sampler_old.py

## class to read simulation dynamics files
## and sample to timeseries, for use by inference calculators

## NEED TO ADD EXTINCTION HANDLING OT THIS CLASS, OR TO TIMME CALCULATE CLASS
## probably best post-interpolation
## i.e. extinction at t=2 => discard interpolate data point at i=1

import numpy as np
#import matplotlib.pyplot as plt

class sampler():
    
    def __init__(self, n_samples, input_file, prey_extinction_file=None, pred_extinction_file=None, plot=False):
        
        self.n_samples = n_samples
        
        self.dynamics = np.genfromtxt(input_file, delimiter=',')
	#print(self.dynamics)
        #self.ext_prey = np.genfromtxt(prey_extinction_file, delimiter=',')
        #self.ext_pred = np.genfromtxt(pred_extinction_file, delimiter=',')
        
        self.sampled_dynamics = np.zeros((3, self.n_samples))
        
        self.plot = plot
        
    def sample(self):
        
        length = np.shape(self.dynamics)[1]
        skip = np.floor( length / self.n_samples)
        
        if skip==0:
            print("warning not enough data for this resolution of sampling")
            return False
        
        s = 0
        s_id = 0
        
        while s < self.n_samples:
            
            self.sampled_dynamics[:,s] = self.dynamics[:,s_id]
            
            s += 1
            s_id += skip
        
        #if self.plot==True:
        #    
        #    plt.subplot(1,2,1)
        #    plt.plot(self.dynamics[0,:], self.dynamics[1,:], 'g')
        #    plt.plot(self.dynamics[0,:], self.dynamics[2,:], 'r')
        #    plt.subplot(1,2,2)
        #    plt.plot(self.sampled_dynamics[0,:], self.sampled_dynamics[1,:], 'go-')
        #    plt.plot(self.sampled_dynamics[0,:], self.sampled_dynamics[2,:], 'ro-')
        #    plt.show()
            
if __name__=='__main__':
    
    S = sampler(100, 'example_run.dynamics', 'example_prey.extinctions', 'example_pred.extinctions', True)
    S.sample()