Merge branch 'develop' into parameters_estimation_by_variable

main_package/classes/amalgamated_cims.py

@@ -20,8 +20,9 @@ class AmalgamatedCims:
             self.sets_of_cims.append(
                 socim.SetOfCims(key, list_of_parents_states_number[indx], states_number_per_node[indx]))
 
-    def get_set_of_cims(self, node_id):
+
-        return self.sets_of_cims[node_id]
+    def get_set_of_cims(self, node_indx):
+        return self.sets_of_cims[node_indx]
 
     def get_cims_of_node(self, node_indx, cim_indx):
         return self.sets_of_cims[node_indx].get_cim(cim_indx)

main_package/classes/conditional_intensity_matrix.py

@@ -18,6 +18,7 @@ class ConditionalIntensityMatrix:
         #print("Time updating In state", state, time)
         self.state_residence_times[state] += time
 
+
     def compute_cim_coefficients(self):
         np.fill_diagonal(self.cim, self.cim.diagonal() * -1)
         self.cim = ((self.cim.T + 1) / (self.state_residence_times + 1)).T

main_package/classes/json_importer.py

@@ -27,6 +27,7 @@ class JsonImporter(AbstractImporter):
         self._df_structure = pd.DataFrame()
         self._df_variables = pd.DataFrame()
         self._concatenated_samples = None
+
         super(JsonImporter, self).__init__(files_path)
 
     def import_data(self):
@@ -115,6 +116,26 @@ class JsonImporter(AbstractImporter):
         for indx in range(len(self.df_samples_list)): # Le singole traj non servono più
             self.df_samples_list[indx] = self.df_samples_list[indx].iloc[0:0]
 
+    def compute_row_delta_sigle_samples_frame(self, sample_frame):
+        columns_header = list(sample_frame.columns.values)
+        #print(columns_header)
+        for col_name in columns_header:
+            if col_name == 'Time':
+                sample_frame[col_name + 'Delta'] = sample_frame[col_name].diff()
+            #else:
+                #sample_frame[col_name + 'Delta'] = (sample_frame[col_name].diff().bfill() != 0).astype(int)
+        #sample_frame['Delta'] = sample_frame['Time'].diff()
+        #print(sample_frame)
+
+    def compute_row_delta_in_all_samples_frames(self):
+        for sample in self.df_samples_list:
+            self.compute_row_delta_sigle_samples_frame(sample)
+        self.concatenated_samples = pd.concat(self.df_samples_list)
+        self.concatenated_samples['Time'] = self.concatenated_samples['TimeDelta']
+        del self.concatenated_samples['TimeDelta']
+        self.concatenated_samples['Time'] = self.concatenated_samples['Time'].fillna(0)
+
+
     def build_list_of_samples_array(self, data_frame):
         """
         Costruisce una lista contenente le colonne presenti nel dataframe data_frame convertendole in numpy_array
@@ -147,6 +168,7 @@ class JsonImporter(AbstractImporter):
     def variables(self):
         return self._df_variables
 
+
     @property
     def structure(self):
         return self._df_structure
@@ -165,3 +187,5 @@ print(ij.df_structure)
 print(ij.df_variables)
 print(ij.concatenated_samples)"""
 
+
+

main_package/classes/parameters_estimator.py

@@ -1,4 +1,5 @@
 import os
+
 from line_profiler import LineProfiler
 
 import numba as nb
@@ -20,6 +21,7 @@ class ParametersEstimator:
                                                      self.net_graph.get_nodes(),
                                                     self.net_graph.get_ordered_by_indx_parents_values_for_all_nodes())
 
+
     def compute_parameters(self):
         for node_indx, set_of_cims in enumerate(self.amalgamated_cims_struct.sets_of_cims):
             self.compute_state_res_time_for_node(node_indx, self.sample_path.trajectories.times,
@@ -86,6 +88,7 @@ class ParametersEstimator:
                     self.transition_scalar_index_converter[node_indx], set_of_cims.transition_matrices)
 
 
+
 # Simple Test #
 os.getcwd()
 os.chdir('..')
@@ -146,3 +149,4 @@ lp_wrapper()
         #print(cond.cim)
 print(pe.amalgamated_cims_struct.get_cims_of_node(1,[2]))
 lp.print_stats()
+

main_package/classes/sample_path.py

@@ -40,6 +40,9 @@ class SamplePath:
     def structure(self):
         return self._structure
 
+"""os.getcwd()
+os.chdir('..')
+path = os.getcwd() + '/data'
 
 
 """os.getcwd()
@@ -50,3 +53,4 @@ s1 = SamplePath(path)
 s1.build_trajectories()
 s1.build_structure()
 print(s1.trajectories[0].get_complete_trajectory())"""
+