fix, clean, add checkpoints

sho/snp.py

@@ -1,31 +1,52 @@
+import sys
 import numpy as np
 import matplotlib.pyplot as plt
 import copy
 
+
 ########################################################################
 # Utilities
 ########################################################################
 
 def x(a):
+    """Return the first element of a 2-tuple.
+    >>> x([1,2])
+    1
+    """
     return a[0]
 
 
 def y(a):
+    """Return the second element of a 2-tuple.
+    >>> y([1,2])
+    2
+    """
     return a[1]
 
 
 def distance(a,b):
-    """Euclidean distance (in pixels)."""
+    """Euclidean distance (in pixels).
+
+    >>> distance( (1,1),(2,2) ) == math.sqrt(2)
+    True
+    """
     return np.sqrt( (x(a)-x(b))**2 + (y(a)-y(b))**2 )
 
 
-def highlight_sensors(domain, sensors):
+def highlight_sensors(domain, sensors, val=2):
+    """Add twos to the given domain, in the cells where the given
+    sensors are located.
+
+    >>> highlight_sensors( [[0,0],[1,1]], [(0,0),(1,1)] )
+    [[2, 0], [1, 2]]
+    """
     for s in sensors:
         # `coverage` fills the domain with ones,
         # adding twos will be visible in an image.
-        domain[y(s)][x(s)] = 2
+        domain[y(s)][x(s)] = val
     return domain
 
+
 ########################################################################
 # Objective functions
 ########################################################################
@@ -133,7 +154,9 @@ def make_init(init, **kwargs):
 def num_neighb_square(sol, scale):
     """Draw a random vector in a square of witdh `scale`
     around the given one."""
-    return sol + np.random.random(len(sol)) * scale - scale/2
+    # TODO handle constraints
+    new = sol + (np.random.random(len(sol)) * scale - scale/2)
+    return new
 
 
 def bit_neighb_square(sol, scale):
@@ -145,6 +168,7 @@ def bit_neighb_square(sol, scale):
         for px in range(len(sol[py])):
             if sol[py][px] == 1:
                 new[py][px] = 0 # Remove original position.
+                # TODO handle constraints
                 d = np.random.randint(-scale//2,scale//2,2)
                 new[py+y(d)][px+x(d)] = 1
     return new
@@ -162,38 +186,81 @@ def make_neig(neighb, **kwargs):
 # Stopping criterions
 ########################################################################
 
-def iter_max(val, sol, nb_it):
-    """Return a generator of nb_it items."""
-    # Directly return the `range` generator.
-    return range(nb_it)
-
+def iter_max(i, val, sol, nb_it):
+    if i < nb_it:
+        return True
+    else:
+        return False
 
 def make_iter(iters, **kwargs):
     """Make an iterations operator from the given function.
     A iter. op. takes a value and a solution and returns
     the current number of iterations."""
-    def cont(val, sol):
-        return iters(val, sol, **kwargs)
-    return cont
+    def f(i, val, sol):
+        return iters(i, val, sol, **kwargs)
+    return f
+
+
+# Stopping criterions that are actually just checkpoints.
+
+def combine(i, val, sol, agains):
+    """Combine  several stopping criterions in one."""
+    res = True
+    for again in agains:
+        res = res and again(i, val, sol)
+    return res
+
+
+def save(i, val, sol, filename="run.csv", fmt="{it} ; {val} ; {sol}\n"):
+    """Save all iterations to a file."""
+    # Append a line at the end of the file.
+    with open(filename.format(it=i), 'a') as fd:
+        fd.write( fmt.format(it=i, val=val, sol=sol) )
+    return True # No incidence on termination.
+
+
+def iter_log(i, val, sol, fmt="{it} {val}\n"):
+    """Print progress on stderr."""
+    sys.stderr.write( fmt.format(it=i, val=val) )
+    return True
 
 
 ########################################################################
 # Algorithms
 ########################################################################
 
