from Cmodel import Cmodel import unittest import copy import os import json class TestCmodel(unittest.TestCase): def setUp(self): dpkgRoot = os.path.join('..' ,'examples', 'foo') dpkg = json.load(open(os.path.join(dpkgRoot, 'ssm.json'))) self.m = Cmodel(dpkgRoot, dpkg) def test_change_user_input(self): x = self.m.change_user_input('r0*2*correct_rate(v)') self.assertEqual(x, ['r0', '*', '2', '*', 'correct_rate', '(', 'v', ')']) def test_par_sv(self): self.assertEqual(self.m.par_sv, ['I_nyc', 'I_paris', 'S_nyc', 'S_paris']) def test_remainder(self): self.assertEqual(self.m.remainder, ['R_nyc', 'R_paris']) def test_par_proc(self): self.assertEqual(self.m.par_proc, ['r0_nyc', 'r0_paris', 'v']) def test_par_disp(self): self.assertEqual(self.m.par_disp, ['vol']) def test_par_obs(self): self.assertEqual(self.m.par_obs, ['phi', 'rep_all_CDC_inc', 'rep_all_google_inc', 'rep_nyc_CDC_inc', 'rep_paris_CDC_prev']) def test_par_forced(self): self.assertEqual(self.m.par_forced, ['N_nyc', 'N_paris', 'mu_b_nyc', 'mu_b_paris', 'mu_d_nyc', 'mu_d_paris', 'prop_all_CDC_inc', 'prop_all_google_inc', 'prop_nyc_CDC_inc', 'prop_paris_CDC_prev']) def test_par_diff(self): self.assertEqual(self.m.par_diff, ['diff__r0_nyc', 'diff__r0_paris']) def test_par_inc(self): self.assertEqual(self.m.par_inc, ['Inc_in_nyc', 'Inc_out']) def test_par_noise(self): self.assertEqual(self.m.par_noise, ['sto']) def test_par_other(self): self.assertEqual(self.m.par_other, []) def test_pow2star(self): self.assertEqual(self.m.pow2star('pow(x, 2)'), '(x)**(2)') self.assertEqual(self.m.pow2star('pow(pow(x,2), pow(2, 3))'), '((x)**(2))**((2)**(3))') self.assertEqual(self.m.pow2star('a+ sin((x))+pow(pow(x,2), pow(2, 3))+cos(x)'), 'a+sin((x))+((x)**(2))**((2)**(3))+cos(x)') def test_make_C_term(self): terms = [ {'x': 'mu_b_paris*(1.0+v*sin((v/N_paris+(mu_b_paris)))) + r0_paris', #input 'h': 'mu_b_paris*(v*sin(mu_b_paris+v/N_paris)+1.0)+r0_paris', #expected human output 'c': 'gsl_spline_eval(calc->spline[ORDER_mu_b_paris],t,calc->acc[ORDER_mu_b_paris])*(gsl_vector_get(par,ORDER_v)*sin(gsl_spline_eval(calc->spline[ORDER_mu_b_paris],t,calc->acc[ORDER_mu_b_paris])+gsl_vector_get(par,ORDER_v)/gsl_spline_eval(calc->spline[ORDER_N_paris],t,calc->acc[ORDER_N_paris]))+1.0)+diffed[ORDER_diff__r0_paris]'}, #expected C output {'x': 'N_paris-S_paris-I_paris+S_paris+I_paris', 'h': 'N_paris', 'c': 'gsl_spline_eval(calc->spline[ORDER_N_paris],t,calc->acc[ORDER_N_paris])'}, {'x': 'rep_all_CDC_inc*(1.0-rep_all_CDC_inc)*prop_all_CDC_inc*x + (rep_all_CDC_inc*phi*prop_all_CDC_inc*x)**2', 'h': 'pow(phi,2)*pow(prop_all_CDC_inc,2)*pow(rep_all_CDC_inc,2)*pow(x,2)+prop_all_CDC_inc*rep_all_CDC_inc*x*(-rep_all_CDC_inc+1.0)', 'c': 