First version of the population model example

tutorials/01_EP_single_cell/11_model_population/run.py

+#!/usr/bin/env python2
+"""
+.. _tutorial_model_population:
+
+EXAMPLE FOR MODEL POPULATION IN BENCH USING A POLLING FILE
+================
+"""
+
+from __future__ import division
+import os
+import sys
+import ast
+import argparse
+import shutil
+import warnings
+warnings.filterwarnings("ignore", category=RuntimeWarning) 
+
+from datetime import date
+from numpy import *
+from numpy.linalg import norm
+import pandas as pd
+
+
+from carputils import settings
+from carputils import bench
+from carputils import testing
+from carputils import tools
+from carputils import mesh
+
+
+def parser():
+
+    parser = tools.standard_parser()    # Generate the standard command line parser
+
+
+
+
+    parser.add_argument('--tolerance' , 
+                        type=float,
+                        default = 0.5,
+                        help='Tolerance to reach limit cycle (%)')    
+
+    parser.add_argument('--model',
+                        type = str,
+                        default = "TT2", 
+                        help='ionic model name ')
+
+    parser.add_argument('--SV-init',
+                        type = str,
+                        default = '', 
+                        help='Initialization file from where to start the simulation to limit cycle')
+
+    parser.add_argument('--bcl',
+                        type = float,
+                        default = 1000.0, 
+                        help='basic cycle length')
+
+    parser.add_argument('--dt',
+                        type = float,
+                        default = 0.01, 
+                        help='simulation time step (ms)')
+
+    parser.add_argument('--parameter' , 
+                        type=ast.literal_eval,
+                        default = ['GNa', 'Gkr','Gto'], 
+                        help='Name of parameters that will be modified for the population models')		
+
+    parser.add_argument('--use_polling_file',
+                        type = str,
+                        default = "None", 
+                        help='ionic model name ')
+
+
+
+    return parser
+
+def jobID(args):
+    ID = 'population_model_{}'.format(args.model)
+
+    return ID
+
+
+@tools.carpexample(parser, jobID)
+def run(args,job):
+    print args.polling_file
+    
+    if args.use_polling_file == "None":
+        cmd = tools.carp_cmd()
+        job.carp(cmd)
+        return
+    
+    
+    polled_param = loadtxt(args.use_polling_file, dtype='str')
+    num_param = shape(polled_param)[1]
+    polled_param = polled_param[:, arange(1,num_param,2)]
+    polled_param.astype('float')
+    
+    num_combinations = len(polled_param)
+    
+    for combination in range(num_combinations):
+    
+        polled_combination = polled_param[combination, :]
+        
+        for k in range(len(args.parameter)):
+            if k != len(args.parameter)-1:
+                modelpar = args.parameter[k] + '*' + str(float(polled_combination[k])/100) + ','
+            else:
+                modelpar = modelpar + args.parameter[k] + '*' + str(float(polled_combination[k])/100)
+        
+
+        cmd = [settings.execs.BENCH,
+            '--imp', 				args.model,
+            '--imp-par',			modelpar,
+            '--bcl', 				args.bcl,
+            '--dt-out',				1,
+            '--stim-curr', 			16,
+            '--stim-dur', 			5,
+            '--numstim', 			1,
+            '--duration', 			args.bcl, 
+            '--stim-start', 		0,
+            '--fout={}/tVI_{}'.format(os.path.join(job.ID),combination),
+            '--no-trace', 'on'
+            '--dt', 				args.dt
+            #'-R', args.SV_init,
+            ]
+        
+        print cmd
+
+        job.bash(cmd)
+
+    
+
+
+if __name__ == '__main__':
+    run()