modifying

algorithms/neat/genome/debug/tools.py

@@ -0,0 +1,88 @@
+from collections import defaultdict
+
+import numpy as np
+
+
+def check_array_valid(nodes, cons, input_keys, output_keys):
+    nodes_dict, cons_dict = array2object(nodes, cons, input_keys, output_keys)
+    # assert is_DAG(cons_dict.keys()), "The genome is not a DAG!"
+
+
+def array2object(nodes, cons, input_keys, output_keys):
+    """
+    Convert a genome from array to dict.
+    :param nodes: (N, 5)
+    :param cons: (C, 4)
+    :param output_keys:
+    :param input_keys:
+    :return: nodes_dict[key: (bias, response, act, agg)], cons_dict[(i_key, o_key): (weight, enabled)]
+    """
+    # update nodes_dict
+    nodes_dict = {}
+    for i, node in enumerate(nodes):
+        if np.isnan(node[0]):
+            continue
+        key = int(node[0])
+        assert key not in nodes_dict, f"Duplicate node key: {key}!"
+
+        if key in input_keys:
+            assert np.all(np.isnan(node[1:])), f"Input node {key} must has None bias, response, act, or agg!"
+            nodes_dict[key] = (None,) * 4
+        else:
+            assert np.all(~np.isnan(node[1:])), f"Normal node {key} must has non-None bias, response, act, or agg!"
+            bias = node[1]
+            response = node[2]
+            act = node[3]
+            agg = node[4]
+            nodes_dict[key] = (bias, response, act, agg)
+
+    # check nodes_dict
+    for i in input_keys:
+        assert i in nodes_dict, f"Input node {i} not found in nodes_dict!"
+
+    for o in output_keys:
+        assert o in nodes_dict, f"Output node {o} not found in nodes_dict!"
+
+    # update connections
+    cons_dict = {}
+    for i, con in enumerate(cons):
+        if np.all(np.isnan(con)):
+            pass
+        elif np.all(~np.isnan(con)):
+            i_key = int(con[0])
+            o_key = int(con[1])
+            if (i_key, o_key) in cons_dict:
+                assert False, f"Duplicate connection: {(i_key, o_key)}!"
+            assert i_key in nodes_dict, f"Input node {i_key} not found in nodes_dict!"
+            assert o_key in nodes_dict, f"Output node {o_key} not found in nodes_dict!"
+            weight = con[2]
+            enabled = (con[3] == 1)
+            cons_dict[(i_key, o_key)] = (weight, enabled)
+        else:
+            assert False, f"Connection {i} must has all None or all non-None!"
+
+    return nodes_dict, cons_dict
+
+
+def is_DAG(edges):
+    all_nodes = set()
+    for a, b in edges:
+        if a == b:  # cycle
+            return False
+        all_nodes.union({a, b})
+
+    for node in all_nodes:
+        visited = {n: False for n in all_nodes}
+        def dfs(n):
+            if visited[n]:
+                return False
+            visited[n] = True
+            for a, b in edges:
+                if a == n:
+                    if not dfs(b):
+                        return False
+            return True
+
+        if not dfs(node):
+            return False
+    return True