0 != am->ArgMgrDefined("listonly") ); + bool seriedescr = ( 0 != am->ArgMgrDefined("seriedescr") ); + int nbSeriesToKeep; int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep); int nbSeriesToDrop; int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop); - + if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0) { std::cout << "KEEP and DROP are mutually exclusive !" << std::endl; delete am; - return 0; + return 0; } - int hasSkel = am->ArgMgrDefined("skel"); + bool hasSkel = ( 0 != am->ArgMgrDefined("hasSkel") ); const char *skel; if (hasSkel) - skel = am->ArgMgrGetString("skel"); + skel = am->ArgMgrGetString("skel"); + const char *input = am->ArgMgrGetString("input","DCM"); // if unused Param we give up if ( am->ArgMgrPrintUnusedLabels() ) - { + { am->ArgMgrUsage(usage); delete am; return 0; @@ -167,7 +179,7 @@ int main(int argc, char *argv[]) } std::string systemCommand; - + std::cout << "Check for output directory :[" << dirNameout << "]." <AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name (false : no convert) // You may prefer 0020 0010 Study ID @@ -244,11 +271,15 @@ int main(int argc, char *argv[]) // use : // s->AddSeriesDetail(0x0020, 0x0011, true); s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID (false : no convert) + + s->AddSeriesDetail(0x0008, 0x103e, false); // Serie Description + s->AddSeriesDetail(0x0020, 0x0011, false); // Serie Number (more than 1 serie may have the same Ser.Nbr don't 'convert!) + // Feel free to add more fields, if they can help a suitable (for you) // image sorting -// Loop on all the gdcm-readable files + // Loop on all the gdcm-readable files for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin(); it != fileNames.end(); ++it) @@ -256,8 +287,17 @@ int main(int argc, char *argv[]) f = GDCM_NAME_SPACE::File::New(); f->SetLoadMode(loadMode); f->SetFileName( *it ); + if (verbose) + std::cout << "Try[" << *it << "]\n"; f->Load(); - + if (!f->Document::IsReadable()) + { + if (verbose) + std::cout << "File : [" << *it << "] not gdcm-readable -> skipped !" << std::endl; + continue; + } + if (verbose) + std::cout << "Loaded!\n"; std::string strSeriesNumber; int seriesNumber; int j; @@ -285,13 +325,13 @@ int main(int argc, char *argv[]) // drop all unrequested Series bool drop = false; if (nbSeriesToDrop != 0) - { + { strSeriesNumber = f->GetEntryString(0x0020, 0x0011 ); seriesNumber = atoi( strSeriesNumber.c_str() ); for (j=0;jDelete(); continue; } - } + } - userFileIdentifier=s->CreateUserDefinedFileIdentifier(f); + userFileIdentifier=s->CreateUserDefinedFileIdentifier(f); + if (verbose) + std::cout << "userFileIdentifier [" << userFileIdentifier << "]" << std::endl; tokens.clear(); - GDCM_NAME_SPACE::Util::Tokenize (userFileIdentifier, tokens, token); - - int imageNum; // Within FileName + GDCM_NAME_SPACE::Util::Tokenize (userFileIdentifier, tokens, token); + char newName[1024]; - - + + ///this is a trick to build up a lexicographical compliant name : + /// eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima + std::string name = GDCM_NAME_SPACE::Util::GetName( *it ); + + std::cout << "name :[" << name << "]\n"; + + if (hasSkel) + { + int imageNum; // Within FileName + GDCM_NAME_SPACE::Util::Tokenize (name, tokensForFileName, skel); + imageNum = atoi ( tokensForFileName[0].c_str() ); + // probabely we could write something much more complicated using C++ ! + sprintf (newName, "%s%06d.dcm", skel, imageNum); + tokens[IND_FileName] = newName; + tokensForFileName.clear(); + } + else + { + tokens[IND_FileName] = name; + } + // Patient's Name - // Study Instance UID + // Study Instance UID // Series Instance UID + // SerieDescription + // Serie Number + // file Name userFileIdentifier = tokens[IND_PatientName] + token + tokens[IND_StudyInstanceUID] + token + - tokens[IND_SerieInstanceUID] + token; - + tokens[IND_SerieInstanceUID] + token + + + tokens[IND_SerieDescription] + token + + tokens[IND_SerieNumber] + token + + tokens[IND_FileName]; + if (verbose) std::cout << "[" << userFileIdentifier << "] : " << *it << std::endl; - - // storing in a map ensures automatic sorting ! + + // storing in a map ensures automatic sorting ! sf[userFileIdentifier] = f; } if (verbose) - std::cout << " " << std::endl; + std::cout << " ==== " << std::endl; std::string fullFilename, lastFilename; std::string previousPatientName, currentPatientName; std::string previousStudyInstanceUID, currentStudyInstanceUID; std::string previousSerieInstanceUID, currentSerieInstanceUID; + std::string currentSerieDescription, currentSerieNumber; std::string writeDir, currentWriteDir; std::string currentPatientWriteDir; - std::string currentStudyWriteDir; + std::string currentStudyWriteDir; std::string currentSerieWriteDir; std::string fullWriteFilename; @@ -368,7 +437,9 @@ int main(int argc, char *argv[]) currentPatientName = tokens[IND_PatientName]; currentStudyInstanceUID = tokens[IND_StudyInstanceUID]; currentSerieInstanceUID = tokens[IND_SerieInstanceUID]; - + currentSerieDescription = tokens[IND_SerieDescription]; + currentSerieNumber = tokens[IND_SerieNumber]; + if (previousPatientName != currentPatientName) { previousPatientName = currentPatientName; @@ -378,42 +449,55 @@ int main(int argc, char *argv[]) previousPatientName = currentPatientName; previousStudyInstanceUID = ""; previousSerieInstanceUID = ""; - + currentPatientWriteDir = writeDir + currentPatientName; systemCommand = "mkdir " + currentPatientWriteDir; - if (verbose) - std::cout << systemCommand << std::endl; - - system ( systemCommand.c_str() ); + if (verbose || listonly) + std::cout << "[" << systemCommand << "]" << std::endl; + if (!listonly) + system ( systemCommand.c_str() ); } - + if (previousStudyInstanceUID != currentStudyInstanceUID) - { - if (verbose) + { + previousStudyInstanceUID = currentStudyInstanceUID; + if (verbose) std::cout << "==== === new Study [" << currentStudyInstanceUID << "]" - << std::endl; + << std::endl; currentStudyWriteDir = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + currentStudyInstanceUID; - systemCommand = "mkdir " + currentStudyWriteDir; - system (systemCommand.c_str()); + systemCommand = "mkdir " + currentStudyWriteDir; + + if (listonly) + std::cout << "[" << systemCommand << "]" << std::endl; + else + system (systemCommand.c_str()); - previousStudyInstanceUID = currentStudyInstanceUID; } if (previousSerieInstanceUID != currentSerieInstanceUID) { + previousSerieInstanceUID = currentSerieInstanceUID; if (verbose) std::cout << "=== ==== === new Serie [" << currentSerieInstanceUID << "]" - << std::endl; - - currentSerieWriteDir = currentStudyWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR - + currentSerieInstanceUID; - systemCommand = "mkdir " + currentSerieWriteDir; - system (systemCommand.c_str()); - - previousSerieInstanceUID = currentSerieInstanceUID; + << std::endl; + + if (seriedescr) // more human readable! + currentSerieWriteDir = currentStudyWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + + currentSerieDescription + "_" + currentSerieNumber + + "_" + currentSerieInstanceUID; + else + currentSerieWriteDir = currentStudyWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + + currentSerieInstanceUID; + + systemCommand = "mkdir " + currentSerieWriteDir; + + if (listonly) + std::cout << "[" << systemCommand << "]" << std::endl; + else + system (systemCommand.c_str()); } if ( GDCM_NAME_SPACE::Debug::GetDebugFlag()) @@ -427,7 +511,11 @@ int main(int argc, char *argv[]) + lastFilename; systemCommand = "cp " + fullFilename + " " + fullWriteFilename; - system ( systemCommand.c_str()); + + if (listonly) + std::cout << "[" << systemCommand << "]" << std::endl; + else + system (systemCommand.c_str()); } return 0;