def setUp(self):
state_init = parameters.COBB_INIT_FIG4A
setup = {'state_init': state_init, 'times': np.linspace(0, 100, 101)}
self.model = ms_approx.MixedStandApprox(setup, ZERO_PARAMS,
np.zeros(7))
def min_func(factor):
"""Function to minimise, SSE between healthy tanoak over range of rates."""
approx_tans = np.zeros_like(test_rates)
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A,
extra_spread=False)
params['max_budget'] = 1000
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12',
'beta_21', 'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
for i, rate in enumerate(test_rates):
params['rogue_rate'] = rate * factor
approx_model = ms_approx.MixedStandApprox(setup, params, beta)
approx_run = approx_model.run_policy(const_rogue_policy)
approx_tans[i] = np.sum(approx_run[0][[6, 8, 9, 11], -1])
logging.info("Approx run, Factor %f, Rate: %f, tans: %f", factor,
rate, approx_tans[i])
return np.sum(np.square(approx_tans - sim_tans))
def test_sis_accuracy(self):
"""Test non-spatial SIS setup matches analytic solution."""
beta = 0.05
mu = 1.0
I0 = 0.1
N = 100
params = get_sis_params(beta, mu)
state_init = np.zeros(15)
state_init[0] = N - I0
state_init[1] = I0
setup = {'state_init': state_init, 'times': np.linspace(0, 10.0, 101)}
inf_rates = np.zeros(7)
inf_rates[0] = beta
model = ms_approx.MixedStandApprox(setup, params, inf_rates)
model_results, *_ = model.run_policy(None)
analytic_results = sis_analytic(setup['times'], beta, mu, I0, N)
print(analytic_results)
print(model_results[1, :])
print(np.isclose(model_results[1, :], analytic_results, atol=1e-5))
self.assertTrue(
np.allclose(model_results[1, :], analytic_results, atol=1e-5))
def setUp(self):
self.params = parameters.CORRECTED_PARAMS
state_init = parameters.COBB_INIT_FIG4A
state_init[1] = state_init[0]/400
state_init[0] *= 399/400
state_init[13] = state_init[12]/400
state_init[12] *= 399/400
# Now initialise space weights and recruitment rates
self.params, state_init = utils.initialise_params(self.params, init_state=state_init)
setup = {
'state_init': state_init,
'times': np.linspace(0, 50.0, 101)
}
beta = 0.5 * np.array([0.88, 0.81, 0.65, 0.48, 5.88, 0.0, 7.37])
self.params['inf_tanoak_tanoak'] = beta[0:4]
self.params['inf_bay_to_tanoak'] = beta[4]
self.params['inf_tanoak_to_bay'] = beta[5]
self.params['inf_bay_to_bay'] = beta[6]
self.params['payoff_factor'] = 1.0
self.params['treat_eff'] = 0.75
self.params['max_budget'] = 100
self.params['rel_small_cost'] = 0.5
self.approx_model = ms_approx.MixedStandApprox(setup, self.params, beta)
def make_data(folder=None):
"""Scan over budgets to analyse change in OL control"""
if folder is None:
folder = os.path.join(os.path.realpath(__file__), '..', '..', 'data',
'budget_scan')
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A)
logging.info("Parameters: %s", params)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_params = copy.deepcopy(params)
approx_params['rogue_rate'] *= scale_and_fit_results['roguing_factor']
approx_params['rogue_cost'] /= scale_and_fit_results['roguing_factor']
approx_model = ms_approx.MixedStandApprox(setup, approx_params, beta)
# budgets = np.array([8, 10, 12, 14, 16, 18, 20])
budgets = np.array([36])
for budget in budgets:
logging.info("Budget: %f", budget)
params['max_budget'] = budget
approx_model.params['max_budget'] = budget
approx_params['max_budget'] = budget
_, control, _ = approx_model.optimise(n_stages=20,
init_policy=even_policy)
approx_model.save_optimisation(
os.path.join(folder, "budget_" + str(int(budget)) + "_OL.pkl"))
mpc_controller = mpc.Controller(setup,
params,
beta,
approx_params=approx_params)
mpc_controller.optimise(horizon=100,
time_step=0.5,
end_time=100,
update_period=20,
rolling_horz=False,
stage_len=5,
init_policy=control,
use_init_first=True)
mpc_controller.save_optimisation(
os.path.join(folder, "budget_" + str(int(budget)) + "_MPC.pkl"))
def run_optimisations(datapath):
"""Run OL and MPC frameworks using newly parameterised roguing rate."""
