generate_pairs: added toggle for distance type.

lib/scripts/generate_pairs.py

@@ -43,6 +43,8 @@ Options:
   -b, --bins <spec>      bin specification in the form of a list of intervals
                          [default: [0.01,0.4],[0.4,0.6],[0.6,2]]
   -s, --bin-size <size>  number of pairs per bin [default: 100]
+  -e, --euclid           use euclidien distance (instead of Jensen-Shannon
+                         distance) [default: False]
   -p, --plot             show plot of pair distributions, otherwise it will
                          be written to a png file [default: False]"""
 
@@ -61,6 +63,8 @@ binspec = args["--bins"][0]
 MESSAGE("Bin specification is " + param(binspec))
 binsize = int(args["--bin-size"][0])
 MESSAGE("Bin size is " + param(binsize))
+disttype = "euclidian" if args["--euclid"] else "Jensen-Shannon"
+MESSAGE("Distance to use is " + param(disttype))
 showplot = args["--plot"]
 MESSAGE("Showing distance histogram is set to " + param(showplot == 1))
 
@@ -150,9 +154,13 @@ while min(map(lambda b: b.shape[0], pair_bins)) < binsize:
     nb_it += 1
     p1 = pick(profiles)
     p2 = pick(profiles)
-    dist = jensen_shannon_distance(p1, p2)
-    # dist = jensen_shannon_divergence(p1, p2)
-    # dist = euclidian_distance(p1, p2)
+    if disttype == "Jensen-Shannon":
+        dist = jensen_shannon_distance(p1, p2)
+        # dist = jensen_shannon_divergence(p1, p2)
+    elif disttype == "euclidian":
+        dist = euclidian_distance(p1, p2)
+    else:
+        FAILURE("Unknown distance type " + data(disttype))
 
     for i in range(nb_bins):
         if in_bin(dist, i) and pair_bins[i].shape[0] < binsize: