--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: SplitIntoDirectories.cxx,v $
+ Language: C++
+ Date: $Date: 2007/09/26 08:14:27 $
+ Version: $Revision: 1.1 $
+
+ 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.
+
+=========================================================================*/
+#include "gdcmDocEntry.h"
+#include "gdcmDicomDir.h"
+#include "gdcmDicomDirPatient.h"
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmDirList.h"
+#include "gdcmDebug.h"
+#include "gdcmArgMgr.h"
+#include "gdcmUtil.h"
+#include "gdcmSerieHelper.h"
+
+#include <iostream>
+
+/**
+ * \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<std::string, GDCM_NAME_SPACE::File*> SortedFiles;
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ " \n SplitIntoDirectories :\n ",
+ " - explores recursively the given directory, ",
+ " - 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, 0x000e) Series Instance UID ",
+ " - fills a tree-like structure of directories as : ",
+ " - Patient ",
+ " -- Study ",
+ " --- Serie ",
+ " ",
+ " usage: ",
+ " ----- ",
+ " SplitIntoDirectories ",
+ " dirin=rootDirectoryName ",
+ " dirout=outputDirectoryName ",
+ " { [keep= list of seriesNumber to process] ",
+ " | [drop= list of seriesNumber to ignore] } ",
+ " [listonly] ",
+ " [noshadowseq][noshadow][noseq] [verbose] [debug] ",
+ " ",
+ " dirout : will be created if doesn't exist ",
+ " keep : if user wants to process a limited number of series ",
+ " he gives the list of 'SeriesNumber' (tag 0020|0011) ",
+ " 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 ",
+ " 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 ",
+ " verbose : user wants to run the program in 'verbose mode' ",
+ " debug : *developer* wants to run the program in 'debug mode' ",
+ FINISH_USAGE
+
+
+ enum Index
+ {
+ IND_PatientName,
+ IND_StudyInstanceUID,
+ IND_SerieInstanceUID
+ };
+
+ 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"))
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ const char *dirNamein;
+ dirNamein = am->ArgMgrGetString("dirin",".");
+
+ const char *dirNameout;
+ dirNameout = am->ArgMgrGetString("dirout",".");
+
+ int loadMode = GDCM_NAME_SPACE::LD_ALL;
+ if ( am->ArgMgrDefined("noshadowseq") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
+ else
+ {
+ if ( am->ArgMgrDefined("noshadow") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
+ if ( am->ArgMgrDefined("noseq") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
+ }
+
+ if (am->ArgMgrDefined("debug"))
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ bool verbose = ( 0 != am->ArgMgrDefined("verbose") );
+ bool listonly = ( 0 != am->ArgMgrDefined("listonly") );
+
+ 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;
+ }
+
+ int hasSkel = am->ArgMgrDefined("skel");
+ const char *skel;
+ if (hasSkel)
+ 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;
+ }
+ delete am; // we don't need Argument Manager any longer
+
+ // ----- Begin Processing -----
+
+
+ // --> Check supposed-to-be-directory names
+
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNamein) )
+ {
+ std::cout << "KO : [" << dirNamein << "] is not a Directory."
+ << std::endl;
+ return 0;
+
+ }
+ else
+ {
+ std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
+ }
+
+ std::string systemCommand;
+
+ std::cout << "Check for output directory :[" << dirNameout << "]."
+ <<std::endl;
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // dirout not found
+ {
+ std::string strDirNameout(dirNameout); // to please gcc 4
+ systemCommand = "mkdir " +strDirNameout; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // be sure it worked
+ {
+ std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)"
+ << std::endl;
+ return 0;
+
+ }
+ else
+ {
+ std::cout << "Directory [" << dirNameout << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ std::cout << "Output Directory [" << dirNameout
+ << "] already exists; Used as is."
+ << std::endl;
+ }
+ // --> End of checking supposed-to-be-directory names
+
+ std::string strDirNamein(dirNamein);
+ // true ; get recursively the list of files
+ GDCM_NAME_SPACE::DirList dirList(strDirNamein, true);
+
+ if (listonly)
+ {
+ std::cout << "------------List of found files ------------" << std::endl;
+ dirList.Print();
+ std::cout << std::endl;
+ }
+
+
+// ======================================= The job starts here =========================
+
+ GDCM_NAME_SPACE::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ GDCM_NAME_SPACE::SerieHelper *s; // Needed to use SerieHelper::AddSeriesDetail()
+ s = GDCM_NAME_SPACE::SerieHelper::New();
+
+ std::string token = "%%%"; // Hope it's enough!
+
+ GDCM_NAME_SPACE::File *f;
+ std::vector<std::string> tokens;
+ std::vector<std::string> tokensForFileName;
+
+ if (verbose)
+ std::cout << "------------------Print Break levels-----------------" << std::endl;
+
+ std::string userFileIdentifier;
+ SortedFiles sf;
+
+ s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name (false : no convert)
+
+ // You may prefer 0020 0010 Study ID
+ // use :
+ // s->AddSeriesDetail(0x0020, 0x0010, true);
+ // Avoid using 0008 0020 Study Date,
+ // since you may have more than one study, for a given Patient, at a given Date!
+ // or the field may be empty!
