Add plot_graph method

PyCTBN/classes/sample_path.py

@@ -66,6 +66,11 @@ class SamplePath(object):
     def total_variables_count(self) -> int:
         return self._total_variables_count
 
+    @property
+    def has_prior_net_structure(self) -> bool:
+        return bool(self._structure.edges)
+
+
 
 
 

PyCTBN/classes/structure_estimator.py

@@ -3,9 +3,11 @@ import itertools
 import json
 import typing
 
+import matplotlib.pyplot as plt
 import networkx as nx
 import numpy as np
 from networkx.readwrite import json_graph
+#import pygraphviz
 from scipy.stats import chi2 as chi2_dist
 from scipy.stats import f as f_dist
 from tqdm import tqdm
@@ -229,11 +231,54 @@ class StructureEstimator(object):
             json.dump(res, f)
 
     def adjacency_matrix(self) -> np.ndarray:
-        """Converts the estimated structrure ``_complete_graph`` to a boolean adjacency matrix representation.
+        """Converts the estimated structure ``_complete_graph`` to a boolean adjacency matrix representation.
 
         :return: The adjacency matrix of the graph ``_complete_graph``
         :rtype: numpy.ndArray
         """
         return nx.adj_matrix(self._complete_graph).toarray().astype(bool)
 
+    def spurious_edges(self) -> typing.List:
+        """Return the spurious edges present in the estimated structure, if a prior net structure is present in
+            ``_sample_path.structure``.
+
+        :return: A list containing the spurious edges
+        :rtype: List
+        """
+        if not self._sample_path.has_prior_net_structure:
+            raise RuntimeError("Can not compute spurious edges with no prior net structure!")
+        real_graph = nx.DiGraph()
+        real_graph.add_nodes_from(self._sample_path.structure.nodes_labels)
+        real_graph.add_edges_from(self._sample_path.structure.edges)
+        return nx.difference(real_graph, self._complete_graph).edges
+
+    def plot_estimated_structure_graph(self) -> None:
+        """Plot the estimated structure in a graphical model style.
+        Spurious edges are colored in red.
+        """
+        graph_to_draw = nx.DiGraph()
+        spurious_edges = self.spurious_edges()
+        non_spurious_edges = list(set(self._complete_graph.edges) - set(spurious_edges))
+        edges_colors = ['red' if edge in spurious_edges else 'black' for edge in self._complete_graph.edges]
+        graph_to_draw.add_edges_from(spurious_edges)
+        graph_to_draw.add_edges_from(non_spurious_edges)
+        pos = nx.spring_layout(graph_to_draw)
+        options = {
+            "node_size": 2500,
+            'linewidths':2,
+            "with_labels":True,
+            "font_size":13,
+            'connectionstyle': 'arc3, rad = 0.1',
+            "arrowsize": 15,
+            "arrowstyle": 'fancy',
+            "width": 1,
+            "edge_color":edges_colors,
+        }
+
+        nx.draw(graph_to_draw, pos, **options)
+        plt.show()
+
+
+
+
 

PyCTBN/tests/test_structure_estimator.py

@@ -20,7 +20,7 @@ class TestStructureEstimator(unittest.TestCase):
     def setUpClass(cls):
         cls.read_files = glob.glob(os.path.join('./data', "*.json"))
         cls.importer = JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
-        cls.importer.import_data(0)
+        cls.importer.import_data(3)
         cls.s1 = SamplePath(cls.importer)
         cls.s1.build_trajectories()
         cls.s1.build_structure()
@@ -72,12 +72,8 @@ class TestStructureEstimator(unittest.TestCase):
         print("Execution Time: ", exec_time)
         for ed in self.s1.structure.edges:
             self.assertIn(tuple(ed), se1._complete_graph.edges)
-        tuples_edges = [tuple(rec) for rec in self.s1.structure.edges]
+        print("Spurious Edges:", se1.spurious_edges())
-        spurious_edges = []
+        se1.plot_estimated_structure_graph()
-        for ed in se1._complete_graph.edges:
-            if not(ed in tuples_edges):
-                spurious_edges.append(ed)
-        print("Spurious Edges:",spurious_edges)
 
     def test_save_results(self):
         se1 = StructureEstimator(self.s1, 0.1, 0.1)