Merge pull request #5 from artificial-life-lab/intergrate

harmonization of simulation solver method imports

causal_inference/base/lv_simulator.py

@@ -6,37 +6,12 @@
 import logging
 import datetime
 
-import h5py
-import matplotlib.pyplot as plt
-
 from causal_inference.config import RESULTS_DIR
 from causal_inference.utils.log_config import log_LV_params
 from causal_inference.base.ode_solver import ODE_solver
 from causal_inference.base.runge_kutta_solver import RungeKuttaSolver
-
-def _save_population(prey_list, predator_list):
-    filename = os.path.join(RESULTS_DIR, 'populations.h5')
-    hf = h5py.File(filename, 'w')
-    hf.create_dataset('prey_pop', data=prey_list)
-    hf.create_dataset('pred_pop', data=predator_list)
-    hf.close()
-
-def plot_population_over_time(prey_list, predator_list, save=True, filename='predator_prey'):
-    fig = plt.figure(figsize=(15, 5))
-    ax = fig.add_subplot(2, 1, 1)
-    PreyLine, = plt.plot(prey_list , color='g')
-    PredatorsLine, = plt.plot(predator_list, color='r')
-    ax.set_xscale('log')
-
-    plt.legend([PreyLine, PredatorsLine], ['Prey', 'Predators'])
-    plt.ylabel('Population')
-    plt.xlabel('Time')
-    if save:
-        plt.savefig(os.path.join(RESULTS_DIR, f"{filename}.svg"),
-                    format='svg', transparent=False, bbox_inches='tight')
-    else:
-        plt.show()
-    plt.close()
+from causal_inference.utils.writer import _save_population
+from causal_inference.utils.visualisations import plot_population_over_time
 
 def get_solver(method):
     '''
@@ -50,15 +25,15 @@ def get_solver(method):
         raise AssertionError(f'{method} is not implemented!')
     return solver
 
-def main(method):
+def main(method, results_dir):
     '''
     Main function that solves LV system.
     '''
     log_LV_params()
     solver = get_solver(method)
     prey_list, predator_list = solver._solve()
-    _save_population(prey_list, predator_list)
-    plot_population_over_time(prey_list, predator_list)
+    _save_population(prey_list, predator_list, solver.time_stamps, results_dir)
+    plot_population_over_time(prey_list, predator_list, solver.time_stamps, results_dir)
 
 if __name__ == '__main__':
     PARSER = argparse.ArgumentParser()
@@ -68,12 +43,12 @@ def main(method):
                         choices=['RK4', 'ODE'], default='RK4')
     ARGS = PARSER.parse_args()
 
-    RESULTS_DIR = os.path.join(RESULTS_DIR, '{}_{}'.format(datetime.datetime.now().strftime("%Y%h%d_%H_%M_%S"), str(ARGS.outdir)))
+    results_dir = os.path.join(RESULTS_DIR, '{}_{}'.format(datetime.datetime.now().strftime("%Y%h%d_%H_%M_%S"), str(ARGS.outdir)))
 
-    if not os.path.exists(RESULTS_DIR):
-        os.makedirs(RESULTS_DIR)
+    if not os.path.exists(results_dir):
+        os.makedirs(results_dir)
 
-    LOG_FILE = os.path.join(RESULTS_DIR, f"{ARGS.logfile}.txt")     # write logg to this file
+    LOG_FILE = os.path.join(results_dir, f"{ARGS.logfile}.txt")     # write logg to this file
     logging.basicConfig(
         level=logging.INFO,
         handlers=[
@@ -82,4 +57,4 @@ def main(method):
         ]
     )
     solver = ARGS.solver
-    main(solver)
+    main(solver, results_dir)

causal_inference/base/lv_system.py

@@ -1,20 +1,31 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 
+import numpy as np
 from causal_inference.config import LV_PARAMS
 