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
with open(os.path.join(datapath, "scaling_results.json"), "r") as infile:
global_scaling = json.load(infile)
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
control_factor = global_scaling['roguing_factor']
approx_params = copy.deepcopy(params)
approx_params['rogue_rate'] *= control_factor
approx_params['rogue_cost'] /= control_factor
approx_model = ms_approx.MixedStandApprox(setup, approx_params, beta)
def even_policy(time):
return np.array([0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1])
_ = approx_model.optimise(n_stages=20, init_policy=even_policy)
approx_model.save_optimisation(
os.path.join(datapath, "OL_GloballyScaledControl.pkl"))
ol_control = interp1d(setup['times'][:-1],
approx_model.optimisation['control'],
kind="zero",
fill_value="extrapolate")
mpc_controller = mpc.Controller(setup,
params,
beta,
approx_params=approx_params)
_ = mpc_controller.optimise(horizon=100,
time_step=0.5,
end_time=100,
update_period=20,
rolling_horz=False,
stage_len=5,
init_policy=ol_control,
use_init_first=True)
mpc_controller.save_optimisation(
os.path.join(datapath, "MPC_GloballyScaledControl.pkl"))
def make_plots(data_folder=None, fig_folder=None):
"""Generate plot of budget scan analysis"""
if data_folder is None:
data_folder = os.path.join(os.path.realpath(__file__), '..', '..',
'data', 'budget_scan')
if fig_folder is None:
fig_folder = os.path.join(os.path.realpath(__file__), '..', '..',
'figures', 'budget_scan')
budgets = np.array([8, 10, 12, 14, 16, 18, 20])
n_budgets = len(budgets)
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A)
model = ms_sim.MixedStandSimulator(setup, params)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_params = copy.deepcopy(params)
approx_params['rogue_rate'] *= scale_and_fit_results['roguing_factor']
approx_params['rogue_cost'] /= scale_and_fit_results['roguing_factor']
approx_model = ms_approx.MixedStandApprox(setup, approx_params, beta)
# Collect control proportions
order = np.array([3, 4, 5, 6, 0, 1, 2, 7, 8])
control_abs_ol = np.zeros((n_budgets, 9))
control_abs_mpc = np.zeros((n_budgets, 9))
real_objectives_ol = np.zeros(n_budgets)
real_objectives_mpc = np.zeros(n_budgets)
approx_objectives_ol = np.zeros(n_budgets)
approx_objectives_mpc = np.zeros(n_budgets)
for i, budget in enumerate(budgets):
logging.info("Budget: %f", budget)
approx_model.load_optimisation(
os.path.join(data_folder,
"budget_" + str(int(budget)) + "_OL.pkl"))
control = approx_model.optimisation['control']
control_policy = interp1d(setup['times'][:-1],
control,
kind="zero",
fill_value="extrapolate")
model.run_policy(control_policy)
approx_model.run_policy(control_policy)
control[0:3] *= params['rogue_rate'] * params['rogue_cost'] * 0.5
control[3:7] *= params['thin_rate'] * params['thin_cost'] * 0.5
control[7:] *= params['protect_rate'] * params['protect_cost'] * 0.5
control[0] *= params['rel_small_cost']
control[3] *= params['rel_small_cost']
control_abs_ol[i] = (np.sum(control, axis=1))[order] / 100
real_objectives_ol[i] = model.run['objective']
approx_objectives_ol[i] = approx_model.run['objective']
mpc_controller = mpc.Controller.load_optimisation(
os.path.join("data", "budget_scan",
"budget_" + str(int(budget)) + "_MPC.pkl"))
sim_run, approx_run = mpc_controller.run_control()
approx_model.run['state'] = approx_run[0]
approx_model.run['objective'] = approx_run[1]
model.run['state'] = sim_run[0]
model.run['objective'] = sim_run[1]
control = mpc_controller.control
control[0:3] *= params['rogue_rate'] * params['rogue_cost'] * 0.5
control[3:7] *= params['thin_rate'] * params['thin_cost'] * 0.5
control[7:] *= params['protect_rate'] * params['protect_cost'] * 0.5
control[0] *= params['rel_small_cost']
control[3] *= params['rel_small_cost']
control_abs_mpc[i] = (np.sum(control, axis=1))[order] / 100
real_objectives_mpc[i] = model.run['objective']
approx_objectives_mpc[i] = approx_model.run['objective']
# Make plot
labels = [
"Thin Tan (Small)", "Thin Tan (Large)", "Thin Bay", "Thin Red",
"Rogue Tan (Small)", "Rogue Tan (Large)", "Rogue Bay",
"Protect Tan (Small)", "Protect Tan (Large)"
]
colors = visualisation.CONTROL_COLOURS
# Open-loop plot
fig = plt.figure()
ax = fig.add_subplot(111)
ax2 = ax.twinx()
color = 'tab:red'
ax2.set_ylabel('Objective', color=color)
ax2.plot(budgets,
-1 * approx_objectives_ol,
'--',
color=color,
label='OL approximate model objective')
ax2.tick_params(axis='y', labelcolor=color)
bars = []
for i in range(9):
b = ax.bar(budgets - 10,
control_abs_ol[:, i],
bottom=np.sum(control_abs_ol[:, :i], axis=1),
color=colors[i],
width=15,
alpha=0.75)
bars.append(b)
ax2.legend(ncol=1)
ax.set_xlabel("Budget")
ax.set_ylabel("Expenditure")
color = 'tab:red'
ax2.set_ylabel('Objective', color=color)
ax2.plot(budgets,
-1 * real_objectives_mpc,
'-',
color=color,
label='MPC simulation objective')
ax2.tick_params(axis='y', labelcolor=color)
bars = []
for i in range(9):
b = ax.bar(budgets + 10,
control_abs_mpc[:, i],
bottom=np.sum(control_abs_mpc[:, :i], axis=1),
color=colors[i],
width=15,
alpha=0.75)
bars.append(b)
ax.legend(bars,
labels,
bbox_to_anchor=(0.5, -0.15),
loc="upper center",
ncol=3,
frameon=True)
ax2.legend(ncol=1, loc='upper left')
ax.set_xlabel("Budget")
ax.set_ylabel("Expenditure")
ax.set_title('Left: OL, right: MPC', fontsize=8)
ax.set_ylim([0, 900])
ax2.set_ylim([0.0, 1.8])
ax.set_xticks([0, 50, 100, 200, 300, 400, 500, 600, 700])
fig.tight_layout()
fig.savefig(os.path.join(fig_folder, "BudgetScan.pdf"), dpi=300)
def main(n_reps=10,
sigma=0.25,
append=False,
folder_name='parameter_sensitivity',
run_mpc=False):
"""Run sensitivity tests."""
