Added standard deviation method to StatisticsReporter.

Updated tests to match current implementation.

Author: CodeReclaimers

neat/statistics.py

@@ -2,7 +2,7 @@
 import copy
 import csv
 
-from neat.math_util import mean
+from neat.math_util import mean, stdev
 from neat.six_util import iteritems
 from neat.reporting import BaseReporter
 
@@ -26,16 +26,23 @@ def post_evaluate(self, config, population, species, best_genome):
         self.generation_statistics.append(species_stats)
         self.generation_cross_validation_statistics.append(species_cross_validation_stats)
 
-    def get_average_fitness(self):
-        """Get the per-generation average fitness."""
-        avg_fitness = []
+    def get_fitness_stat(self, f):
+        stat = []
         for stats in self.generation_statistics:
             scores = []
             for species_stats in stats.values():
                 scores.extend(species_stats.values())
-            avg_fitness.append(mean(scores))
+            stat.append(f(scores))
+
+        return stat
+
+    def get_fitness_mean(self):
+        """Get the per-generation average fitness."""
+        return self.get_fitness_stat(mean)
 
-        return avg_fitness
+    def get_fitness_stdev(self):
+        """Get the per-generation standard deviation of the fitness."""
+        return self.get_fitness_stat(stdev)
 
     def get_average_cross_validation_fitness(self):
         """Get the per-generation average cross_validation fitness."""

tests/test_activation.py

@@ -13,7 +13,7 @@ def assert_almost_equal(a, b):
         max_abs = max(abs(a), abs(b))
         abs_rel_err = abs(a - b) / max_abs
         if abs_rel_err > 1e-6:
-            raise NotAlmostEqualException()
+            raise NotAlmostEqualException("{0:.4f} !~= {1:.4f}".format(a, b))
 
 
 def test_sigmoid():
@@ -29,7 +29,7 @@ def test_sin():
 
 
 def test_gauss():
-    assert_almost_equal(activations.gauss_activation(0.0), 0.398942280401)
+    assert_almost_equal(activations.gauss_activation(0.0), 1.0)
     assert_almost_equal(activations.gauss_activation(-1.0),
                         activations.gauss_activation(1.0))
 
@@ -131,6 +131,7 @@ def test_function_set():
 
     assert not s.is_valid('foo')
 
+
 if __name__ == '__main__':
     test_sigmoid()
     test_tanh()
@@ -146,3 +147,4 @@ def test_function_set():
     test_hat()
     test_square()
     test_cube()
+

tests/test_feedforward_network.py

@@ -31,15 +31,15 @@ def test_basic():
 
     assert r.values[0] == 0.0
 
-    result = r.activate([1.0])
+    result = r.activate([0.2])
 
-    assert r.values[-1] == 1.0
+    assert r.values[-1] == 0.2
     assert_almost_equal(r.values[0], 0.731, 0.001)
     assert result[0] == r.values[0]
 
-    result = r.activate([2.0])
+    result = r.activate([0.4])
 
-    assert r.values[-1] == 2.0
+    assert r.values[-1] == 0.4
     assert_almost_equal(r.values[0], 0.881, 0.001)
     assert result[0] == r.values[0]
 
@@ -54,7 +54,7 @@ def test_basic():
 #         'compatibility_threshold':3.0,
 #         'excess_coefficient':1.0,
 #         'disjoint_coefficient':1.0,
-#         'weight_coefficient':1.0,
+#         'compatibility_weight_coefficient':1.0,
 #         'conn_add_prob':0.5,
 #         'conn_delete_prob':0.05,
 #         'node_add_prob':0.1,

tests/test_recurrent_network.py

@@ -39,21 +39,21 @@ def test_basic():
     assert len(r.values[0]) == 2
     assert len(r.values[1]) == 2
 
-    result = r.activate([1.0])
+    result = r.activate([0.2])
 
     assert r.active == 1
-    assert r.values[1][-1] == 1.0
+    assert r.values[1][-1] == 0.2
     assert_almost_equal(r.values[1][0], 0.731, 0.001)
     assert result[0] == r.values[1][0]
 
-    result = r.activate([2.0])
+    result = r.activate([0.4])
 
     assert r.active == 0
-    assert r.values[0][-1] == 2.0
+    assert r.values[0][-1] == 0.4
     assert_almost_equal(r.values[0][0], 0.881, 0.001)
     assert result[0] == r.values[0][0]
 
 
 if __name__ == '__main__':
+    test_unconnected()
     test_basic()
-    test_unconnected()