+ s->AddSeriesDetail(0x0020, 0x000d, false); // Study Instance UID (false : no convert)
+
+
+ // You may prefer 0020 0011 Series Number
+ // use :
+ // s->AddSeriesDetail(0x0020, 0x0011, true);
+ s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID (false : no convert)
+
+ // Feel free to add more fields, if they can help a suitable (for you)
+ // image sorting
+
+// Loop on all the gdcm-readable files
+ for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ f = GDCM_NAME_SPACE::File::New();
+ f->SetLoadMode(loadMode);
+ f->SetFileName( *it );
+ f->Load();
+
+ std::string strSeriesNumber;
+ int seriesNumber;
+ int j;
+
+ // keep only requested Series
+ bool keep = false;
+ if (nbSeriesToKeep != 0)
+ {
+ strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
+ seriesNumber = atoi( strSeriesNumber.c_str() );
+ for (j=0; j<nbSeriesToKeep; j++)
+ {
+ if(seriesNumber == seriesToKeep[j])
+ {
+ keep = true;
+ break;
+ }
+ }
+ if ( !keep)
+ {
+ f->Delete();
+ continue;
+ }
+ }
+ // drop all unrequested Series
+ bool drop = false;
+ if (nbSeriesToDrop != 0)
+ {
+ strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
+ seriesNumber = atoi( strSeriesNumber.c_str() );
+ for (j=0;j<nbSeriesToDrop; j++)
+ {
+ if(seriesNumber == seriesToDrop[j])
+ {
+ drop = true;
+ break;
+ }
+ }
+ if (drop)
+ {
+ f->Delete();
+ continue;
+ }
+ }
+
+ userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
+ tokens.clear();
+ GDCM_NAME_SPACE::Util::Tokenize (userFileIdentifier, tokens, token);
+
+ int imageNum; // Within FileName
+ char newName[1024];
+
+
+ // Patient's Name
+ // Study Instance UID
+ // Series Instance UID
+
+ userFileIdentifier = tokens[IND_PatientName] + token +
+ tokens[IND_StudyInstanceUID] + token +
+ tokens[IND_SerieInstanceUID] + token;
+
+ if (verbose)
+ std::cout << "[" << userFileIdentifier << "] : " << *it << std::endl;
+
+ // storing in a map ensures automatic sorting !
+ sf[userFileIdentifier] = f;
+ }
+
+ if (verbose)
+ std::cout << " " << std::endl;
+
+ std::string fullFilename, lastFilename;
+ std::string previousPatientName, currentPatientName;
+ std::string previousStudyInstanceUID, currentStudyInstanceUID;
+ std::string previousSerieInstanceUID, currentSerieInstanceUID;
+
+
+ std::string writeDir, currentWriteDir;
+ std::string currentPatientWriteDir;
+ std::string currentStudyWriteDir;
+ std::string currentSerieWriteDir;
+
+ std::string fullWriteFilename;
+
+ writeDir = GDCM_NAME_SPACE::Util::NormalizePath(dirNameout);
+ SortedFiles::iterator it2;
+
+ previousPatientName = "";
+ previousStudyInstanceUID = "";
+ previousSerieInstanceUID = "";
+
+ GDCM_NAME_SPACE::File *currentFile;
+
+ for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
+ {
+ currentFile = it2->second;
+
+ fullFilename = currentFile->GetFileName();
+ lastFilename = GDCM_NAME_SPACE::Util::GetName( fullFilename );
+ if (verbose)
+ std::cout <<" ------------------------------------------------------------------------------"
+ << std::endl << " Deal with [" << it2->first << "] : [" <<fullFilename << "]"
+ << std::endl;
+
+ tokens.clear();
+ GDCM_NAME_SPACE::Util::Tokenize (it2->first, tokens, token);
+
+ currentPatientName = tokens[IND_PatientName];
+ currentStudyInstanceUID = tokens[IND_StudyInstanceUID];
+ currentSerieInstanceUID = tokens[IND_SerieInstanceUID];
+
+ if (previousPatientName != currentPatientName)
+ {
+ previousPatientName = currentPatientName;
+ if (verbose)
+ std::cout << "==== new Patient [" << currentPatientName << "]" << std::endl;
+
+ previousPatientName = currentPatientName;
+ previousStudyInstanceUID = "";
+ previousSerieInstanceUID = "";
+
+ currentPatientWriteDir = writeDir + currentPatientName;
+
+ systemCommand = "mkdir " + currentPatientWriteDir;
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+
+ system ( systemCommand.c_str() );
+ }
+
+ if (previousStudyInstanceUID != currentStudyInstanceUID)
+ {
+ if (verbose)
+ std::cout << "==== === new Study [" << currentStudyInstanceUID << "]"
+ << std::endl;
+
+ currentStudyWriteDir = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
+ + currentStudyInstanceUID;
+ systemCommand = "mkdir " + currentStudyWriteDir;
+ system (systemCommand.c_str());
+
+ previousStudyInstanceUID = currentStudyInstanceUID;
+ }
+
+ if (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;
+ }
+
+ if ( GDCM_NAME_SPACE::Debug::GetDebugFlag())
+ std::cout << "--- --- --- --- --- " << it2->first << " "
+ << (it2->second)->GetFileName() << " "
+ << GDCM_NAME_SPACE::Util::GetName( fullFilename ) << std::endl;
+
+ // If you want to create file names of your own, here is the place!
+ // Just replace 'lastFilename' by anything that's better for you.
+ fullWriteFilename = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
+ + lastFilename;
+
+ systemCommand = "cp " + fullFilename + " " + fullWriteFilename;
+ system ( systemCommand.c_str());
+
+ }
+ return 0;
+ }
+
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