/*=========================================================================
-
+
Program: gdcm
Module: $RCSfile: exXCoherentFileSet.cxx,v $
Language: C++
- Date: $Date: 2005/10/25 15:57:20 $
- Version: $Revision: 1.1 $
+ 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.
#include "gdcmFile.h"
#include "gdcmDebug.h"
#include <iostream>
-
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+#include "gdcmArgMgr.h"
int main(int argc, char *argv[])
-{
- gdcm::SerieHelper *s;
+{
+ 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} ",
+ " dirout=outputDirectoryName ",
+ " { tag=group-elem | pos | ori } [sort] [write] ",
+ " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] ",
+ " ",
+ " 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 ",
+ " 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_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
- std::string dirName;
- if (argc > 1)
- dirName = argv[1];
- else
+ if (am->ArgMgrDefined("usage") || argc == 1)
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ if (am->ArgMgrDefined("debug"))
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ 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;
+ }
+
+ const char *dirName = am->ArgMgrGetString("dirin");
+ if (dirName == 0)
{
- dirName = GDCM_DATA_ROOT;
+ std::cout <<std::endl
+ << "'dirin=' must be present;"
+ << std::endl;
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
}
- if (argc > 2)
- gdcm::Debug::DebugOn();
+ const char *dirNameout;
+ dirNameout = am->ArgMgrGetString("dirout",".");
+
+ 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;
+ 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_NAME_SPACE::SerieHelper *s;
+
+ 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 = new gdcm::SerieHelper();
- s->SetLoadMode(gdcm::LD_ALL); // Load everything for each File
- //s->AddRestriction(tagKey, valueToCheck); // 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 :["
<< dirName << "]" << std::endl;
s->Print();
std::cout << " ------------------------------------- Result after splitting"
<< std::endl;
+*/
+
+ std::string systemCommand;
+ std::string filenameout;
+ if (write) {
+ if (verbose)
+ 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
+ {
+ if (verbose)
+ std::cout << "Directory [" << dirNameout << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Output Directory [" << dirNameout
+ << "] already exists; Used as is."
+ << std::endl;
+ }
+ }
+ // --> 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();
- 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 " <<systemCommand << std::endl;
+ }
+ }
+ // --- end for write
+
std::cout << "Split the 'Single SerieUID' FileSet :["
- << s->GetCurrentSerieUIDFileSetUID()
- << "] " << nbFiles << " long" << std::endl;
- std::cout << "-----------------------------------" << std::endl;
- gdcm::XCoherentFileSetmap xcm = s->SplitOnOrientation(l);
- //gdcm::XCoherentFileSetmap xcm = s->SplitOnPosition(l);
-
- for (gdcm::XCoherentFileSetmap::iterator i = xcm.begin();
+ << serieUID
+ << "] " << nbFiles << " long" << std::endl;
+ std::cout << "-----------------------------------" << std::endl;
+
+ if (ori)
+ xcm = s->SplitOnOrientation(l);
+ else if (pos)
+ xcm = s->SplitOnPosition(l);
+ else if (groupelem != 0) {
+ xcm = s->SplitOnTagValue(l, groupelem[0],groupelem[1] );
+ }
+
+ for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
i != xcm.end();
++i)
{
- std::cout << "Orientation : [" << (*i).first << "]" << std::endl;
-
- // Nowadays OrderFileList() causes trouble, since some files
- // (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<gdcm::File* >::iterator it = ((*i).second)->begin();
- it != ((*i).second)->end();
- ++it)
+ 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 : ";
+ else if (pos)
+ std::cout << "Position : ";
+ 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.
+
+ 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;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff