diff --git a/main_package/classes/conditional_intensity_matrix.py b/main_package/classes/conditional_intensity_matrix.py index 82445dd..7523c8e 100644 --- a/main_package/classes/conditional_intensity_matrix.py +++ b/main_package/classes/conditional_intensity_matrix.py @@ -15,6 +15,7 @@ class ConditionalIntensityMatrix: def update_state_residence_time_for_state(self, state, time): #print("Time updating In state", state, time) + #print(state) self.state_residence_times[state] = self.state_residence_times[state] + time def compute_cim_coefficients(self): diff --git a/main_package/classes/json_importer.py b/main_package/classes/json_importer.py index cbe1631..ebbb7eb 100644 --- a/main_package/classes/json_importer.py +++ b/main_package/classes/json_importer.py @@ -96,8 +96,8 @@ class JsonImporter(AbstractImporter): 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) + #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) @@ -134,9 +134,10 @@ class JsonImporter(AbstractImporter): """ for indx in range(len(self.df_samples_list)): self.df_samples_list[indx] = self.df_samples_list[indx].iloc[0:0] + self.concatenated_samples = self.concatenated_samples.iloc[0:0] -ij = JsonImporter("../data") +"""ij = JsonImporter("../data") ij.import_data() #print(ij.df_samples_list[7]) print(ij.df_structure) @@ -144,4 +145,4 @@ print(ij.df_variables) #print((ij.build_list_of_samples_array(0)[1].size)) #ij.compute_row_delta_sigle_samples_frame(ij.df_samples_list[0]) ij.compute_row_delta_in_all_samples_frames() -print(ij.concatenated_samples.to_numpy()) +print(ij.concatenated_samples.to_numpy())""" diff --git a/main_package/classes/parameters_estimator.py b/main_package/classes/parameters_estimator.py index 370b5f2..9a2032f 100644 --- a/main_package/classes/parameters_estimator.py +++ b/main_package/classes/parameters_estimator.py @@ -1,6 +1,7 @@ import os import time as tm from line_profiler import LineProfiler +import numpy as np import network_graph as ng import sample_path as sp @@ -30,12 +31,18 @@ class ParametersEstimator: #print("Elapsed Time ", t1) def parameters_estimation_single_trajectory(self, trajectory): + tr_len = trajectory.shape[0] + row_length = trajectory.shape[1] + print(tr_len) + print(row_length) t0 = tm.time() for indx, row in enumerate(trajectory): - if trajectory[indx][1] == -1: + """ #if int(trajectory[indx][1]) == -1: + #break + if indx == tr_len - 2: break if trajectory[indx + 1][1] != -1: - transition = self.find_transition(trajectory[indx], trajectory[indx + 1]) + transition = self.find_transition(trajectory[indx], trajectory[indx + 1], row_length) which_node = transition[0] # print(which_node) which_matrix = self.which_matrix_to_update(row, transition[0]) @@ -43,7 +50,9 @@ class ParametersEstimator: self.amalgamated_cims_struct.update_state_transition_for_matrix(which_node, which_matrix, which_element) #changed_node = which_node - time = self.compute_time_delta(trajectory[indx], trajectory[indx + 1]) + if int(trajectory[indx][0]) == 0: + time = trajectory[indx + 1][0] + #time = self.compute_time_delta(trajectory[indx], trajectory[indx + 1]) which_element = transition[1][0] self.amalgamated_cims_struct.update_state_residence_time_for_matrix(which_node, which_matrix, which_element, time) @@ -53,20 +62,19 @@ class ParametersEstimator: # print(node) which_node = node_indx which_matrix = self.which_matrix_to_update(row, node_indx) - which_element = row[node_indx + 1] + which_element = int(row[node_indx + 1]) # print("State res time element " + str(which_element) + node) # print("State res time matrix indx" + str(which_matrix)) self.amalgamated_cims_struct.update_state_residence_time_for_matrix(which_node, which_matrix, which_element, time) t1 = tm.time() - t0 - print("Elapsed Time ", t1) + print("Elapsed Time ", t1)""" - def find_transition(self, current_row, next_row): - for indx in range(1, len(current_row)): + def find_transition(self, current_row, next_row, row_length): + for indx in range(1, row_length): if current_row[indx] != next_row[indx]: return [indx - 1, (current_row[indx], next_row[indx])] - def compute_time_delta(self, current_row, next_row): return next_row[0] - current_row[0] @@ -97,7 +105,7 @@ print(pe.amalgamated_cims_struct.get_set_of_cims(2).get_cims_number()) #pe.parameters_estimation_single_trajectory(pe.sample_path.trajectories[0].get_trajectory()) lp = LineProfiler() lp_wrapper = lp(pe.parameters_estimation_single_trajectory) -lp_wrapper(pe.sample_path.trajectories[0].get_trajectory()) +lp_wrapper(pe.sample_path.trajectories.get_trajectory()) lp.print_stats() #pe.parameters_estimation() """for matrix in pe.amalgamated_cims_struct.get_set_of_cims(1).actual_cims: diff --git a/main_package/classes/sample_path.py b/main_package/classes/sample_path.py index 9f5b7dc..a7f2be3 100644 --- a/main_package/classes/sample_path.py +++ b/main_package/classes/sample_path.py @@ -21,14 +21,16 @@ class SamplePath: def __init__(self, files_path): print() self.importer = imp.JsonImporter(files_path) - self.trajectories = [] + self.trajectories = None self.structure = None def build_trajectories(self): self.importer.import_data() - for traj_data_frame in self.importer.df_samples_list: - trajectory = tr.Trajectory(self.importer.build_list_of_samples_array(traj_data_frame)) - self.trajectories.append(trajectory) + self.importer.compute_row_delta_in_all_samples_frames() + #self.trajectories = self.importer.concatenated_samples.to_numpy() + #for traj_data_frame in self.importer.df_samples_list: + self.trajectories = tr.Trajectory(self.importer.build_list_of_samples_array(self.importer.concatenated_samples)) + #self.trajectories.append(trajectory) self.importer.clear_data_frames() def build_structure(self): @@ -38,4 +40,11 @@ class SamplePath: return len(self.trajectories) +"""os.getcwd() +os.chdir('..') +path = os.getcwd() + '/data' +s1 = SamplePath(path) +s1.build_trajectories() +s1.build_structure() +print(s1.trajectories.get_trajectory())"""