os.makedirs(os.path.join('data', folder_name), exist_ok=True)
# Analysis:
# 1. First construct default parameters (corrected and scaled Cobb)
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A)
mpc_args = {
'horizon': 100,
'time_step': 0.5,
'end_time': 100,
'update_period': 20,
'rolling_horz': False,
'stage_len': 5,
'init_policy': None,
'use_init_first': True
}
ncells = np.product(setup['landscape_dims'])
# Baseline no control run
model = ms_sim.MixedStandSimulator(setup, params)
model.run_policy(control_policy=None, n_fixed_steps=None)
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
if not append:
model.save_run(
os.path.join("data", folder_name, "no_control_baseline.pkl"))
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12',
'beta_21', 'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_params = copy.deepcopy(params)
approx_params['rogue_rate'] *= scale_and_fit_results['roguing_factor']
approx_params['rogue_cost'] /= scale_and_fit_results['roguing_factor']
approx_model = ms_approx.MixedStandApprox(setup, approx_params, beta)
logging.info("Running baseline OL control")
_, baseline_ol_control_policy, exit_text = approx_model.optimise(
n_stages=20, init_policy=even_policy)
approx_model.save_optimisation(
os.path.join("data", folder_name, "ol_control_baseline.pkl"))
if run_mpc:
logging.info("Running baseline MPC control")
mpc_args['init_policy'] = baseline_ol_control_policy
mpc_controller = mpc.Controller(setup,
params,
beta,
approx_params=approx_params)
mpc_controller.optimise(**mpc_args)
mpc_controller.save_optimisation(
os.path.join("data", folder_name, "mpc_control_baseline.pkl"))
# Which parameters to perturb:
# First single numbers that can be perturbed
perturbing_params_numbers = [
'inf_bay_to_bay', 'inf_bay_to_tanoak', 'inf_tanoak_to_bay',
'nat_mort_bay', 'nat_mort_redwood', 'recov_tanoak', 'recov_bay',
'resprout_tanoak'
]
# And lists of parameters
perturbing_params_lists = [
'inf_tanoak_tanoak', 'nat_mort_tanoak', 'inf_mort_tanoak',
'trans_tanoak', 'recruit_tanoak'
]
if append:
logging.info("Loading previous dataset to append new data to")
# Read in summary data already generated
with open(os.path.join("data", folder_name, "summary.json"),
"r") as infile:
summary_results = json.load(infile)
approx_model = ms_approx.MixedStandApprox.load_optimisation_class(
os.path.join("data", folder_name, "ol_control_baseline.pkl"))
baseline_ol_control_policy = interp1d(
approx_model.setup['times'][:-1],
approx_model.optimisation['control'],
kind="zero",
fill_value="extrapolate")
n_reps = (len(summary_results), len(summary_results) + n_reps)
ol_alloc_results = np.load(
os.path.join("data", folder_name, "ol_alloc_results.npy"))
mpc_alloc_results = np.load(
os.path.join("data", folder_name, "mpc_alloc_results.npy"))
else:
# Otherwise start afresh
summary_results = []
ol_alloc_results = np.zeros((0, 9, len(setup['times']) - 1))
mpc_alloc_results = np.zeros((0, 9, len(setup['times']) - 1))
n_reps = (0, n_reps)
error_dist = truncnorm(-1.0 / sigma, np.inf, loc=1.0, scale=sigma)
for i in range(*n_reps):
# 2. Perturb these parameters using Normal distribution, sigma 25%
logging.info("Perturbing parameter set %d of %d with sigma %f", i + 1,
n_reps[1], sigma)
new_params = copy.deepcopy(params)
for param_key in perturbing_params_numbers:
new_params[param_key] = new_params[param_key] * error_dist.rvs()
for param_key in perturbing_params_lists:
new_params[param_key] = (
new_params[param_key] *
error_dist.rvs(size=len(new_params[param_key])))
# Set space weights and recruitment rates to NaN so can be recaluclated for dyn equilibrium
new_params['recruit_bay'] = np.nan
new_params['recruit_redwood'] = np.nan
new_params['space_tanoak'] = np.full(4, np.nan)
# 3. Recalculate space weights & recruitment rates to give dynamic equilibrium
new_params, _ = utils.initialise_params(
new_params, host_props=parameters.COBB_PROP_FIG4A)
# 4. Run simulation model with no control policy
model = ms_sim.MixedStandSimulator(setup, new_params)
model.run_policy(control_policy=None, n_fixed_steps=None)
model.save_run(
os.path.join("data", folder_name, "no_control_{}.pkl".format(i)))
# 5. Fit approximate model
_, beta = scale_and_fit.fit_beta(setup, new_params)
approx_new_params = copy.deepcopy(params)
approx_new_params['rogue_rate'] *= scale_and_fit_results[
'roguing_factor']
approx_new_params['rogue_cost'] /= scale_and_fit_results[
'roguing_factor']
# 6. Optimise control (open-loop)
approx_model = ms_approx.MixedStandApprox(setup, approx_new_params,
beta)
*_, exit_text = approx_model.optimise(
n_stages=20, init_policy=baseline_ol_control_policy)
if exit_text not in [
"Optimal Solution Found.", "Solved To Acceptable Level."