-def search(func, init, neighb, iters):
-    """Iterative randomized heuristic template."""
+def random(func, init, again):
+    """Iterative random search template."""
+    best_sol = None
+    best_val = - np.inf
+    val,sol = best_val,best_sol
+    i = 0
+    while again(i, val, sol):
+        sol = init()
+        val = func(sol)
+        if val > best_val:
+            best_val = val
+            best_sol = sol
+        i += 1
+    return best_val, best_sol
+
+
+def greedy(func, init, neighb, again):
+    """Iterative randomized greedy heuristic template."""
     best_sol = init()
     best_val = func(best_sol)
-    for i in iters(best_val, best_sol):
+    val,sol = best_val,best_sol
+    i = 1
+    while again(i, val, sol):
         sol = neighb(best_sol)
         val = func(sol)
         if val > best_val:
             best_val = val
             best_sol = sol
-    return val,sol
-
+        i += 1
+    return best_val, best_sol
 
+# TODO add a simulated annealing solver.
 # TODO add a population-based stochastic heuristic template.
 
 
@@ -221,8 +288,8 @@ if __name__=="__main__":
     can.add_argument("-i", "--iters", metavar="NB", default=100, type=int,
             help="Maximum number of iterations")
 
-    can.add_argument("-s", "--seed", metavar="VAL", default=0, type=int,
-            help="Random pseudo-generator seed (0 for epoch)")
+    can.add_argument("-s", "--seed", metavar="VAL", default=None, type=int,
+            help="Random pseudo-generator seed (none for current epoch)")
 
     solvers = ["num_greedy","bit_greedy"]
     can.add_argument("-m", "--solver", metavar="NAME", choices=solvers, default="num_greedy",
@@ -244,10 +311,31 @@ if __name__=="__main__":
     # in case you would start "runs" in parallel.
     np.random.seed(the.seed)
 
+    # Weird numpy way to ensure single line print of array.
+    np.set_printoptions(linewidth = np.inf)
+
     domain = np.zeros((the.domain_width, the.domain_width))
 
+    # Common termination and checkpointing.
+    iters = make_iter(
+                combine,
+                agains = [
+                    make_iter(iter_max,
+                        nb_it = the.iters),
+                    make_iter(save,
+                        filename = the.solver+".csv",
+                        fmt = "{it} ; {val} ; {sol}\n"),
+                    make_iter(iter_log,
+                        fmt="\r{it} {val}")
+                ]
+            )
+
+    # Erase the previous file.
+    with open(the.solver+".csv", 'w') as fd:
+        fd.write("# {} {}\n".format(the.solver,the.domain_width))
+
     if the.solver == "num_greedy":
-        val,sol = search(
+        val,sol = greedy(
                 make_func(num_cover_sum,
                     domain_width = the.domain_width,
                     sensor_range = the.sensor_range * the.domain_width),
@@ -256,13 +344,12 @@ if __name__=="__main__":
                     scale = the.domain_width),
                 make_neig(num_neighb_square,
                     scale = the.domain_width/10), # TODO think of an alternative.
-                make_iter(iter_max,
-                    nb_it = the.iters)
+                iters
             )
         sensors = num_to_sensors(sol)
 
     elif the.solver == "bit_greedy":
-        val,sol = search(
+        val,sol = greedy(
                 make_func(bit_cover_sum,
                     domain_width = the.domain_width,
                     sensor_range = the.sensor_range),
@@ -271,15 +358,13 @@ if __name__=="__main__":
                     nb_sensors = the.nb_sensors),
                 make_neig(bit_neighb_square,
                     scale = the.domain_width/10),
-                make_iter(iter_max,
-                    nb_it = the.iters)
+                iters
             )
         sensors = bit_to_sensors(sol)
 
-    # TODO add a simulated annealing solver.
 
     # Fancy output.
-    print(val,":",sensors)
+    print("\n",val,":",sensors)
 
     domain = coverage(domain, sensors,
             the.sensor_range * the.domain_width)