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- import numpy as np
- from brian2.units import *
- from pypet import Environment, cartesian_product, Trajectory
- from pypet.brian2.parameter import Brian2MonitorResult
- from scripts.interneuron_placement import create_grid_of_excitatory_neurons, \
- create_interneuron_sheet_entropy_max_orientation, get_excitatory_neurons_in_inhibitory_axonal_clouds
- from scripts.ring_network.head_direction import ex_in_network
- from scripts.spatial_maps.orientation_map import OrientationMap
- from scripts.spatial_maps.orientation_map_generator_pypet import TRAJ_NAME_ORIENTATION_MAPS
- from scripts.spatial_network.head_direction_index_over_noise_scale import excitatory_eqs, excitatory_params, \
- lif_interneuron_eqs, lif_interneuron_params, lif_interneuron_options, ei_synapse_model, ei_synapse_on_pre, \
- ei_synapse_param, ie_synapse_model, ie_synapse_on_pre, ie_synapse_param, get_synaptic_weights, \
- create_head_direction_input
- DATA_FOLDER = "../../data/"
- LOG_FOLDER = "../../logs/"
- TRAJ_NAME = "entropy_maximisation_orientation_map_placement_jitter"
- def get_orientation_map(correlation_length, seed, sheet_size, N_E, data_folder=None):
- if data_folder is None:
- data_folder = DATA_FOLDER
- traj = Trajectory(filename=data_folder + TRAJ_NAME_ORIENTATION_MAPS + ".hdf5")
- traj.f_load(index=-1, load_parameters=2, load_results=2)
- available_lengths = sorted(list(set(traj.f_get("corr_len").f_get_range())))
- closest_length = available_lengths[np.argmin(np.abs(np.array(available_lengths)-correlation_length))]
- if closest_length!=correlation_length:
- print("Warning: desired correlation length {:.1f} not available. Taking {:.1f} instead".format(
- correlation_length, closest_length))
- corr_len = closest_length
- seed = seed
- map_by_params = lambda x, y: x == corr_len and y == seed
- idx_iterator = traj.f_find_idx(['corr_len', 'seed'], map_by_params)
- # TODO: Since it has only one entry, maybe iterator can be replaced
- for idx in idx_iterator:
- traj.v_idx = idx
- map_angle_grid = traj.crun.map
- number_of_excitatory_neurons_per_row = int(np.sqrt(N_E))
- map = OrientationMap(number_of_excitatory_neurons_per_row + 1, number_of_excitatory_neurons_per_row + 1,
- corr_len, sheet_size, sheet_size, seed)
- map.angle_grid = map_angle_grid
- return map.tuning
- def spatial_network_with_entropy_maximisation(traj):
- sheet_size = traj.orientation_map.sheet_size
- N_E = traj.network.N_E
- N_I = traj.network.N_I
- orientation_map = get_orientation_map(traj.orientation_map.correlation_length, traj.orientation_map.seed,
- sheet_size, N_E)
- ex_positions, ex_tunings = create_grid_of_excitatory_neurons(sheet_size,
- sheet_size,
- int(np.sqrt(N_E)), orientation_map)
- inhibitory_axon_long_axis = traj.morphology.long_axis
- inhibitory_axon_short_axis = traj.morphology.short_axis
- entropy_maximisation_steps = traj.simulation.entropy_maximisation.steps if inhibitory_axon_long_axis != \
- inhibitory_axon_short_axis else 1
- inhibitory_axonal_clouds, ellipse_single_trial_entropy = create_interneuron_sheet_entropy_max_orientation(
- ex_positions, ex_tunings, N_I, inhibitory_axon_long_axis,
- inhibitory_axon_short_axis, sheet_size,
- sheet_size, trial_orientations=entropy_maximisation_steps,
- placement_jitter=traj.interneuron.placement_jitter)
- ie_connections = get_excitatory_neurons_in_inhibitory_axonal_clouds(ex_positions, inhibitory_axonal_clouds)
- inhibitory_synapse_strength = traj.synapse.inhibitory * nS
- excitatory_synapse_strength = traj.synapse.excitatory * mV
- if inhibitory_synapse_strength != 0.0 * nS and excitatory_synapse_strength != 0.0 * mV \