]:
logging.warning(
"Failed optimisation. Trying intialisation from previous solution."
)
filename = os.path.join(
os.path.dirname(os.path.realpath(__file__)), '..',
'mixed_stand_model', "BOCOP", "problem.def")
with open(filename, "r") as infile:
all_lines = infile.readlines()
all_lines[31] = "# " + all_lines[31]
all_lines[32] = "# " + all_lines[32]
all_lines[33] = all_lines[33][2:]
all_lines[34] = all_lines[34][2:]
with ms_approx._try_file_open(filename) as outfile:
outfile.writelines(all_lines)
*_, exit_text = approx_model.optimise(
n_stages=20, init_policy=baseline_ol_control_policy)
all_lines[31] = all_lines[31][2:]
all_lines[32] = all_lines[32][2:]
all_lines[33] = "# " + all_lines[33]
all_lines[34] = "# " + all_lines[34]
with ms_approx._try_file_open(filename) as outfile:
outfile.writelines(all_lines)
if exit_text not in [
"Optimal Solution Found.", "Solved To Acceptable Level."
]:
logging.error(
"Failed optimisation. Falling back to init policy.")
approx_model.save_optimisation(
os.path.join("data", folder_name, "ol_control_{}.pkl".format(i)))
# Run OL control to get objective
ol_control_policy = interp1d(setup['times'][:-1],
approx_model.optimisation['control'],
kind="zero",
fill_value="extrapolate")
sim_run = model.run_policy(ol_control_policy)
ol_obj = model.run['objective']
sim_state = np.sum(np.reshape(sim_run[0],
(ncells, 15, -1)), axis=0) / ncells
allocation = (np.array([
sim_state[1] + sim_state[4], sim_state[7] + sim_state[10],
sim_state[13],
np.sum(sim_state[0:6], axis=0),
np.sum(sim_state[6:12],
axis=0), sim_state[12] + sim_state[13], sim_state[14],
sim_state[0] + sim_state[3], sim_state[6] + sim_state[9]
])[:, :-1] * approx_model.optimisation['control'])
allocation[0:3] *= params['rogue_rate'] * params['rogue_cost']
allocation[3:7] *= params['thin_rate'] * params['thin_cost']
allocation[7:] *= params['protect_rate'] * params['protect_cost']
allocation[0] *= params['rel_small_cost']
allocation[3] *= params['rel_small_cost']
expense = utils.control_expenditure(
approx_model.optimisation['control'], new_params,
sim_state[:, :-1])
for j in range(len(setup['times']) - 1):
if expense[j] > new_params['max_budget']:
allocation[:, j] *= new_params['max_budget'] / expense[j]
ol_alloc_results = np.concatenate([ol_alloc_results, [allocation]],
axis=0)
if run_mpc:
mpc_args['init_policy'] = ol_control_policy
# Optimise control (MPC)
mpc_controller = mpc.Controller(setup,
new_params,
beta,
approx_params=approx_new_params)
*_, mpc_obj = mpc_controller.optimise(**mpc_args)
mpc_controller.save_optimisation(
os.path.join("data", folder_name,
"mpc_control_{}.pkl".format(i)))
sim_run, _ = mpc_controller.run_control()
sim_state = np.sum(np.reshape(sim_run[0], (ncells, 15, -1)),
axis=0) / ncells
allocation = (np.array([
sim_state[1] + sim_state[4], sim_state[7] + sim_state[10],
sim_state[13],
np.sum(sim_state[0:6], axis=0),
np.sum(sim_state[6:12],
axis=0), sim_state[12] + sim_state[13], sim_state[14],
sim_state[0] + sim_state[3], sim_state[6] + sim_state[9]
])[:, :-1] * mpc_controller.control)
allocation[0:3] *= params['rogue_rate'] * params['rogue_cost']
allocation[3:7] *= params['thin_rate'] * params['thin_cost']
allocation[7:] *= params['protect_rate'] * params['protect_cost']
allocation[0] *= params['rel_small_cost']
allocation[3] *= params['rel_small_cost']
expense = utils.control_expenditure(mpc_controller.control,
new_params, sim_state[:, :-1])
for j in range(len(setup['times']) - 1):
if expense[j] > new_params['max_budget']:
allocation[:, j] *= new_params['max_budget'] / expense[j]
mpc_alloc_results = np.concatenate(
[mpc_alloc_results, [allocation]], axis=0)
list_keys = [
'inf_tanoak_tanoak', 'nat_mort_tanoak', 'inf_mort_tanoak',
'trans_tanoak', 'recruit_tanoak', 'space_tanoak'
]
for key in list_keys:
new_params[key] = new_params[key].tolist()
summary_results.append({
'iteration': i,
'params': new_params,
'beta': beta.tolist(),
'ol_objective': ol_obj,
'mpc_objective': mpc_obj
})
# Write summary results to file
with open(os.path.join("data", folder_name, "summary.json"),
"w") as outfile:
json.dump(summary_results, outfile, indent=4)
# Save control allocations to file
np.save(os.path.join("data", folder_name, "ol_alloc_results.npy"),
ol_alloc_results)
np.save(os.path.join("data", folder_name, "mpc_alloc_results.npy"),
mpc_alloc_results)
def run_optimisations(ensemble_and_fit,
params,
setup,
n_optim_runs,
standard_dev,
mpc_args,
ol_pol=None):
"""Run open-loop and MPC optimisations over parameter distributions"""
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
approx_params = copy.deepcopy(params)
approx_params['rogue_rate'] *= scale_and_fit_results['roguing_factor']
approx_params['rogue_cost'] /= scale_and_fit_results['roguing_factor']
approx_model = ms_approx.MixedStandApprox(setup, approx_params,
ensemble_and_fit['fit'])
sim_model = ms_sim.MixedStandSimulator(setup, params)
if ol_pol is None:
_, ol_control, exit_text = approx_model.optimise(
n_stages=20, init_policy=even_policy)
if exit_text not in [
"Optimal Solution Found.", "Solved To Acceptable Level."
