MIND is default in site search. Bugfix: CLI sites.

src/tirl/scripts/mnd/block_to_slice.py

@@ -377,9 +377,9 @@ def jiggle(fixed, moving, cnf):
 
     # Measure grid cost: find N best location + rotation parameters
     # cost = CostMSD(moving, fixed, normalise=True)
-    # cost = CostMIND(moving, fixed, normalise=False, kernel=MK_FULL, sigma=1,
-    #                 truncate=1.5)
-    cost = CostMI(moving, fixed, normalise=False)
+    cost = CostMIND(moving, fixed, normalise=True, kernel=MK_FULL, sigma=1,
+                    truncate=1.5)
+    # cost = CostMI(moving, fixed, normalise=False)
     gridcost = []
     for y in yy:
         for x in xx:
@@ -590,7 +590,7 @@ def block_to_slice(args):
     if args.init:
         if len(args.init) > 1:
             y, x = args.init
-            cnf["regparams"]["sites"] = np.atleast_2d([float(y), float(x)])
+            cnf["regparams"]["sites"] = np.atleast_2d([float(y), float(x)]).tolist()
         elif os.path.isfile(args.init[0]):
             sites = np.loadtxt(args.init[0])
             cnf["regparams"]["sites"] = np.atleast_2d(sites).tolist()