Add refactors

main_package/classes/json_importer.py

@@ -102,8 +102,9 @@ class JsonImporter(AbstractImporter):
         Returns:
             void
         """
-        for sample_indx, sample in enumerate(raw_data[indx][trajectories_key]):
+        self.df_samples_list = [pd.DataFrame(sample) for sample in raw_data[indx][trajectories_key]]
-            self.df_samples_list.append(pd.DataFrame(sample))
+        #for sample_indx, sample in enumerate(raw_data[indx][trajectories_key]):
+            #self.df_samples_list.append(pd.DataFrame(sample))
         self.sorter = list(self.df_samples_list[0].columns.values)[1:]
 
     def compute_row_delta_sigle_samples_frame(self, sample_frame: pd.DataFrame, time_header_label: str,
@@ -135,9 +136,9 @@ class JsonImporter(AbstractImporter):
             :columns_list: la lista contenente le colonne convertite in numpyarray
 
         """
-        columns_list = []
+        columns_list = [data_frame[column].to_numpy() for column in data_frame]
-        for column in data_frame:
+        #for column in data_frame:
-            columns_list.append(data_frame[column].to_numpy())
+            #columns_list.append(data_frame[column].to_numpy())
         return columns_list
 
     def clear_concatenated_frame(self):

main_package/classes/network_graph.py

@@ -22,10 +22,10 @@ class NetworkGraph():
         self._nodes_labels = self.graph_struct.list_of_nodes_labels()
         self.aggregated_info_about_nodes_parents = None
         self._fancy_indexing = None
-        self._time_scalar_indexing_structure = []
+        self._time_scalar_indexing_structure = None
-        self._transition_scalar_indexing_structure = []
+        self._transition_scalar_indexing_structure = None
-        self._time_filtering = []
+        self._time_filtering = None
-        self._transition_filtering = []
+        self._transition_filtering = None
 
     def init_graph(self):
         self.add_nodes(self.graph_struct.list_of_nodes_labels())
@@ -54,9 +54,11 @@ class NetworkGraph():
         sorted_parents = [x for _, x in sorted(zip(self.graph_struct.list_of_nodes_labels(), parents))]
         #print(sorted_parents)
         #print(parents)
-        p_indxes= []
+        #p_indxes= []
-        p_values = []
+        #p_values = []
-        for n in parents:
+        p_indxes = [self.get_node_indx(node) for node in parents]
+        p_values = [self.get_states_number_by_indx(indx) for indx in p_indxes]
+        """for n in parents:
             #indx = self.graph_struct.get_node_indx(n)
 
             #print(indx)
@@ -64,7 +66,7 @@ class NetworkGraph():
             node_indx = self.get_node_indx(n)
             p_indxes.append(node_indx)
             #p_values.append(self.graph_struct.get_states_number(n))
-            p_values.append(self.get_states_number_by_indx(node_indx))
+            p_values.append(self.get_states_number_by_indx(node_indx))"""
         ordered_set = (sorted_parents, p_indxes, p_values)
         #print(ordered_set)
 
@@ -73,9 +75,9 @@ class NetworkGraph():
 
     def get_ord_set_of_par_of_all_nodes(self):
         result = []
-        for node in self._nodes_labels:
+        #for node in self._nodes_labels:
-            result.append(self.get_ordered_by_indx_set_of_parents(node))
+            #result.append(self.get_ordered_by_indx_set_of_parents(node))
-        #print(result)
+        result = [self.get_ordered_by_indx_set_of_parents(node) for node in self._nodes_labels]
         return result
 