]:
logging.warning(
"Failed optimisation. Trying intialisation from previous solution."
)
filename = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..",
"mixed_stand_model", "BOCOP", "problem.def")
with open(filename, "r") as infile:
all_lines = infile.readlines()
all_lines[31] = "# " + all_lines[31]
all_lines[32] = "# " + all_lines[32]
all_lines[33] = all_lines[33][2:]
all_lines[34] = all_lines[34][2:]
with ms_approx._try_file_open(filename) as outfile:
outfile.writelines(all_lines)
_, ol_control, exit_text = approx_model.optimise(
n_stages=20, init_policy=even_policy)
all_lines[31] = all_lines[31][2:]
all_lines[32] = all_lines[32][2:]
all_lines[33] = "# " + all_lines[33]
all_lines[34] = "# " + all_lines[34]
with ms_approx._try_file_open(filename) as outfile:
outfile.writelines(all_lines)
if exit_text not in [
"Optimal Solution Found.", "Solved To Acceptable Level."
]:
raise RuntimeError("Open loop optimisation failed!!")
else:
ol_control = ol_pol
# Create parameter error distribution
if standard_dev != 0.0:
error_dist = truncnorm(-1.0 / standard_dev,
np.inf,
loc=1.0,
scale=standard_dev)
error_samples = np.reshape(error_dist.rvs(size=n_optim_runs * 7),
(n_optim_runs, 7))
else:
n_optim_runs = 1
error_samples = np.ones((n_optim_runs, 7))
# Sample from parameter distribution and run simulations
baseline_beta = np.zeros(7)
baseline_beta[:4] = params['inf_tanoak_tanoak']
baseline_beta[4] = params['inf_bay_to_tanoak']
baseline_beta[5] = params['inf_tanoak_to_bay']
baseline_beta[6] = params['inf_bay_to_bay']
parameter_samples = error_samples * baseline_beta
logging.info("Generated ensemble parameters for optimisation runs")
ol_objs = np.zeros(n_optim_runs)
for i in range(n_optim_runs):
logging.info("Using parameter set: %s", parameter_samples[i])
sim_model.params['inf_tanoak_tanoak'] = parameter_samples[i, 0:4]
sim_model.params['inf_bay_to_tanoak'] = parameter_samples[i, 4]
sim_model.params['inf_tanoak_to_bay'] = parameter_samples[i, 5]
sim_model.params['inf_bay_to_bay'] = parameter_samples[i, 6]
_, obj, _ = sim_model.run_policy(control_policy=ol_control)
ol_objs[i] = obj
logging.info("Open-loop run %d of %d done.", i + 1, n_optim_runs)
mpc_args['init_policy'] = ol_control
mpc_objs = np.zeros(n_optim_runs)
mpc_controls = np.zeros((n_optim_runs, 9, len(setup['times']) - 1))
for i in range(n_optim_runs):
logging.info("Using parameter set: %s", parameter_samples[i])
sim_model.params['inf_tanoak_tanoak'] = parameter_samples[i, 0:4]
sim_model.params['inf_bay_to_tanoak'] = parameter_samples[i, 4]
sim_model.params['inf_tanoak_to_bay'] = parameter_samples[i, 5]
sim_model.params['inf_bay_to_bay'] = parameter_samples[i, 6]
mpc_controller = mpc.Controller(setup,
sim_model.params,
ensemble_and_fit['fit'],
approx_params=approx_params)
_, _, mpc_control, mpc_obj = mpc_controller.optimise(**mpc_args)
mpc_objs[i] = mpc_obj
mpc_controls[i] = mpc_control
logging.info("MPC run %d of %d done.", i + 1, n_optim_runs)
ret_dict = {
'params': parameter_samples,
'ol_control': np.array([ol_control(t) for t in setup['times'][:-1]]).T,
'ol_objs': ol_objs,
'mpc_control': mpc_controls,
'mpc_objs': mpc_objs
}
return ret_dict
def make_data(folder=None):
"""Scan over budgets to analyse change in OL control"""
if folder is None:
folder = os.path.join(os.path.realpath(__file__), '..', '..', 'data',
'div_cost_scan')
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A)
logging.info("Parameters: %s", params)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_params = copy.deepcopy(params)
approx_params['rogue_rate'] *= scale_and_fit_results['roguing_factor']
approx_params['rogue_cost'] /= scale_and_fit_results['roguing_factor']
approx_model = ms_approx.MixedStandApprox(setup, approx_params, beta)
div_prop = np.array(
[0.0, 0.125, 0.25, 0.375, 0.5, 0.625, 0.75, 0.875, 1.0])
div_costs = div_prop / (setup['times'][-1] * np.log(3))
for div_cost, prop in zip(div_costs, div_prop):
logging.info("Diversity cost: %f", div_cost)
params['div_cost'] = div_cost
approx_params['div_cost'] = div_cost
approx_model.params['div_cost'] = div_cost
_, control, exit_text = approx_model.optimise(n_stages=20,
init_policy=even_policy)
if exit_text not in [
"Optimal Solution Found.", "Solved To Acceptable Level."
