Change in options (now mask is optional)

fslmeants.cc

@@ -18,9 +18,12 @@ using namespace MISCMATHS;
 
 
 void print_usage(const string& progname) {
-  cerr << "Usage: " << progname << " <input 4D volume> <mask volume> <output text file>" 
+  cerr << "Usage: " << progname << " <input 4D volume> <output text file> [<mask volume>] " 
        << endl << endl;
-  cerr << "e.g.   " << progname << " filtered_func_data  my_mask  meants.txt" << endl;
+  cerr << "e.g.   " << progname << " filtered_func_data meants.txt my_mask" 
+       << endl;
+  cerr << "e.g.   " << progname << " filtered_func_data meants.txt" 
+       << endl;
 }
 
 
@@ -31,7 +34,7 @@ int main(int argc,char *argv[])
   Tracer tr("main");
 
   string progname=argv[0];
-  if (argc<4) { 
+  if (argc<3) { 
     print_usage(progname);
     return -1; 
   }
@@ -39,8 +42,12 @@ int main(int argc,char *argv[])
   volume4D<float> vin;
   read_volume4D(vin,argv[1]);
 
+  bool use_mask = false;
   volume<float> mask;
-  read_volume(mask,argv[2]);
+  if (argc>=4) {
+    use_mask = true;
+    read_volume(mask,argv[3]);
+  }
 
   if (!samesize(vin[0],mask)) {
     cerr << "ERROR: Mask and Input volumes have different (x,y,z) size." 
@@ -56,7 +63,8 @@ int main(int argc,char *argv[])
   for (int z=mask.minz(); z<mask.maxz(); z++) {
     for (int y=mask.miny(); y<mask.maxy(); y++) {
       for (int x=mask.minx(); x<mask.maxx(); x++) {
-	if (fabs(mask(x,y,z))>1e-8) {  // arbitrary "0" threshold
+	if ( (!use_mask) || (fabs(mask(x,y,z))>1e-8)) {  
+	    // arbitrary "0" threshold
 	  meants += vin.voxelts(x,y,z);
 	  num++;
 	}
@@ -68,7 +76,7 @@ int main(int argc,char *argv[])
   meants /= (float) num;
 
   // save the result
-  write_ascii_matrix(meants,argv[3]);
+  write_ascii_matrix(meants,argv[2]);
 
   return 0;
 }