     """def get_ordered_by_indx_parents_values(self, node):
@@ -95,8 +97,9 @@ class NetworkGraph():
 
     def get_states_number_of_all_nodes_sorted(self):
         states_number_list = []
-        for node in self._nodes_labels:
+        #for node in self._nodes_labels:
-            states_number_list.append(self.get_states_number(node))
+            #states_number_list.append(self.get_states_number(node))
+        states_number_list = [self.get_states_number(node) for node in self._nodes_labels]
         return states_number_list
 
     def build_fancy_indexing_structure(self, start_indx):
@@ -132,13 +135,12 @@ class NetworkGraph():
 
     def build_time_scalar_indexing_structure(self):
         #parents_indexes_list = self._fancy_indexing
-        for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
+        """for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
-            #if not p_indxs:
-                #self._time_scalar_indexing_structure.append(np.array([self.get_states_number_by_indx(node_indx)],
-                                                                     #dtype=np.int))
-            #else:
                 self._time_scalar_indexing_structure.append(
-                    self.build_time_scalar_indexing_structure_for_a_node(node_indx, p_indxs))
+                    self.build_time_scalar_indexing_structure_for_a_node(node_indx, p_indxs))"""
+        self._time_scalar_indexing_structure = [self.build_time_scalar_indexing_structure_for_a_node(node_indx, p_indxs)
+                                                for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(),
+                                                                              self._fancy_indexing)]
 
     def build_transition_scalar_indexing_structure_for_a_node(self, node_indx, parents_indxs):
         #M_vector = np.array([self.graph_struct.variables_frame.iloc[node_id, 1],
@@ -151,23 +153,30 @@ class NetworkGraph():
 
     def build_transition_scalar_indexing_structure(self):
         #parents_indexes_list = self._fancy_indexing
-        for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
+        """for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
             self._transition_scalar_indexing_structure.append(
-                self.build_transition_scalar_indexing_structure_for_a_node(node_indx, p_indxs))
+                self.build_transition_scalar_indexing_structure_for_a_node(node_indx, p_indxs))"""
+        self._transition_scalar_indexing_structure = \
+            [self.build_transition_scalar_indexing_structure_for_a_node(node_indx, p_indxs)
+                                                      for node_indx, p_indxs in
+                                                      zip(self.graph_struct.list_of_nodes_indexes(),
+                                                          self._fancy_indexing) ]
 
     def build_time_columns_filtering_structure(self):
         #parents_indexes_list = self._fancy_indexing
-        for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
+        """for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
-            #if p_indxs.size == 0:
+                self._time_filtering.append(np.append(np.array([node_indx], dtype=np.int), p_indxs).astype(np.int))"""
-                #self._time_filtering.append(np.append(p_indxs, np.array([node_indx], dtype=np.int)))
+        self._time_filtering = [np.append(np.array([node_indx], dtype=np.int), p_indxs).astype(np.int)
-            #else:
+            for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing)]
-                self._time_filtering.append(np.append(np.array([node_indx], dtype=np.int), p_indxs).astype(np.int))
 
     def build_transition_columns_filtering_structure(self):
         #parents_indexes_list = self._fancy_indexing
         nodes_number = self.graph_struct.total_variables_number
-        for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
+        """for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(), self._fancy_indexing):
-            self._transition_filtering.append(np.array([node_indx + nodes_number, node_indx, *p_indxs], dtype=np.int))
+            self._transition_filtering.append(np.array([node_indx + nodes_number, node_indx, *p_indxs], dtype=np.int))"""
+        self._transition_filtering = [np.array([node_indx + nodes_number, node_indx, *p_indxs], dtype=np.int)
+                                      for node_indx, p_indxs in zip(self.graph_struct.list_of_nodes_indexes(),
+                                                                    self._fancy_indexing)]
 
     def get_nodes(self):
         return list(self.graph.nodes)

main_package/classes/parameters_estimator.py

@@ -2,7 +2,7 @@ import os
 
 from line_profiler import LineProfiler
 
-import numba as nb
+from numba.experimental import jitclass
 import numpy as np
 import network_graph as ng
 import sample_path as sp
@@ -63,7 +63,6 @@ class ParametersEstimator:
             self.sets_of_cims_struct.sets_of_cims[pos_index].state_residence_times,
             self.sets_of_cims_struct.sets_of_cims[pos_index].transition_matrices)
 