 class LotkaVolterra():
     '''
-    Class simulates predator-prey dynamics and solves it with 4th order Runge-Kutta method.
+    Base Lotka-Volterra Class that defines a predator-prey system.
     '''
-    def __init__(self):
-        self.A = LV_PARAMS['A']
-        self.B = LV_PARAMS['B']
-        self.C = LV_PARAMS['C']
-        self.D = LV_PARAMS['D']
-        self.time = LV_PARAMS['INITIAL_TIME']
-        self.step_size = LV_PARAMS['STEP_SIZE']
-        self.max_iterations = LV_PARAMS['MAX_ITERATIONS']
+    def __init__(self,
+                 A=LV_PARAMS['A'], B=LV_PARAMS['B'], C=LV_PARAMS['C'], D=LV_PARAMS['D'],
+                 prey_population=LV_PARAMS['INITIAL_PREY_POPULATION'],
+                 pred_population=LV_PARAMS['INITIAL_PREDATOR_POPULATION'],
+                 total_time=LV_PARAMS['TOTAL_TIME'], step_size=LV_PARAMS['STEP_SIZE'],
+                 max_iter=LV_PARAMS['MAX_ITERATIONS']):
+        # Lotka-Volterra parameters
+        self.A = A
+        self.B = B
+        self.C = C
+        self.D = D
 
-        self.prey_population = LV_PARAMS['INITIAL_PREY_POPULATION']
-        self.predator_population = LV_PARAMS['INITIAL_PREDATOR_POPULATION']
+        self.prey_population = prey_population          # Initial prey population
+        self.predator_population = pred_population      # Initial predator population
+
+        self.init_time = 0                       # initial time
+        self.total_time = total_time        # total time in units
+        self.step_size = step_size          # increment for each time step
+        self.max_iterations = max_iter      # tolerance parameter
+
+        self.time_stamps = np.arange(self.init_time, self.total_time, self.step_size)

causal_inference/base/ode_solver.py

@@ -5,7 +5,6 @@
 import numpy as np
 from scipy import integrate
 
-from causal_inference.config import LV_PARAMS
 from causal_inference.base.lv_system import LotkaVolterra
 
 class ODE_solver(LotkaVolterra):
@@ -14,20 +13,28 @@ class ODE_solver(LotkaVolterra):
     '''
     def __init__(self):
         super().__init__()
-        logging.info('Solving Lotka-Volterra predator-prey dynamics odeint solver')
+        logging.info('Simulating Lotka-Volterra predator-prey dynamics with odeint solver')
 
     @staticmethod
-    def LV_derivative(X, t, alpha, beta, delta, gamma):
-        x, y = X
-        dotx = x * (alpha - beta * y)
-        doty = y * (-delta + gamma * x)
+    def LV_derivative(t, Z, A, B, C, D):
+        '''
+        Returns the rate of change of predator and prey population
+        '''
+        x, y = Z
+        dotx = x * (A - B * y)
+        doty = y * (-C + D * x)
         return np.array([dotx, doty])
 
     def _solve(self):
-        logging.info('Computing population over time...')
-        t = np.arange(0.,self.max_iterations, self.step_size)
-        X0 = [self.prey_population, self.predator_population]
-        res = integrate.odeint(self.LV_derivative, X0, t, args=(self.A, self.B, self.C, self.D))
-        prey_list, predator_list = res.T
+        '''
+        ODE solver that returns the predator and prey populations at each time step in time series.
+        '''
+        logging.info(f'Computing population over {self.total_time} generation with step size of {self.step_size}...')
+
+        INIT_POP = [self.prey_population, self.predator_population]
+        sol = integrate.solve_ivp(self.LV_derivative, [self.init_time, self.total_time], INIT_POP, args=(self.A, self.B, self.C, self.D), dense_output=True)
+        prey_list, predator_list = sol.sol(self.time_stamps)
+
         logging.info('done!')
-        return prey_list, predator_list
+
+        return prey_list, predator_list

causal_inference/base/runge_kutta_solver.py

@@ -1,7 +1,6 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 import logging
-from math import ceil
 from causal_inference.base.lv_system import LotkaVolterra
 
 class RungeKuttaSolver(LotkaVolterra):
@@ -11,7 +10,6 @@ class RungeKuttaSolver(LotkaVolterra):
     def __init__(self):
         super().__init__()
         logging.info('Solving Lotka-Volterra predator-prey dynamics with 4th order Runge-Kutta method')
-        self.time_stamp = [self.time]
         self.prey_list = [self.prey_population]
         self.predator_list = [self.predator_population]
 