'pow(gsl_vector_get(par,ORDER_phi),2)*pow(gsl_spline_eval(calc->spline[ORDER_prop_all_CDC_inc],t,calc->acc[ORDER_prop_all_CDC_inc]),2)*pow(gsl_vector_get(par,ORDER_rep_all_CDC_inc),2)*pow(x,2)+gsl_spline_eval(calc->spline[ORDER_prop_all_CDC_inc],t,calc->acc[ORDER_prop_all_CDC_inc])*gsl_vector_get(par,ORDER_rep_all_CDC_inc)*x*(-gsl_vector_get(par,ORDER_rep_all_CDC_inc)+1.0)'}, ] for t in terms: self.assertEqual(self.m.make_C_term(t['x'], False, human=True), t['h']) self.assertEqual(self.m.make_C_term(t['x'], False, human=False), t['c']) def test_make_C_term_nested(self): self.assertEqual(self.m.make_C_term('correct_rate(correct_rate(x))', False, human=False), 'ssm_correct_rate(ssm_correct_rate(x,dt),dt)') self.assertEqual(self.m.make_C_term('pow(correct_rate(correct_rate(x)),2)', False, human=False), 'pow(ssm_correct_rate(ssm_correct_rate(x,dt),dt),2)') self.assertEqual(self.m.make_C_term('(correct_rate(correct_rate(x)))**(2)', False, human=False), 'pow(ssm_correct_rate(ssm_correct_rate(x,dt),dt),2)') self.assertEqual(self.m.make_C_term('correct_rate(x) + correct_rate(correct_rate(x))', False, human=False), 'ssm_correct_rate(x,dt)+ssm_correct_rate(ssm_correct_rate(x,dt),dt)') self.assertEqual(self.m.make_C_term('correct_rate(correct_rate(x))+ sin(v*x+(3*sin(r0_paris)))', False, human=False), 'ssm_correct_rate(ssm_correct_rate(x,dt),dt)+sin(gsl_vector_get(par,ORDER_v)*x+3*sin(diffed[ORDER_diff__r0_paris]))') def test_make_C_term_derivate(self): x = 'sin(2*PI*(t +r0_paris))' h = '2*PI*cos(2*PI*(r0_paris+t))' c = '2*PI*cos(2*PI*(diffed[ORDER_diff__r0_paris]+t))' self.assertEqual(self.m.make_C_term(x, False, human=True, derivate='r0_paris'), h) self.assertEqual(self.m.make_C_term(x, False, human=False, derivate='r0_paris'), c) def test_make_C_term_skip_correct_rate(self): #correct_rate is only skipped for C code x = 'mu_b_paris*(1.0+correct_rate(v)*sin((correct_rate(v)/N_paris+(mu_b_paris)))) + r0_paris' c = 'gsl_spline_eval(calc->spline[ORDER_mu_b_paris],t,calc->acc[ORDER_mu_b_paris])*((gsl_vector_get(par,ORDER_v))*sin(gsl_spline_eval(calc->spline[ORDER_mu_b_paris],t,calc->acc[ORDER_mu_b_paris])+(gsl_vector_get(par,ORDER_v))/gsl_spline_eval(calc->spline[ORDER_N_paris],t,calc->acc[ORDER_N_paris]))+1.0)+diffed[ORDER_diff__r0_paris]' self.assertEqual(self.m.make_C_term(x, True, human=False), c) def test_make_C_term_extra_terms(self): terms = [ {'x': 'heaviside(t-v)', 'c': 'heaviside(t-gsl_vector_get(par,ORDER_v))'}, {'x': 'heaviside((t-v))', 'c': 'heaviside(t-gsl_vector_get(par,ORDER_v))'}, {'x': 'ramp(t-v)', 'c': 'ramp(t-gsl_vector_get(par,ORDER_v))'}, {'x': 'correct_rate(v)', 'c': 'ssm_correct_rate(gsl_vector_get(par,ORDER_v),dt)'}, ] for t in terms: self.assertEqual(self.m.make_C_term(t['x'], False, human=False), t['c']) if __name__ == '__main__': unittest.main()