diff --git a/src/miv_simulator/optimization.py b/src/miv_simulator/optimization.py index 34af701..e4b1b53 100644 --- a/src/miv_simulator/optimization.py +++ b/src/miv_simulator/optimization.py @@ -317,6 +317,7 @@ def update_network_params(env, param_tuples): continue biophys_cell = biophys_cell_dict[gid] + biophys_cell.pop_name = population is_reduced = False if hasattr(biophys_cell, "is_reduced"): is_reduced = biophys_cell.is_reduced @@ -334,7 +335,7 @@ def update_network_params(env, param_tuples): filters={"sources": sources} if sources is not None else None, - origin=None if is_reduced else "soma", + # origin=None if is_reduced else "soma", update_targets=True, ) @@ -395,9 +396,7 @@ def update_run_params(env, param_tuples): ) -def network_features( - env, target_trj_rate_map_dict, t_start, t_stop, target_populations -): +def network_features(env, t_start, t_stop, target_populations): features_dict = dict() temporal_resolution = float(env.stimulus_config["Temporal Resolution"]) @@ -406,8 +405,6 @@ def network_features( pop_spike_dict = spikedata.get_env_spike_dict(env, include_artificial=False) for pop_name in target_populations: - has_target_trj_rate_map = pop_name in target_trj_rate_map_dict - n_active = 0 sum_mean_rate = 0.0 spike_density_dict = spikedata.spike_density_estimate( @@ -423,27 +420,6 @@ def network_features( n_target_rate_map = 0 sum_snr = None - if has_target_trj_rate_map: - pop_target_trj_rate_map_dict = target_trj_rate_map_dict[pop_name] - n_target_rate_map = len(pop_target_trj_rate_map_dict) - snrs = [] - for gid in pop_target_trj_rate_map_dict: - target_trj_rate_map = pop_target_trj_rate_map_dict[gid] - rate_map_len = len(target_trj_rate_map) - if gid in spike_density_dict: - measured_rate = spike_density_dict[gid]["rate"][ - :rate_map_len - ] - ref_signal = target_trj_rate_map - np.mean( - target_trj_rate_map - ) - signal = measured_rate - np.mean(measured_rate) - noise = signal - ref_signal - snr = np.var(signal) / max(np.var(noise), 1e-6) - else: - snr = 0.0 - snrs.append(snr) - sum_snr = np.sum(snrs) pop_features_dict = {} pop_features_dict["n_total"] = n_total diff --git a/src/miv_simulator/optimize_network.py b/src/miv_simulator/optimize_network.py index 7c5396e..4abc6e9 100644 --- a/src/miv_simulator/optimize_network.py +++ b/src/miv_simulator/optimize_network.py @@ -341,7 +341,6 @@ def from_param_dict(params_dict): env, operational_config, opt_targets, - target_trj_rate_map_dict, from_param_dict, t_start, t_stop, @@ -360,7 +359,6 @@ def network_objfun( env, operational_config, opt_targets, - target_trj_rate_map_dict, from_param_dict, t_start, t_stop, @@ -371,11 +369,9 @@ def network_objfun( update_network_params(env, param_tuple_values) env.tstop = t_stop - network.run(env, output=False, shutdown=False) + network.run(env, output=False) - return network_features( - env, target_trj_rate_map_dict, t_start, t_stop, target_populations - ) + return network_features(env, t_start, t_stop, target_populations) def compute_objectives(local_features, operational_config, opt_targets):