X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FexXCoherentFileSet.cxx;h=8f22110c07ab4351c0172118a301ecfe08df978c;hb=6fc9a59ce58ba4bb71d63a57e6b1ef2c3c87292a;hp=c60915dd3deea2e7d555aa5d5b2ad6ad9536e4e4;hpb=1f4b804082d56e199031a5380165eff84750f8a8;p=gdcm.git diff --git a/Example/exXCoherentFileSet.cxx b/Example/exXCoherentFileSet.cxx index c60915dd..8f22110c 100755 --- a/Example/exXCoherentFileSet.cxx +++ b/Example/exXCoherentFileSet.cxx @@ -1,15 +1,15 @@ /*========================================================================= - + Program: gdcm Module: $RCSfile: exXCoherentFileSet.cxx,v $ Language: C++ - Date: $Date: 2005/11/08 16:40:02 $ - Version: $Revision: 1.5 $ + Date: $Date: 2009/05/28 15:44:34 $ + Version: $Revision: 1.16 $ 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. @@ -19,36 +19,43 @@ #include "gdcmFile.h" #include "gdcmDebug.h" #include - +#include "gdcmDirList.h" +#include "gdcmUtil.h" #include "gdcmArgMgr.h" - int main(int argc, char *argv[]) -{ - +{ START_USAGE(usage) "\n exXCoherentFileSet :\n ", "Shows the various 'XCoherent' Filesets within a directory ", + "Optionaly copies the images in a Directories tree ", "usage: exXCoherentFileSet {dirin=inputDirectoryName} ", - " { tag= group-elem | pos | ori } ", + " dirout=outputDirectoryName ", + " { tag=group-elem | pos | ori } [sort] [write] ", " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] ", " ", - " inputDirectoryName : user wants to analyze *all* the files ", + " dirin : user wants to analyze *all* the files ", " within the directory ", + " write : user wants to create directories ", + " dirout : will be created if doesn't exist ", " pos : user wants to split each Single SerieUID Fileset on the ", " 'Image Position ' ", " ori : user wants to split each Single SerieUID Fileset on the ", " 'Image Orientation ' ", " tag : group-elem (in hexa, no space) ", " the user wants to split on ", + " sort : user wants FileHelper to sort the images ", + " Warning : will probabely crah if sort has no meaning ", + " (not only look at image names) ", " 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 ", - " debug : user wants to run the program in 'debug mode' ", + " verbose : user wants to run the program in 'verbose mode' ", + " debug : developper wants to run the program in 'debug mode' ", FINISH_USAGE // ----- Initialize Arguments Manager ------ - - gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv); + + GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv); if (am->ArgMgrDefined("usage") || argc == 1) { @@ -58,70 +65,92 @@ int main(int argc, char *argv[]) } if (am->ArgMgrDefined("debug")) - gdcm::Debug::DebugOn(); - - int loadMode = gdcm::LD_ALL; + GDCM_NAME_SPACE::Debug::DebugOn(); + + int loadMode = GDCM_NAME_SPACE::LD_ALL; if ( am->ArgMgrDefined("noshadowseq") ) - loadMode |= gdcm::LD_NOSHADOWSEQ; - else + loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ; + else { if ( am->ArgMgrDefined("noshadow") ) - loadMode |= gdcm::LD_NOSHADOW; + loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW; if ( am->ArgMgrDefined("noseq") ) - loadMode |= gdcm::LD_NOSEQ; + loadMode |= GDCM_NAME_SPACE::LD_NOSEQ; } - char *dirName = am->ArgMgrGetString("dirin",(char *)0); + const char *dirName = am->ArgMgrGetString("dirin"); if (dirName == 0) { std::cout <ArgMgrUsage(usage); // Display 'usage' delete am; return 0; - } + } - // FIXME : check only one of them is set ! + const char *dirNameout; + dirNameout = am->ArgMgrGetString("dirout","."); - int pos = am->ArgMgrDefined("pos"); - int ori = am->ArgMgrDefined("ori"); + bool