@@ -22,8 +20,6 @@ def compute_predator_rate(self, current_prey, current_predators):
         return - self.C * current_predators + self.D * current_prey * current_predators
 
     def runge_kutta_update(self, current_prey, current_predators):
-        self.time = self.time + self.step_size
-        self.time_stamp.append(self.time)
 
         k1_prey = self.step_size * self.compute_prey_rate(current_prey, current_predators)
         k1_pred = self.step_size * self.compute_predator_rate(current_prey, current_predators)
@@ -46,11 +42,17 @@ def runge_kutta_update(self, current_prey, current_predators):
         return new_prey_population, new_predator_population
 
     def _solve(self):
+        '''
+        Runge-Kutta solver that returns the predator and prey populations at each time step in time series.
+        '''
+        #initial population
         current_prey, current_predators = self.prey_population, self.predator_population
-        logging.info('Computing population over time...')
-        for gen_idx in range(ceil(self.max_iterations/self.step_size)):
+
+        logging.info(f'Computing population over {self.total_time} generation with step size of {self.step_size}...')
+
+        for step_idx in self.time_stamps[1:]:
             current_prey, current_predators = self.runge_kutta_update(current_prey, current_predators)
-            msg= f'Gen: {gen_idx} | Prey population: {current_prey} | Predator population: {current_predators}'
+            msg= f'Step: {step_idx} | Prey population: {current_prey} | Predator population: {current_predators}'
             logging.info(msg)
         print('Done!')
         return self.prey_list, self.predator_list

causal_inference/config.py

@@ -12,7 +12,7 @@
 'C' : 3.0,
 'D' : 5.0,
 'STEP_SIZE' : 0.01,
-'INITIAL_TIME' : 0,
+'TOTAL_TIME' : 20,
 'INITIAL_PREY_POPULATION' : 60,
 'INITIAL_PREDATOR_POPULATION' : 25,
 'MAX_ITERATIONS' : 200

causal_inference/utils/visualisations.py

@@ -0,0 +1,21 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+from os.path import join
+import matplotlib.pyplot as plt
+
+def plot_population_over_time(prey_list, predator_list, time_stamps, results_dir, save=True, filename='predator_prey'):
+    fig = plt.figure(figsize=(15, 5))
+    ax = fig.add_subplot(2, 1, 1)
+    PreyLine, = plt.plot(time_stamps, prey_list, color='g')
+    PredatorsLine, = plt.plot(time_stamps, predator_list, color='r')
+    ax.set_xscale('log')
+
+    plt.legend([PreyLine, PredatorsLine], ['Prey', 'Predators'])
+    plt.ylabel('Population')
+    plt.xlabel('Time')
+    if save:
+        plt.savefig(join(results_dir, f"{filename}.svg"),
+                    format='svg', transparent=False, bbox_inches='tight')
+    else:
+        plt.show()
+    plt.close()

causal_inference/utils/writer.py

@@ -0,0 +1,12 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+from os.path import join
+import h5py
+
+def _save_population(prey_list, predator_list, time_stamps, results_dir):
+    filename = join(results_dir, 'populations.h5')
+    hf = h5py.File(filename, 'w')
+    hf.create_dataset('time_stamp', data=time_stamps)
+    hf.create_dataset('prey_pop', data=prey_list)
+    hf.create_dataset('pred_pop', data=predator_list)
+    hf.close()