]:
logging.warning(
"Failed optimisation. Trying intialisation from previous solution."
)
filename = os.path.join(
os.path.dirname(os.path.realpath(__file__)), '..',
'mixed_stand_model', "BOCOP", "problem.def")
with open(filename, "r") as infile:
all_lines = infile.readlines()
all_lines[31] = "# " + all_lines[31]
all_lines[32] = "# " + all_lines[32]
all_lines[33] = all_lines[33][2:]
all_lines[34] = all_lines[34][2:]
with ms_approx._try_file_open(filename) as outfile:
outfile.writelines(all_lines)
_, control, exit_text = approx_model.optimise(
n_stages=20, init_policy=even_policy)
all_lines[31] = all_lines[31][2:]
all_lines[32] = all_lines[32][2:]
all_lines[33] = "# " + all_lines[33]
all_lines[34] = "# " + all_lines[34]
with ms_approx._try_file_open(filename) as outfile:
outfile.writelines(all_lines)
if exit_text not in [
"Optimal Solution Found.", "Solved To Acceptable Level."
]:
logging.error("Failed optimisation in OL optimisation.")
approx_model.save_optimisation(
os.path.join(folder, "div_cost_" + str(prop) + "_OL.pkl"))
mpc_controller = mpc.Controller(setup,
params,
beta,
approx_params=approx_params)
mpc_controller.optimise(horizon=100,
time_step=0.5,
end_time=100,
update_period=20,
rolling_horz=False,
stage_len=5,
init_policy=control,
use_init_first=True)
mpc_controller.save_optimisation(
os.path.join(folder, "div_cost_" + str(prop) + "_MPC.pkl"))
def make_plots(data_folder=None, fig_folder=None):
"""Generate plot of diversity cost scan."""
if data_folder is None:
data_folder = os.path.join(os.path.realpath(__file__), '..', '..',
'data', 'div_cost_scan')
if fig_folder is None:
fig_folder = os.path.join(os.path.realpath(__file__), '..', '..',
'figures', 'div_cost_scan')
div_props = np.array(
[0.0, 0.125, 0.25, 0.375, 0.5, 0.625, 0.75, 0.875, 1.0])
n_costs = len(div_props)
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_model = ms_approx.MixedStandApprox(setup, params, beta)
model = ms_sim.MixedStandSimulator(setup, params)
ncells = np.product(setup['landscape_dims'])
# Collect control proportions
order = np.array([3, 4, 5, 6, 0, 1, 2, 7, 8])
control_abs_ol = np.zeros((n_costs, 9))
control_abs_mpc = np.zeros((n_costs, 9))
objectives_ol = np.zeros(n_costs)
objectives_mpc = np.zeros(n_costs)
for i, div_prop in enumerate(div_props):
div_cost = div_prop / (setup['times'][-1] * np.log(3))
logging.info("Diversity cost: %f", div_cost)
approx_model.load_optimisation(
os.path.join(data_folder, "div_cost_" + str(div_prop) + "_OL.pkl"))
control = approx_model.optimisation['control']
control_policy = interp1d(setup['times'][:-1],
control,
kind="zero",
fill_value="extrapolate")
sim_run, obj, objs = model.run_policy(control_policy)
sim_state = np.sum(np.reshape(sim_run,
(ncells, 15, -1)), axis=0) / ncells
allocation = np.array([
sim_state[1] + sim_state[4], sim_state[7] + sim_state[10],
sim_state[13],
np.sum(sim_state[0:6], axis=0),
np.sum(sim_state[6:12],
axis=0), sim_state[12] + sim_state[13], sim_state[14],
sim_state[0] + sim_state[3], sim_state[6] + sim_state[9]
])[:, :-1] * control
allocation[0:3] *= params['rogue_rate'] * params['rogue_cost']
allocation[3:7] *= params['thin_rate'] * params['thin_cost']
allocation[7:] *= params['protect_rate'] * params['protect_cost']
allocation[0] *= params['rel_small_cost']
allocation[3] *= params['rel_small_cost']
expense = utils.control_expenditure(control, params, sim_state[:, :-1])
for j in range(len(setup['times']) - 1):
if expense[j] > params['max_budget']:
allocation[:, j] *= params['max_budget'] / expense[j]
control_abs_ol[i] = (np.sum(allocation, axis=1))[order] / 200
objectives_ol[i] = -1 * (obj - objs[-1])
mpc_controller = mpc.Controller.load_optimisation(
os.path.join(data_folder,
"div_cost_" + str(div_prop) + "_MPC.pkl"))
sim_run, approx_run = mpc_controller.run_control()
control = mpc_controller.control
sim_state = np.sum(np.reshape(sim_run[0],
(ncells, 15, -1)), axis=0) / ncells
allocation = np.array([
sim_state[1] + sim_state[4], sim_state[7] + sim_state[10],
sim_state[13],
np.sum(sim_state[0:6], axis=0),
np.sum(sim_state[6:12],
axis=0), sim_state[12] + sim_state[13], sim_state[14],
sim_state[0] + sim_state[3], sim_state[6] + sim_state[9]
])[:, :-1] * control
allocation[0:3] *= params['rogue_rate'] * params['rogue_cost']
allocation[3:7] *= params['thin_rate'] * params['thin_cost']
allocation[7:] *= params['protect_rate'] * params['protect_cost']
allocation[0] *= params['rel_small_cost']
