Fixed problems with initial masking - bugs now gone from -P and -k and -l and -u

fslstats.cc

@@ -18,6 +18,8 @@ using namespace NEWIMAGE;
 using namespace MISCMATHS;
 
 bool masks_used=false;
+bool lthr_used=false;
+bool uthr_used=false;
 
 void print_usage(const string& progname) {
   cout << "Usage: avwstats++ <input> [options]" << endl << endl;
@@ -124,10 +126,8 @@ template <class T>
 int generate_masks(volume4D<T> &mask, volume4D<T> &masknz, const volume4D<T> &vin,
 		   T& lthr, T& uthr) 
 {
-  if ((lthr==42) && (uthr==8)) {  // my case of "uninitialised"
-    lthr=vin.min()-1;
-    uthr=vin.max()+1;
-  }
+  if (!lthr_used) { lthr=vin.min()-1; }
+  if (!uthr_used) { uthr=vin.max()+1; }
   mask = binarise(vin,lthr,uthr,exclusive);
   masknz = mask * ((T) 1 - binarise(vin,(T) 0.0, (T) 0.0));
   return 0;
@@ -153,11 +153,9 @@ int fmrib_main(int argc, char* argv[])
   volume4D<T> vin, vol, mask, masknz;
   read_volume4D(vol,argv[1]);
 
-  T lthr=42, uthr=8;  // special "uninitialised" codes
+  T lthr=0, uthr=0;  // these initial values are not used
   if (masks_used) {
     vin = vol;
-    lthr=vin.min()-1;
-    uthr=vin.max()+1;
     generate_masks(mask,masknz,vin,lthr,uthr);
     vol = vin * mask;
   }
@@ -197,6 +195,7 @@ int fmrib_main(int argc, char* argv[])
     } else if (sarg=="-w") {
       if (!masks_used) { 
 	if (vin.nvoxels()<1) { vin = vol; }
+	masks_used=true;
 	generate_masks(mask,masknz,vin,lthr,uthr); 
 	vol = vin * mask; 
       }
@@ -225,6 +224,7 @@ int fmrib_main(int argc, char* argv[])
     } else if (sarg=="-e") {
       if (!masks_used) { 
 	if (vin.nvoxels()<1) { vin = vol; }
+	masks_used=true;
 	generate_masks(mask,masknz,vin,lthr,uthr); 
 	vol = vin * mask; 
       }
@@ -260,10 +260,20 @@ int fmrib_main(int argc, char* argv[])
 	exit(2);
       }
       read_volume4D(mask,argv[narg]);
-      if (!samesize(mask,vol)) {
+      if (!samesize(mask[0],vol[0])) {
 	cerr << "Mask and image must be the same size" << endl;
 	exit(3);
       }
+      if ( mask.tsize() > vol.tsize() ) {
+	cerr << "Mask and image must be the same size" << endl;
+	exit(3);
+      }
+      if ( mask.tsize() != vol.tsize() ) {
+	// copy the last max volume until the correct size is reached
+	while (mask.tsize() < vol.tsize() ) {
+   	  mask.addvolume(mask[mask.maxt()]);
+        }
+      }
       if (!masks_used) {
 	masks_used=true;
 	vin = vol;
@@ -284,6 +294,7 @@ int fmrib_main(int argc, char* argv[])
 	cerr << "Must specify an argument to -l" << endl;
 	exit(2);
       }
+      lthr_used=true;
       if (!masks_used) {
 	masks_used=true;
 	vin = vol;
@@ -298,6 +309,7 @@ int fmrib_main(int argc, char* argv[])
 	cerr << "Must specify an argument to -u" << endl;
 	exit(2);
       }
+      uthr_used=true;
       if (!masks_used) {
 	masks_used=true;
 	vin = vol;
@@ -389,6 +401,12 @@ int fmrib_main(int argc, char* argv[])
     	cerr << "Percentile must be between 0 and 100" << endl;
     	exit(1);
       }
+      if (!masks_used) {
+	if (vin.nvoxels()<1) { vin = vol; }
+	masks_used=true;
+	generate_masks(mask,masknz,vin,lthr,uthr); 
+	vol = vin * mask; 
+      }
       cout << vol.percentile((float) n/100.0,masknz) << " ";
     } else {
 	cerr << "Unrecognised option: " << sarg << endl;