- and inhibitory_axon_long_axis == inhibitory_axon_short_axis:
- traj.f_add_derived_parameter("morphology.morph_label", 'circular',
- comment="Interneuron morphology of this run is circular")
- elif inhibitory_synapse_strength != 0.0 * nS and excitatory_synapse_strength != 0.0 * mV:
- traj.f_add_derived_parameter("morphology.morph_label", 'ellipsoid',
- comment="Interneuron morphology of this run is ellipsoid")
- else:
- traj.f_add_derived_parameter("morphology.morph_label", 'no conn',
- comment="There are no interneurons")
- ex_in_weights, in_ex_weights = get_synaptic_weights(N_E, N_I, ie_connections, excitatory_synapse_strength,
- inhibitory_synapse_strength)
- sharpness = 1.0 / (traj.input.width) ** 2
- directions = np.linspace(-np.pi, np.pi, traj.input.number_of_directions, endpoint=False)
- for idx, dir in enumerate(directions):
- # We recreate the network here for every dir, which slows down the simulation quite considerably. Otherwise,
- # we get a problem with saving and restoring the spike times (0s spike for neuron 0)
- net = ex_in_network(N_E, N_I, excitatory_eqs, excitatory_params, lif_interneuron_eqs,
- lif_interneuron_params,
- lif_interneuron_options, ei_synapse_model, ei_synapse_on_pre,
- ei_synapse_param,
- ex_in_weights, ie_synapse_model, ie_synapse_on_pre,
- ie_synapse_param, in_ex_weights, random_seed=2)
- input_to_excitatory_population = create_head_direction_input(traj.input.baseline * nA, ex_tunings,
- sharpness,
- traj.input.amplitude * nA, dir)
- excitatory_neurons = net["excitatory_neurons"]
- excitatory_neurons.I = input_to_excitatory_population
- inhibitory_neurons = net["interneurons"]
- inhibitory_neurons.u_ext = traj.inh_input.baseline * mV
- inhibitory_neurons.tau = traj.interneuron.tau * ms
- net.run(traj.simulation.duration * ms)
- direction_id = 'dir{:d}'.format(idx)
- traj.f_add_result(Brian2MonitorResult, '{:s}.spikes.e'.format(direction_id), net["excitatory_spike_monitor"],
- comment='The spiketimes of the excitatory population')
- traj.f_add_result(Brian2MonitorResult, '{:s}.spikes.i'.format(direction_id), net["inhibitory_spike_monitor"],
- comment='The spiketimes of the inhibitory population')
- traj.f_add_result('ex_positions', np.array(ex_positions),
- comment='The positions of the excitatory neurons on the sheet')
- traj.f_add_result('ex_tunings', np.array(ex_tunings),
- comment='The input tunings of the excitatory neurons')
- ie_connections_save_array = np.zeros((N_I, N_E))
- for i_idx, ie_conn in enumerate(ie_connections):
- for e_idx in ie_conn:
- ie_connections_save_array[i_idx, e_idx] = 1
- traj.f_add_result('ie_adjacency', ie_connections_save_array,
- comment='Recurrent connection adjacency matrix')
- axon_cloud_save_list = [[p.x, p.y, p.phi] for p in inhibitory_axonal_clouds]
- axon_cloud_save_array = np.array(axon_cloud_save_list)
- traj.f_add_result('inhibitory_axonal_cloud_array', axon_cloud_save_array,
- comment='The inhibitory axonal clouds')
- return 1
- def main():
- env = Environment(trajectory=TRAJ_NAME,
- comment="Compare the head direction tuning for circular and ellipsoid interneuron morphology, "
- "when tuning orientations to maximise entropy of connected excitatory tunings.",
- multiproc=True, filename=DATA_FOLDER, ncores=30, overwrite_file=True, log_folder=LOG_FOLDER)
- traj = env.trajectory
- traj.f_add_parameter_group("orientation_map")
- traj.f_add_parameter("orientation_map.correlation_length", 200.0,
- comment="Correlation length of orientations in um")
- traj.f_add_parameter("orientation_map.seed", 1, comment="Random seed for map generation.")
