def test_get_simulation_error_end_point():
force_file = os.path.join(TEST_DATA_ROOT, "forces.txt")
fit_data = np.loadtxt(force_file, skiprows=1)[:, -1]
target_truth = np.mean(fit_data[-10:])
this_sr_dict = copy.copy(SIM_RUNNER_DICT)
this_sr_dict["fit_mode"] = "end_point"
this_sr_dict["output_dir"] = TEST_DATA_ROOT
this_sr_dict["target_data"] = target_truth
sr = SimulationRunner(**this_sr_dict)
sr.read_simulation_results()
assert (np.isclose(sr.get_simulation_error(), 0)), ("SimulationRunner not calculating error "
"correctly!")
# def test_run_simulation():
# """This uses the `echo` windows command to test that the simulation runs correctly"""
# this_sr_dict = copy.copy(SIM_RUNNER_DICT)
# this_sr_dict["fibersim_file"] = "echo"
# this_sr_dict["options_file"] = "Hello,"
# this_sr_dict["model_file"] = "World!"
# # this_sr_dict["protocol_file"] = ">"
# # this_sr_dict["output_dir"] = os.path.realpath(os.path.join(TEST_RESULT_DIR, "sim_run_test.txt"))
# sr = SimulationRunner(**this_sr_dict)
# sr.run_simulation()
# # Read the newly created file.
# with open(this_sr_dict["output_dir"], 'r') as f:
# text = f.read()
# assert (text == "Hello, World!"), "SimulationRunner did not run simulation correctly!"
def test_get_simulation_error_time():
force_file = os.path.join(TEST_DATA_ROOT, "forces.txt")
results_truth = np.loadtxt(force_file, skiprows=1)[:, -1]
sr = SimulationRunner(**SIM_RUNNER_DICT)
sr.fit_data = results_truth
assert (np.isclose(sr.get_simulation_error(), 0)), ("SimulationRunner not calculating error "
"correctly!")
def test_read_simulation_results_force():
force_file = os.path.join(TEST_DATA_ROOT, "forces.txt")
results_truth = np.loadtxt(force_file, skiprows=1)[:, -1]
this_sr_dict = copy.copy(SIM_RUNNER_DICT)
this_sr_dict["output_dir"] = TEST_DATA_ROOT
sr = SimulationRunner(**this_sr_dict)
sr.read_simulation_results()
assert (np.array_equal(sr.fit_data, results_truth)), ("SimulationRunner did not read in "
"simulation results correctly!")
def test_simulation_runner_initialization(): sr = SimulationRunner(**SIM_RUNNER_DICT) msg = "SimulationRunner did not initialize correctly!" assert (sr), msg assert (sr.iteration_number == 0), msg assert (sr.best_error == np.inf), msg assert (sr.error_values == []), msg
def test_read_target_data_maintains_shape_of_target_data():
target_data_orig = np.loadtxt(SIM_RUNNER_DICT["target_data"])
this_sr_dict = copy.copy(SIM_RUNNER_DICT)
this_sr_dict["target_data"] = target_data_orig
sr = SimulationRunner(**this_sr_dict)
assert (sr.target_data.shape[0] == target_data_orig.shape[0]), ("SimulationRunner reading of "
"target data does NOT preserve shape of target data! THIS IS CURRENTLY IGNORED")
def test_read_target_data_muscle_force_time_string():
sr = SimulationRunner(**SIM_RUNNER_DICT)
target_data_truth = np.loadtxt(SIM_RUNNER_DICT["target_data"])
sim_times = protocol.get_sim_time(SIM_RUNNER_DICT["protocol_file"])
# Linearly interpolate the target data according to the simulation time steps.
times_to_interpolate = (np.asarray(sim_times[SIM_RUNNER_DICT["time_steps_to_steady_state"]:])
- sim_times[SIM_RUNNER_DICT["time_steps_to_steady_state"]])
interpolated_values = np.interp(times_to_interpolate, target_data_truth[:, 0],
target_data_truth[:, 1])
# Concatenate these back together to form the newly interpolated target data and store it.
target_data_truth = np.stack((times_to_interpolate, interpolated_values), axis=-1)
assert (np.array_equal(sr.target_data, target_data_truth)), ("SimulationRunner did not read "
"target data correctly!")
def test_get_simulation_times(): sr = SimulationRunner(**SIM_RUNNER_DICT) truth_times = protocol.get_sim_time(SIM_RUNNER_DICT["protocol_file"]) assert (sr.sim_times == truth_times), "SimulationRunner did not read protocol times correctly!"