-
     def compute_state_res_time_for_node(self, node_indx, times, trajectory, cols_filter, scalar_indexes_struct, T):
         #print(times.size)
         #print(trajectory)

main_package/classes/sets_of_cims_container.py

@@ -8,14 +8,16 @@ class SetsOfCimsContainer:
     """
     # list_of_vars_orders contiene tutte le liste con i parent ordinati secondo il valore indx
     def __init__(self, list_of_keys, states_number_per_node, list_of_parents_states_number):
-        self.sets_of_cims = []
+        self.sets_of_cims = None
         self.init_cims_structure(list_of_keys, states_number_per_node, list_of_parents_states_number)
         #self.states_per_variable = states_number
 
     def init_cims_structure(self, keys, states_number_per_node, list_of_parents_states_number):
-        for indx, key in enumerate(keys):
+        """for indx, key in enumerate(keys):
             self.sets_of_cims.append(
-                socim.SetOfCims(key, list_of_parents_states_number[indx], states_number_per_node[indx]))
+                socim.SetOfCims(key, list_of_parents_states_number[indx], states_number_per_node[indx]))"""
+        self.sets_of_cims = [socim.SetOfCims(pair[1], list_of_parents_states_number[pair[0]], states_number_per_node[pair[0]])
+                             for pair in enumerate(keys)]
 
     def get_set_of_cims(self, node_indx):
         return self.sets_of_cims[node_indx]

main_package/classes/structure_estimator.py

@@ -4,6 +4,7 @@ import itertools
 import networkx as nx
 from scipy.stats import f as f_dist
 from scipy.stats import chi2 as chi2_dist
+from numba import njit
 
 
 
@@ -133,29 +134,17 @@ class StructureEstimator:
         return True
 
     def independence_test(self, tested_child, cim1, cim2):
-        # Fake exp test
         r1s = cim1.state_transition_matrix.diagonal()
         r2s = cim2.state_transition_matrix.diagonal()
         F_stats = cim2.cim.diagonal() / cim1.cim.diagonal()
         child_states_numb = self.sample_path.structure.get_states_number(tested_child)
-        for val in range(0, child_states_numb):  # i possibili valori di tested child TODO QUESTO CONTO DEVE ESSERE VETTORIZZATO
+        for val in range(0, child_states_numb):
-            #r1 = cim1.state_transition_matrix[val][val]
-            #r2 = cim2.state_transition_matrix[val][val]
-            #print("No Test Parent:",cim1.cim[val][val],"With Test Parent", cim2.cim[val][val])
-            #F = cim2.cim[val][val] / cim1.cim[val][val]
-
-            #print("Exponential test", F_stats[val], r1s[val], r2s[val])
-            #print(f_dist.ppf(1 - self.exp_test_sign / 2, r1, r2))
-            #print(f_dist.ppf(self.exp_test_sign / 2, r1, r2))
             if F_stats[val] < f_dist.ppf(self.exp_test_sign / 2, r1s[val], r2s[val]) or \
                     F_stats[val] > f_dist.ppf(1 - self.exp_test_sign / 2, r1s[val], r2s[val]):
                 print("CONDITIONALLY DEPENDENT EXP")
                 return False
-        # fake chi test
         M1_no_diag = self.remove_diagonal_elements(cim1.state_transition_matrix)
         M2_no_diag = self.remove_diagonal_elements(cim2.state_transition_matrix)
-        #print("M1 no diag", M1_no_diag)
-        #print("M2 no diag", M2_no_diag)
         chi_2_quantile = chi2_dist.ppf(1 - self.chi_test_alfa, child_states_numb - 1)
         """
         Ks = np.sqrt(cim1.state_transition_matrix.diagonal() / cim2.state_transition_matrix.diagonal())
@@ -181,6 +170,8 @@ class StructureEstimator:
 
     def one_iteration_of_CTPC_algorithm(self, var_id):
         u = list(self.complete_graph.predecessors(var_id))
+        #TODO aggiungere qui il filtraggio del complete_graph_frame verso il nodo di arrivo 'To' var_id e passare il frame a complete test
+        #TODO trovare un modo per passare direttamente anche i valori delle variabili comprese nel test del nodo var_id
         tests_parents_numb = len(u)
         #print(u)
         b = 0

main_package/tests/test_structure_estimator.py

@@ -1,5 +1,6 @@
 import unittest
 from line_profiler import LineProfiler
+from multiprocessing import  Pool
 
 import sample_path as sp
 import structure_estimator as se