allocation[3] *= params['rel_small_cost']
expense = utils.control_expenditure(control, params, sim_state[:, :-1])
for j in range(len(setup['times']) - 1):
if expense[j] > params['max_budget']:
allocation[:, j] *= params['max_budget'] / expense[j]
control_abs_mpc[i] = (np.sum(allocation, axis=1))[order] / 200
objectives_mpc[i] = -1 * (sim_run[1] - sim_run[2][-1])
# Make plot
labels = [
"Thin Tan (Small)", "Thin Tan (Large)", "Thin Bay", "Thin Red",
"Rogue Tan (Small)", "Rogue Tan (Large)", "Rogue Bay",
"Protect Tan (Small)", "Protect Tan (Large)"
]
colors = visualisation.CONTROL_COLOURS
fig = plt.figure()
gs = gridspec.GridSpec(3,
2,
width_ratios=[2, 1],
height_ratios=[0.2, 3, 1],
top=0.95,
left=0.1,
wspace=0.3,
bottom=0.3)
ax = fig.add_subplot(gs[:, 0])
ax2 = fig.add_subplot(gs[1, 1])
color = 'tab:red'
ax2.set_ylabel('Large healthy tanoak')
ax2.plot(div_props,
objectives_ol,
'--',
color=color,
label='OL tanoak objective')
bars = []
for i in range(9):
b = ax.bar(div_props - 0.015,
control_abs_ol[:, i],
bottom=np.sum(control_abs_ol[:, :i], axis=1),
color=colors[i],
width=0.015,
alpha=0.75)
bars.append(b)
ax2.plot(div_props,
objectives_mpc,
'-',
color=color,
label='MPC tanoak objective')
bars = []
for i in range(9):
b = ax.bar(div_props + 0.015,
control_abs_mpc[:, i],
bottom=np.sum(control_abs_mpc[:, :i], axis=1),
color=colors[i],
width=0.015,
alpha=0.75)
bars.append(b)
ax.legend(bars,
labels,
bbox_to_anchor=(-0.1, -0.15),
loc="upper left",
ncol=3,
frameon=True)
ax2.legend(bbox_to_anchor=(0.5, -0.3),
loc="upper center",
ncol=1,
frameon=True,
fontsize=8)
ax.set_xlabel("Diversity benefit")
ax.set_ylabel("Expenditure")
ax2.set_xlabel("Diversity benefit")
x_ticks = np.array([0.0, 0.25, 0.5, 0.75, 1.0])
offset = 0.025
ax.set_xticks(x_ticks)
ax2.set_xticks(x_ticks)
ax.tick_params(axis='x',
direction='out',
pad=7,
length=5,
color='darkgray')
ax2.tick_params(axis='x',
direction='out',
pad=7,
length=5,
color='darkgray')
data_to_axis = ax.transData + ax.transAxes.inverted()
for x_tick in x_ticks:
ax.text(data_to_axis.transform((x_tick - offset, 0))[0],
-0.025,
'OL',
ha='center',
transform=ax.transAxes,
fontsize=5)
ax.text(data_to_axis.transform((x_tick + (offset / 2), 0))[0],
-0.025,
'MPC',
ha='left',
transform=ax.transAxes,
fontsize=5)
ax.set_ylim([0, 15])
fig.text(0.01,
0.95,
"(a)",
transform=fig.transFigure,
fontsize=11,
fontweight="semibold")
fig.text(0.57,
0.95,
"(b)",
transform=fig.transFigure,
fontsize=11,
fontweight="semibold")
fig.savefig(os.path.join(fig_folder, "DivCostScan.pdf"), dpi=300)
def run_scan(datapath):
"""Scan over control scaling factor."""
factors = np.arange(0.05, 1.11, 0.01)
diff_results = np.zeros_like(factors)
# Run simulations using open-loop control policy
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A,
extra_spread=True)
approx_model = ms_approx.MixedStandApprox.load_optimisation_class(
os.path.join('data', 'ol_mpc_control', 'ol_control.pkl'))
ol_control = interp1d(setup['times'][:-1],
approx_model.optimisation['control'],
kind="zero",
fill_value="extrapolate")
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
ncells = np.product(setup['landscape_dims'])
model = ms_sim.MixedStandSimulator(setup, params)
sim_run = model.run_policy(ol_control)
sim_state = np.sum(sim_run[0].reshape((ncells, 15, -1)), axis=0) / ncells
sim_tans = np.sum(sim_state[[6, 8, 9, 11], -1])
logging.info("Sim run, healthy tans: %f", sim_tans)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_model = ms_approx.MixedStandApprox(setup, params, beta)
def min_func(factor):
"""Function to minimise, SSE between healthy tanoak using OL control."""
approx_model.params['rogue_rate'] = factor * params['rogue_rate']
approx_run = approx_model.run_policy(ol_control)
approx_tans = np.sum(approx_run[0][[6, 8, 9, 11], -1])
logging.info("Approx run, Factor %f, tans: %f", factor, approx_tans)
return np.sum(np.square(approx_tans - sim_tans))
for i, factor in enumerate(factors):
diff = min_func(factor)
diff_results[i] = diff
csv_file = os.path.join(datapath, 'scan_control.csv')
with open(csv_file, 'w', newline='') as csvfile:
spamwriter = csv.writer(csvfile,
delimiter=',',
quotechar='|',
quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow(['ControlScalingFactor', 'SSE'])
for i, factor in enumerate(factors):
spamwriter.writerow([factor, diff_results[i]])
def scale_control(datapath):
"""Parameterise roguing control in approximate model to match simulations."""
