def default_evaluation():
"""Default evaluation of current model:
* runs particle swarm for 600 iterations followed by
* levelberg marquardt
:return: found parameter values
"""
basico.run_parameter_estimation(method='Particle Swarm', update_model=True,
settings={'method': {'Iteration Limit': 600}})
sol = basico.run_parameter_estimation(method='Levenberg - Marquardt', update_model=True)
return sol
def test_change_bounds(self):
basico.set_fit_parameters([{
'name': '(R1).k2',
'lower': 1,
'upper': 0.01
}])
with self.assertLogs(level='ERROR') as cm:
sol = basico.as_dict(basico.run_parameter_estimation())
self.assertTrue(np.isnan(sol['sol']))
def test_get_data(self):
data = basico.get_experiment_data_from_model()
self.assertEqual(len(data), 5)
set_1 = data[0]
self.assertEqual(set_1.shape, (100, 3))
names = basico.get_experiment_names()
self.assertIn('Experiment', names)
files = basico.get_experiment_filenames()
self.assertEqual(len(files), len(names))
set_2 = basico.get_data_from_experiment('Experiment')
self.assertEqual(set_2.shape, (100, 3))
sol_before = basico.run_parameter_estimation(
method=basico.PE.CURRENT_SOLUTION)
# remove data
basico.remove_experiments()
# add data back
for exp, name in zip(data, names):
basico.add_experiment(name, exp)
# since we have affected experiments, reset them
basico.set_fit_parameters(basico.get_fit_parameters())
# save to temp file
main_file = tempfile.mktemp()
basico.save_model_and_data(main_file, delete_data_on_exit=True)
# ensure it still works
sol_after = basico.run_parameter_estimation(
method=basico.PE.CURRENT_SOLUTION)
self.assertListEqual(basico.as_dict(sol_before[['sol']]),
basico.as_dict(sol_after[['sol']]))
def evaluate(self):
if self.settings is not None:
basico.set_task_settings('Parameter Estimation', self.settings)
return basico.run_parameter_estimation()
def test_statistic(self):
basico.run_parameter_estimation(method=basico.PE.CURRENT_SOLUTION)
result = basico.get_fit_statistic()
self.assertTrue(result is not None)
self.assertTrue(result['obj'] < 0.2)
def test_run(self):
sol = basico.run_parameter_estimation(
method=basico.PE.CURRENT_SOLUTION)
self.assertTrue(sol is not None)
self.assertAlmostEqual(sol.loc['(R1).k2'].sol, 1.0, places=2)