Merge pull request #206 from sherryzyh/main

Graph operations compatible with np array

causallearn/graph/Dag.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 from itertools import combinations
-from typing import List
+from typing import List, Optional, Union
 
 import networkx as nx
 import numpy as np
@@ -18,8 +18,23 @@
 # or latent, with at most one edge per node pair, and no edges to self.
 class Dag(GeneralGraph):
 
-    def __init__(self, nodes: List[Node]):
-
+    def __init__(self, nodes: Optional[List[Node]]=None, graph: Union[np.ndarray, nx.Graph, None]=None):
+        if nodes is not None:
+            self._init_from_nodes(nodes)
+        elif graph is not None:
+            if isinstance(graph, np.ndarray):
+                nodes = [Node(node_name=str(i)) for i in range(len(graph))]
+                self._init_from_nodes(nodes)
+                for i in range(len(nodes)):
+                    for j in range(len(nodes)):
+                        if graph[i, j] == 1:
+                            self.add_directed_edge(nodes[i], nodes[j])
+            else:
+                pass
+        else:
+            raise ValueError("Dag.__init__() requires argument 'nodes' or 'graph'")
+
+    def _init_from_nodes(self, nodes: List[Node]):
         # for node in nodes:
         #     if not isinstance(node, type(GraphNode)):
         #         raise TypeError("Graphs must be instantiated with a list of GraphNodes")

causallearn/graph/Node.py

@@ -2,27 +2,34 @@
 
 # Represents an object with a name, node type, and position that can serve as a
 # node in a graph.
+from typing import Optional
 from causallearn.graph.NodeType import NodeType
 from causallearn.graph.NodeVariableType import NodeVariableType
 
 
 class Node:
+    node_type: NodeType
+    node_name: str
 
+    def __init__(self, node_name: Optional[str] = None, node_type: Optional[NodeType] = None) -> None:
+        self.node_name = node_name
+        self.node_type = node_type
+
     #  @return the name of the variable.
     def get_name(self) -> str:
-        pass
+        return self.node_name
 
     # set the name of the variable
     def set_name(self, name: str):
-        pass
+        self.node_name = name
 
     # @return the node type of the variable
     def get_node_type(self) -> NodeType:
-        pass
+        return self.node_type
 
     # set the node type of the variable
     def set_node_type(self, node_type: NodeType):
-        pass
+        self.node_type = node_type
 
     # @return the intervention type
     def get_node_variable_type(self) -> NodeVariableType:
@@ -35,7 +42,7 @@ def set_node_variable_type(self, var_type: NodeVariableType):
 
     # @return the name of the node as its string representation
     def __str__(self):
-        pass
+        return self.node_name
 
     # @return the x coordinate of the center of the node
     def get_center_x(self) -> int:
@@ -59,7 +66,7 @@ def set_center(self, center_x: int, center_y: int):
 
     # @return a hashcode for this variable
     def __hash__(self):
-        pass
+        return hash(self.node_name)
 
     # @return true iff this variable is equal to the given variable
     def __eq__(self, other):

causallearn/utils/DAG2CPDAG.py

@@ -1,3 +1,4 @@
+from typing import Union
 import numpy as np
 
 from causallearn.graph.Dag import Dag
@@ -6,7 +7,7 @@
 from causallearn.graph.GeneralGraph import GeneralGraph
 
 
-def dag2cpdag(G: Dag) -> GeneralGraph:
+def dag2cpdag(G: Union[Dag, np.ndarray]) -> GeneralGraph:
     """
     Convert a DAG to its corresponding PDAG
 
@@ -22,7 +23,13 @@ def dag2cpdag(G: Dag) -> GeneralGraph:
     -------
     Yuequn Liu@dmirlab, Wei Chen@dmirlab, Kun Zhang@CMU
     """
-
+
+    if isinstance(G, np.ndarray):
+        # convert np array to Dag graph
+        G = Dag(graph=G)
+    elif not isinstance(G, Dag):
+        raise TypeError("parameter graph should be `Dag` or `np.ndarry`")
+
     # order the edges in G
     nodes_order = list(
         map(lambda x: G.node_map[x], G.get_causal_ordering())