pos = ( 0 != am->ArgMgrDefined("pos") ); + bool ori = ( 0 != am->ArgMgrDefined("ori") ); + bool sort = ( 0 != am->ArgMgrDefined("sort") ); + bool write = ( 0 != am->ArgMgrDefined("write") ); + bool verbose = ( 0 != am->ArgMgrDefined("verbose") ); + bool tag = ( 0 != am->ArgMgrDefined("tag") ); + + if( (tag && (pos || ori)) || (pos && (tag || ori)) || (ori && (tag || pos)) ) + { + std::cout << " POS, ORI and TAG are mutually exclusive" << std::endl; + delete am; + return 0; + } + if( (!tag && !pos && !ori)) + { + std::cout << " One of POS, ORI and TAG is mandatory!" << std::endl; + delete am; + return 0; + } int nb; uint16_t *groupelem; - groupelem = am->ArgMgrGetXInt16Enum("tag", &nb); - - if (groupelem != 0) + if (tag) { + groupelem = am->ArgMgrGetXInt16Enum("tag", &nb); if (nb != 1) { std::cout << "TAG : one and only one group,elem!" << std::endl; delete am; return 0; } - } - - + } + /* if unused Param we give up */ if ( am->ArgMgrPrintUnusedLabels() ) { am->ArgMgrUsage(usage); delete am; return 0; - } - + } + delete am; // ------ we don't need Arguments Manager any longer ------ - - gdcm::SerieHelper *s; + GDCM_NAME_SPACE::SerieHelper *s; - s = new gdcm::SerieHelper(); - s->SetLoadMode(gdcm::LD_ALL); // Load everything for each File - //gdcm::TagKey t(0x0020,0x0013); - //s->AddRestriction(t, "340", gdcm::GDCM_LESS); // Keep only files where - // restriction is true + s = GDCM_NAME_SPACE::SerieHelper::New(); + s->SetLoadMode(GDCM_NAME_SPACE::LD_ALL); // Load everything for each File + + //GDCM_NAME_SPACE::TagKey t(0x0020,0x0013); + //s->AddRestriction(t, "340", GDCM_NAME_SPACE::GDCM_LESS); // Keep only files where + // restriction is true + s->SetDirectory(dirName, true); // true : recursive exploration + // The Dicom file set is splitted into several 'Single SerieUID Files Sets' + // (a 'Single SerieUID Files Set' per SerieUID) + // In some cases, it's not enough, since, in some cases + // we can find scout view with the same SerieUID + /* std::cout << " ---------------------------------------- " << "'Single UID' Filesets found in :[" @@ -131,63 +160,176 @@ int main(int argc, char *argv[]) std::cout << " ------------------------------------- Result after splitting" << std::endl; */ + + std::string systemCommand; + std::string filenameout; + if (write) { + if (verbose) + std::cout << "Check for output directory :[" << dirNameout << "]." + < End of checking supposed-to-be-directory names + int nbFiles; std::string fileName; - // For all the Single SerieUID Files Sets of the gdcm::Serie - gdcm::FileList *l = s->GetFirstSingleSerieUIDFileSet(); - - gdcm::XCoherentFileSetmap xcm; - while (l) + + // For all the Single SerieUID Files Sets of the GDCM_NAME_SPACE::Serie + GDCM_NAME_SPACE::FileList *l = s->GetFirstSingleSerieUIDFileSet(); + GDCM_NAME_SPACE::XCoherentFileSetmap xcm; + + std::string serieUID; + std::string currentSerieWriteDir = ""; + std::string xCoherentWriteDir = ""; + std::string xCoherentName = ""; + std::string serieDirectory; + std::string lastFilename; + std::string rep("_"); + int controlCount = 0; + + while (l) // for each 'Single SerieUID FileSet' { nbFiles = l->size() ; - if ( l->size() > 3 ) // Why not ? Just an example, for testing + if ( l->size() > 0 ) // ignore Series with less than 2 images. + // Why not ? Just an example, for testing! { + serieUID = s->GetCurrentSerieUIDFileSetUID(); + GDCM_NAME_SPACE::Util::ReplaceSpecChar(serieUID, rep); + + // --- for write + if (write) + { + currentSerieWriteDir = currentSerieWriteDir + dirNameout; + unsigned int lg = strlen(dirNameout)-1; + if ( dirNameout[lg] != '/' && dirNameout[lg] != '\\') + currentSerieWriteDir = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR; + + currentSerieWriteDir = currentSerieWriteDir + serieUID; + if (verbose) + std::cout << "[" << currentSerieWriteDir<< "]" << std::endl; + // if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(currentSerieWriteDir) ) + { + systemCommand = "mkdir " + currentSerieWriteDir; + system( systemCommand.c_str()); + if (verbose) + std::cout << "1 " <GetCurrentSerieUIDFileSetUID() + << serieUID << "] " << nbFiles << " long" << std::endl; std::cout << "-----------------------------------" << std::endl; - + if (ori) xcm = s->SplitOnOrientation(l); - if (pos) + else if (pos) xcm = s->SplitOnPosition(l); - if (groupelem != 0) + else if (groupelem != 0) { xcm = s->SplitOnTagValue(l, groupelem[0],groupelem[1] ); - - for (gdcm::XCoherentFileSetmap::iterator i = xcm.begin(); + } + + for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin(); i != xcm.end(); ++i) { + xCoherentName = (*i).first; + if (verbose) + std::cout << "xCoherentName = " << xCoherentName << std::endl; + GDCM_NAME_SPACE::Util::ReplaceSpecChar(serieUID, rep); + // --- for write + if (write) + { + xCoherentWriteDir = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR+ xCoherentName; + // if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(xCoherentWriteDir) ) + { + systemCommand = "mkdir " + xCoherentWriteDir; + system( systemCommand.c_str()); + if (verbose) + std::cout << systemCommand << std::endl; + } + } + // --- end for write + if (ori) std::cout << "Orientation : "; - if (pos) + else if (pos) std::cout << "Position : "; - if (groupelem != 0) - std::cout << "Tag (" << std::hex << groupelem[0] - << "|" << groupelem[1] << ") value : "; - - std::cout << "[" << (*i).first << "]" << std::endl; - - // Nowadays OrderFileList() causes trouble, since some files - // (MIP views) don't have 'Position', now considered as mandatory + else if (groupelem != 0) + std::cout << "Tag (" << std::hex << groupelem[0] + << "|" << groupelem[1] << ") value : "; + std::cout << "[" << (*i).first << "]" << std::endl; + + if (verbose) + std::cout << "xCoherentName [" << xCoherentName << "]" << std::endl; + + // Within a 'just to see' program, + // OrderFileList() causes trouble, since some files + // (eg:MIP views) don't have 'Position', now considered as mandatory // Commented out for the moment. - - //s->OrderFileList((*i).second); // sort the XCoherent Fileset - - for (std::vector::iterator it = ((*i).second)->begin(); - it != ((*i).second)->end(); - ++it) + + if (sort) { + s->OrderFileList((*i).second); // sort the XCoherent Fileset + std::cout << "ZSpacing for the file set " << s->GetZSpacing() + << std::endl; + } + + for (GDCM_NAME_SPACE::FileList::iterator it = ((*i).second)->begin(); + it != ((*i).second)->end(); + ++it) { + controlCount ++; fileName = (*it)->GetFileName(); std::cout << " " << fileName << std::endl; - } - std::cout << std::endl; + + // --- for write + if (write) + { + lastFilename = GDCM_NAME_SPACE::Util::GetName( fileName ); + filenameout = xCoherentWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR+ lastFilename; + systemCommand = "cp " + fileName + " " + filenameout; + system( systemCommand.c_str()); + if (verbose) + std::cout << "3 " << systemCommand << std::endl; + } + // --- end for write + } + std::cout << std::endl; } } l = s->GetNextSingleSerieUIDFileSet(); - } - - delete s; + } + + if ( controlCount == 0 ) + std::cout << "No suitable file was found!" << std::endl; + + s->Delete(); return 0; }