Program: gdcm
Module: $RCSfile: exXCoherentFileSet.cxx,v $
Language: C++
- Date: $Date: 2007/06/15 13:18:51 $
- Version: $Revision: 1.10 $
+ Date: $Date: 2007/09/28 14:08:08 $
+ Version: $Revision: 1.11 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmFile.h"
#include "gdcmDebug.h"
#include <iostream>
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
#include "gdcmArgMgr.h"
+void removeSpecChar(std::string &s);
+
+void removeSpecChar(std::string &s) {
+ unsigned int s_size = s.size();
+ for(unsigned int i=0; i<s_size; i++)
+ {
+ if (
+ /*while(i<s_size
+ && */!( s[i] == '.' || s[i] == '%' || s[i] == '_'
+ || (s[i] >= '+' && s[i] <= '-')
+ || (s[i] >= 'a' && s[i] <= 'z')
+ || (s[i] >= '0' && s[i] <= '9')
+ || (s[i] >= 'A' && s[i] <= 'Z')))
+ {
+ s.replace(i, 1, "_"); // ImagePositionPatient related stuff will be more human readable
+ }
+ }
+
+ // deal with Dicom strings trailing '\0'
+ if(s[s_size-1] == '_')
+ s.erase(s_size-1, 1);
+
+}
+
int main(int argc, char *argv[])
{
START_USAGE(usage)
"\n exXCoherentFileSet :\n ",
"Shows the various 'XCoherent' Filesets within a directory ",
+ "Optionaly copis the images in a Directories tree ",
"usage: exXCoherentFileSet {dirin=inputDirectoryName} ",
- " { tag= group-elem | pos | ori } sort ",
+ " 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 ",
" 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 ------
am->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");
- int sort = am->ArgMgrDefined("sort");
-
+ 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;
return 0;
}
}
-
-
+
/* if unused Param we give up */
if ( am->ArgMgrPrintUnusedLabels() )
{
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);
+
+ //GDCM_NAME_SPACE::TagKey t(0x0020,0x0013);
//s->AddRestriction(t, "340", GDCM_NAME_SPACE::GDCM_LESS); // Keep only files where
- // restriction is true
+ // restriction is true
+
s->SetDirectory(dirName, true); // true : recursive exploration
// The Dicom file set is splitted into several 'Single SerieUID Files Sets'
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_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;
+
+ 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();
+ removeSpecChar(serieUID);
+
+ // --- for write
+ if (write)
+ {
+ currentSerieWriteDir = currentSerieWriteDir + dirNameout;
+ unsigned int l = strlen(dirNameout)-1;
+ if ( dirNameout[l] != '/' && dirNameout[l] != '\\')
+ 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()
+ << 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_NAME_SPACE::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;
+ removeSpecChar(xCoherentName);
+ // --- 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 << "2 " << 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;
+ 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) {
+ if (sort) {
s->OrderFileList((*i).second); // sort the XCoherent Fileset
std::cout << "ZSpacing for the file set " << s->GetZSpacing()
<< std::endl;
it != ((*i).second)->end();
++it)
{
+ controlCount ++;
fileName = (*it)->GetFileName();
std::cout << " " << fileName << 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();
- }
-
+ }
+
+ if ( controlCount == 0 )
+ std::cout << "No suitable file was found!" << std::endl;
+
s->Delete();
return 0;
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff