Added results and simulators

main_package/classes/estimators/fam_score_calculator.py

@@ -31,7 +31,7 @@ class FamScoreCalculator:
     """
 
     def __init__(self):
-        np.seterr('raise')
+        #np.seterr('raise')
         pass
 
     # region theta

main_package/classes/estimators/structure_constraint_based_estimator.py

@@ -19,6 +19,8 @@ import structure_graph.sample_path as sp
 import structure_graph.structure as st
 import optimizers.constraint_based_optimizer as optimizer
 
+from utility.decorators import timing,timing_write
+
 
 class StructureConstraintBasedEstimator(se.StructureEstimator):
     """
@@ -209,6 +211,7 @@ class StructureConstraintBasedEstimator(se.StructureEstimator):
                                                             tot_vars_count = tot_vars_count)
         optimizer_obj.optimize_structure()
 
+    @timing_write
     def ctpc_algorithm(self):
         """
         Compute the CTPC algorithm.

main_package/classes/estimators/structure_score_based_estimator.py

@@ -22,7 +22,7 @@ import estimators.fam_score_calculator as fam_score
 import optimizers.hill_climbing_search as hill
 import optimizers.tabu_search as tabu
 
-from utility.decorators import timing
+from utility.decorators import timing,timing_write
 
 
 
@@ -33,10 +33,6 @@ from multiprocessing import Pool
 
 
 
-'''
-#TODO: Create a parent class StructureEstimator and Two Subclasses (Score-Based and Constraint-Based)
-#TODO: Evaluate if it could be better to change list_edges to set for improve the performance
-'''
 
 class StructureScoreBasedEstimator(se.StructureEstimator):
     """
@@ -49,10 +45,10 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
         super().__init__(sample_path)
 
 
-    @timing
+    @timing_write
     def estimate_structure(self, max_parents:int = None, iterations_number:int= 40,
                          patience:int = None, tabu_length:int = None, tabu_rules_duration:int = None,
-                         optimizer: str = 'hill' ):
+                         optimizer: str = 'hill',disable_multiprocessing:bool= False ):
         """
         Compute the score-based algorithm to find the optimal structure
 
@@ -60,6 +56,10 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
             max_parents: maximum number of parents for each variable. If None, disabled
             iterations_number: maximum number of optimization algorithm's iteration
             patience: number of iteration without any improvement before to stop the search.If None, disabled
+            tabu_length: maximum lenght of the data structures used in the optimization process
+            tabu_rules_duration: number of iterations in which each rule keeps its value 
+            optimzer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search)
+            disable_multiprocessing: true if you desire to disable the multiprocessing operations
         Returns:
             void
 
@@ -86,7 +86,8 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
         'get the number of CPU'
         cpu_count = multiprocessing.cpu_count()
 
-        #cpu_count = 1
+        if disable_multiprocessing:
+            cpu_count = 1
 
         'Estimate the best parents for each node'
         with multiprocessing.Pool(processes=cpu_count) as pool:

main_package/classes/utility/cache.py

@@ -32,7 +32,7 @@ class Cache:
             #print("Cache State:", self.list_of_sets_of_indxs)
             #print("Look For:", parents_comb)
             result = self.actual_cache[self.list_of_sets_of_parents.index(parents_comb)]
-            print("CACHE HIT!!!!", parents_comb)
+            #print("CACHE HIT!!!!", parents_comb)
             return result
         except ValueError:
             return None

main_package/classes/utility/decorators.py

@@ -9,5 +9,20 @@ def timing(f):
         te = time()
         print (f"{f.__name__} args:[{args},{kw}] took: {te-ts} sec") 
           
+        return result
+    return wrap
+
+
+def timing_write(f):
+    @wraps(f)
+    def wrap(*args, **kw):
+        ts = time()
+        result = f(*args, **kw)
+        te = time()
+        print (f"{f.__name__} args:[{args},{kw}] took: {te-ts} sec") 
+
+        with open("../results/results.csv", 'a+') as fi:
+            fi.write(f"\n{round(te-ts,3)},")
+          
         return result
     return wrap

main_package/tests/simulators/test_simulation_constraint.py

@@ -0,0 +1,108 @@
+import sys
+sys.path.append("../../classes/")
+import glob
+import math
+import os
+import unittest
+
+import networkx as nx
+import numpy as np
+import psutil
+from line_profiler import LineProfiler
+import copy
+
+import utility.cache as ch
+import structure_graph.sample_path as sp
+import estimators.structure_constraint_based_estimator as se
+import utility.json_importer as ji
+
+
+
+class TestTabuSearch(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        pass
+
+
+
+    def test_constr(self):
+
+        list_vals= [3,4,5,6,10,15]
+        
+        list_dens = [["0.1","_01"],["0.2","_02"], ["0.3",""], ["0.4","_04"] ]
+        
+        for dens in list_dens:
+            for var_n in list_vals:
+
+                var_number= var_n
+
+                cardinality = 4
+                cardinality_string = "quaternary"
+
+                density= dens[0]
+                density_string = dens[1]
+
+
+
+                constraint = 1
+
+
+
+                index = 0 
+                num_networks=10
+
+                if var_number > 9:
+                    num_networks=3
+
+                while index < num_networks:
+                    #cls.read_files = glob.glob(os.path.join('../../data', "*.json"))
+                    self.importer = ji.JsonImporter(f"../../data/networks_and_trajectories_{cardinality_string}_data{density_string}_{var_number}.json", 
+                                                'samples', 'dyn.str', 'variables', 'Time', 'Name', index )
+                    self.s1 = sp.SamplePath(self.importer)
+                    self.s1.build_trajectories()
+                    self.s1.build_structure()
+
+
+                    true_edges = copy.deepcopy(self.s1.structure.edges)
+                    true_edges = set(map(tuple, true_edges))
+
+                    se1 = se.StructureConstraintBasedEstimator(self.s1, 0.1, 0.1)
+                    se1.ctpc_algorithm()
+
+                                    
+                    set_list_edges = set(se1.complete_graph.edges)
+
+                    
+                    n_added_fake_edges = len(set_list_edges.difference(true_edges))
+
+                    n_missing_edges = len(true_edges.difference(set_list_edges))
+
+                    n_true_positive = len(true_edges) - n_missing_edges
+
+                    precision = n_true_positive / (n_true_positive + n_added_fake_edges)
+
+                    recall = n_true_positive / (n_true_positive + n_missing_edges)
+
+                    f1_measure = round(2* (precision*recall) / (precision+recall),3)
+
+                    # print(f"n archi reali non trovati: {n_missing_edges}")
+                    # print(f"n archi non reali aggiunti: {n_added_fake_edges}")
+                    print(true_edges)
+                    print(set_list_edges)
+                    print(f"precision: {precision} ")
+                    print(f"recall: {recall} ")
+
+
+                    with open("../results/results.csv", 'a+') as fi:
+                        fi.write(f"{constraint},{var_number},{density},{cardinality},{index},{f1_measure},{round(precision,3)},{round(recall,3)}")
+
+                    index += 1
+
+        self.assertEqual(set_list_edges, true_edges)
+                
+
+
+if __name__ == '__main__':
+    unittest.main()
+

main_package/tests/simulators/test_simulation_score.py

@@ -0,0 +1,121 @@
+import sys
+sys.path.append("../../classes/")
+import glob
+import math
+import os
+import unittest
+
+import networkx as nx
+import numpy as np
+import psutil
+from line_profiler import LineProfiler
+import copy
+
+import utility.cache as ch
+import structure_graph.sample_path as sp
+import estimators.structure_score_based_estimator as se
+import utility.json_importer as ji
+
+
+
+class TestTabuSearch(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        pass
+
+
+
+    def test_constr(self):
+
+
+        list_vals= [3,4,5,6,10,15]
+        
+        list_dens = [["0.1","_01"],["0.2","_02"], ["0.3",""], ["0.4","_04"] ]
+        
+        for dens in list_dens:
+            for var_n in list_vals:
+
+                patience = 20
+
+                var_number= var_n
+
+                if var_number > 11:
+                    patience = 25
+
+                if var_number > 16:
+                    patience = 35
+
+
+                cardinality = 4
+                cardinality_string = "quaternary"
+
+                density= dens[0]
+                density_string = dens[1]
+
+                constraint = 0
+
+                index = 0 
+                num_networks=10
+
+                if var_number > 9:
+                    num_networks=3
+
+                while index < num_networks:
+                    #cls.read_files = glob.glob(os.path.join('../../data', "*.json"))
+                    self.importer = ji.JsonImporter(f"../../data/networks_and_trajectories_{cardinality_string}_data{density_string}_{var_number}.json", 
+                                                'samples', 'dyn.str', 'variables', 'Time', 'Name', index )
+                    self.s1 = sp.SamplePath(self.importer)
+                    self.s1.build_trajectories()
+                    self.s1.build_structure()
+
+
+                    true_edges = copy.deepcopy(self.s1.structure.edges)
+                    true_edges = set(map(tuple, true_edges))
+
+                    se1 = se.StructureScoreBasedEstimator(self.s1)
+                    set_list_edges = se1.estimate_structure(
+                                        max_parents = None,
+                                        iterations_number = 100,
+                                        patience = patience,
+                                        tabu_length = var_number,
+                                        tabu_rules_duration = var_number,
+                                        optimizer = 'tabu'
+                                        )
+
+                                    
+                    
+
+                    
+                    n_added_fake_edges = len(set_list_edges.difference(true_edges))
+
+                    n_missing_edges = len(true_edges.difference(set_list_edges))
+
+                    n_true_positive = len(true_edges) - n_missing_edges
+
+                    precision = n_true_positive / (n_true_positive + n_added_fake_edges)
+
+                    recall = n_true_positive / (n_true_positive + n_missing_edges)
+
+                    f1_measure = round(2* (precision*recall) / (precision+recall),3)
+
+                    # print(f"n archi reali non trovati: {n_missing_edges}")
+                    # print(f"n archi non reali aggiunti: {n_added_fake_edges}")
+                    print(true_edges)
+                    print(set_list_edges)
+                    print(f"precision: {precision} ")
+                    print(f"recall: {recall} ")
+
+                    with open("../results/results.csv", 'a+') as fi:
+                        fi.write(f"{constraint},{var_number},{density},{cardinality},{index},{f1_measure},{round(precision,3)},{round(recall,3)}")
+
+                    index += 1
+
+        self.assertEqual(set_list_edges, true_edges)
+                
+                
+
+
+if __name__ == '__main__':
+    unittest.main()
+