MNT: Use a namespace, as there are other things in the world called "data",

"glm", etc etc.

fsl_glm.cc

@@ -21,6 +21,8 @@ using namespace std;
 // The two strings below specify the title and example usage that is
 // printed out as the help or usage message
 
+namespace FSL_GLM {
+
   string title=string("fsl_glm")+
     string("\nAuthor: Christian F. Beckmann \nCopyright(C) 2006-2013 University of Oxford \n")+
     string(" \n Simple GLM allowing temporal or spatial regression on either text data or images\n");
@@ -309,57 +311,58 @@ using namespace std;
     write_res();
     return 0;
   }
+}
 
-  ////////////////////////////////////////////////////////////////////////////
+using namespace FSL_GLM;
 
-  int main(int argc,char *argv[]){
-    Tracer tr("main");
-    OptionParser options(title, examples);
-    try{
-      // must include all wanted options here (the order determines how
-      //  the help message is printed)
-      options.add(fnin);
-      options.add(fnout);
-      options.add(fndesign);
-      options.add(fncontrasts);
-      options.add(fnmask);
-      options.add(fnftest);
-      options.add(dofset);
-      options.add(normdes);
-      options.add(normdat);
-      options.add(perfvn);
-      options.add(perf_demean);
-      options.add(help);
-      options.add(debug);
-      options.add(outcope);
-      options.add(outz);
-      options.add(outt);
-      options.add(outp);
-      options.add(outf);
-      options.add(outpf);
-      options.add(outres);
-      options.add(outvarcb);
-      options.add(outsigsq);
-      options.add(outdata);
-      options.add(outvnscales);
-      options.add(textConfounds);
-      options.add(voxelwiseConfounds);
-      options.parse_command_line(argc, argv);
+int main(int argc,char *argv[]){
+  Tracer tr("main");
+  OptionParser options(title, examples);
+  try{
+    // must include all wanted options here (the order determines how
+    //  the help message is printed)
+    options.add(fnin);
+    options.add(fnout);
+    options.add(fndesign);
+    options.add(fncontrasts);
+    options.add(fnmask);
+    options.add(fnftest);
+    options.add(dofset);
+    options.add(normdes);
+    options.add(normdat);
+    options.add(perfvn);
+    options.add(perf_demean);
+    options.add(help);
+    options.add(debug);
+    options.add(outcope);
+    options.add(outz);
+    options.add(outt);
+    options.add(outp);
+    options.add(outf);
+    options.add(outpf);
+    options.add(outres);
+    options.add(outvarcb);
+    options.add(outsigsq);
+    options.add(outdata);
+    options.add(outvnscales);
+    options.add(textConfounds);
+    options.add(voxelwiseConfounds);
+    options.parse_command_line(argc, argv);
 
-      // line below stops the program if the help was requested or
-      //  a compulsory option was not set
-      if ( (help.value()) || (!options.check_compulsory_arguments(true)) ){
-        options.usage();
-        exit(EXIT_FAILURE);
-      }else{
-        // Call the local functions
-        return do_work(argc,argv);
-      }
-    }catch(X_OptionError& e) {
+    // line below stops the program if the help was requested or
+    //  a compulsory option was not set
+    if ( (help.value()) || (!options.check_compulsory_arguments(true)) ){
       options.usage();
-      cerr << endl << e.what() << endl;
       exit(EXIT_FAILURE);
-    }catch(std::exception &e) {
-      cerr << e.what() << endl;
+    }else{
+      // Call the local functions
+      return do_work(argc,argv);
     }
+  }catch(X_OptionError& e) {
+    options.usage();
+    cerr << endl << e.what() << endl;
+    exit(EXIT_FAILURE);
+  }catch(std::exception &e) {
+    cerr << e.what() << endl;
   }
+}