# First run simulation using open-loop policy
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A,
extra_spread=True)
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
approx_model = ms_approx.MixedStandApprox.load_optimisation_class(
os.path.join('data', 'ol_mpc_control', 'ol_control.pkl'))
ol_control = interp1d(setup['times'][:-1],
approx_model.optimisation['control'],
kind="zero",
fill_value="extrapolate")
ncells = np.product(setup['landscape_dims'])
model = ms_sim.MixedStandSimulator(setup, params)
sim_run = model.run_policy(ol_control)
sim_state = np.sum(sim_run[0].reshape((ncells, 15, -1)), axis=0) / ncells
sim_tans = np.sum(sim_state[[6, 8, 9, 11], -1])
logging.info("Sim run, healthy tans: %f", sim_tans)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_model = ms_approx.MixedStandApprox(setup, params, beta)
def min_func(factor):
"""Function to minimise, SSE between healthy tanoak over range of rates."""
approx_model.params['rogue_rate'] = factor * params['rogue_rate']
approx_run = approx_model.run_policy(ol_control)
approx_tans = np.sum(approx_run[0][[6, 8, 9, 11], -1])
logging.info("Approx run, Factor %f, tans: %f, rate: %f", factor,
approx_tans, factor * params['rogue_rate'])
return abs(approx_tans - sim_tans)
ret = minimize(min_func, [0.25], bounds=[(0, 2)])
logging.info(ret)
# Write scaling results to file
results = {'roguing_factor': ret.x[0], 'tan_diff': ret.fun}
with open(os.path.join(datapath, 'scaling_results.json'), "w") as outfile:
json.dump(results, outfile, indent=4)
def make_data(n_reps=10, folder=None, append=False):
"""Generate data analysing effect of sampling effort."""
if folder is None:
folder = os.path.join(os.path.realpath(__file__), '..', '..', 'data',
'obs_uncert')
setup, params = utils.get_setup_params(
parameters.CORRECTED_PARAMS,
scale_inf=True,
host_props=parameters.COBB_PROP_FIG4A)
ncells = np.product(setup['landscape_dims'])
# Use population size of 500 as 500m2 per cell
pop_size = 500
sampling_nums = np.array(
[1, 2, 3, 5, 7, 10, 15, 25, 35, 50, 70, 100, 150, 250, 350, 500])
with open(os.path.join("data", "scale_and_fit_results.json"),
"r") as infile:
scale_and_fit_results = json.load(infile)
beta_names = [
'beta_1,1', 'beta_1,2', 'beta_1,3', 'beta_1,4', 'beta_12', 'beta_21',
'beta_2'
]
beta = np.array([scale_and_fit_results[x] for x in beta_names])
approx_params = copy.deepcopy(params)
approx_params['rogue_rate'] *= scale_and_fit_results['roguing_factor']
approx_params['rogue_cost'] /= scale_and_fit_results['roguing_factor']
mpc_args = {
'horizon': 100,
'time_step': 0.5,
'end_time': 100,
'update_period': 20,
'rolling_horz': False,
'stage_len': 5,
'use_init_first': True
}
approx_model = ms_approx.MixedStandApprox(setup, approx_params, beta)
_, baseline_ol_control, _ = approx_model.optimise(n_stages=20,
init_policy=even_policy)
mpc_args['init_policy'] = baseline_ol_control
for n_samples in sampling_nums:
logging.info("Running with %d/%d stems sampled, %f%%", n_samples,
pop_size, 100 * n_samples / pop_size)
observer = observer_factory(pop_size, n_samples)
mpc_controls = np.zeros((n_reps, 9, len(setup['times']) - 1))
mpc_objs = np.zeros(n_reps)
# For storing observed states:
mpc_approx_states = np.zeros(
(n_reps, 4, 15)) # 4 as 4 update steps excluding the start
mpc_actual_states = np.zeros((n_reps, 4, 15))
# MPC runs - approximate model initialised correctly, & then observed at update steps
for i in range(n_reps):
mpc_controller = mpc.Controller(setup,
params,
beta,
approx_params=approx_params)
_, _, mpc_control, mpc_obj = mpc_controller.optimise(
**mpc_args, observer=observer)
mpc_objs[i] = mpc_obj
mpc_controls[i] = mpc_control
mpc_approx_states[i] = mpc_controller.approx_update_states
sim_run, approx_run = mpc_controller.run_control()
sim_state = np.sum(np.reshape(sim_run[0], (ncells, 15, -1)),
axis=0) / ncells
mpc_actual_states[i] = sim_state[:, [40, 80, 120, 160]].T
logging.info("MPC run %d of %d done", i + 1, n_reps)
# Append to existing data
if append:
old_filename = os.path.join(
folder, "sampled_data_" + str(n_samples) + ".npz")
with np.load(old_filename) as old_dataset:
mpc_controls = np.append(old_dataset['mpc_controls'],
mpc_controls,
axis=0)
mpc_objs = np.append(old_dataset['mpc_objs'], mpc_objs, axis=0)
mpc_approx_states = np.append(old_dataset['mpc_approx_states'],
mpc_approx_states,
axis=0)
# Store data
dataset = {
'mpc_controls': mpc_controls,
'mpc_objs': mpc_objs,
'mpc_approx_states': mpc_approx_states,
'mpc_actual_states': mpc_actual_states
}
np.savez_compressed(
os.path.join(folder, "sampled_data_" + str(n_samples)), **dataset)