- traj.f_add_parameter("orientation_map.sheet_size", 450, comment="Sheet size in um")
- traj.f_add_parameter_group("network")
- traj.f_add_parameter("network.N_E", 900, comment="Number of excitatory neurons")
- traj.f_add_parameter("network.N_I", 100, comment="Number of inhibitory neurons")
- traj.f_add_parameter_group("interneuron")
- traj.f_add_parameter("interneuron.tau", 7., comment="Interneuron timescale in ms")
- traj.f_add_parameter("interneuron.placement_jitter", 10.0, comment="Interneuron placement random component length")
- traj.f_add_parameter_group("synapse")
- traj.f_add_parameter("synapse.inhibitory", 30.0, "Strength of conductance-based inhibitory synapse in nS.")
- traj.f_add_parameter("synapse.excitatory", 2.5, "Strength of conductance-based inhibitory synapse in mV.")
- traj.f_add_parameter_group("input")
- traj.f_add_parameter("input.width", 1. / np.sqrt(2.5), comment="Standard deviation of incoming head direction input.")
- traj.f_add_parameter("input.baseline", 0.05, comment="Head direction input baseline")
- traj.f_add_parameter("input.amplitude", 0.6, comment="Head direction input amplitude")
- traj.f_add_parameter("input.number_of_directions", 12, comment="Number of probed directions")
- traj.f_add_parameter_group("inh_input")
- traj.f_add_parameter("inh_input.baseline", -50., comment="Head direction input baseline")
- traj.f_add_parameter("inh_input.amplitude", 0., comment="Head direction input amplitude")
- traj.f_add_parameter_group("morphology")
- traj.f_add_parameter("morphology.long_axis", 100.0, comment="Long axis of axon ellipsoid")
- traj.f_add_parameter("morphology.short_axis", 25.0, comment="Short axis of axon ellipsoid")
- traj.f_add_parameter_group("simulation")
- traj.f_add_parameter("simulation.entropy_maximisation.steps", 30, comment="Steps for entropy maximisation")
- traj.f_add_parameter("simulation.dt", 0.1, comment="Network simulation time step in ms")
- traj.f_add_parameter("simulation.duration", 1000, comment="Network simulation duration in ms")
- correlation_length_range = [200.0]
- seed_range = [1]
- placement_jitter_range = [0.0, 10.0, 20.0]
- ellipsoid_parameter_exploration = {
- "morphology.long_axis": [100.0],
- "morphology.short_axis": [25.0],
- "orientation_map.correlation_length": correlation_length_range,
- "orientation_map.seed": seed_range,
- "synapse.inhibitory": [30.],
- "synapse.excitatory": [2.5],
- "interneuron.placement_jitter": placement_jitter_range
- # "orientation_map.correlation_length": np.arange(0.0, 200.0, 50).tolist()
- }
- corresponding_circular_radius = float(np.sqrt(ellipsoid_parameter_exploration[
- "morphology.long_axis"][0] * ellipsoid_parameter_exploration[
- "morphology.short_axis"][0]))
- circle_parameter_exploration = {
- "morphology.long_axis": [corresponding_circular_radius],
- "morphology.short_axis": [corresponding_circular_radius],
- "orientation_map.correlation_length": ellipsoid_parameter_exploration["orientation_map.correlation_length"],
- "orientation_map.seed": ellipsoid_parameter_exploration["orientation_map.seed"],
- "synapse.inhibitory": ellipsoid_parameter_exploration["synapse.inhibitory"],
- "synapse.excitatory": ellipsoid_parameter_exploration["synapse.excitatory"],
- "interneuron.placement_jitter": placement_jitter_range
- }
- no_conn_parameter_exploration = {
- "morphology.long_axis": [corresponding_circular_radius],
- "morphology.short_axis": [corresponding_circular_radius],
- "orientation_map.correlation_length": ellipsoid_parameter_exploration["orientation_map.correlation_length"],
- "orientation_map.seed": ellipsoid_parameter_exploration["orientation_map.seed"],
- "synapse.inhibitory": [0.],
- "synapse.excitatory": [0.],
- "interneuron.placement_jitter": placement_jitter_range
- }
- expanded_dicts = [cartesian_product(dict) for dict in [ellipsoid_parameter_exploration,
- circle_parameter_exploration,
- no_conn_parameter_exploration]]
- final_dict = {}
- for key in expanded_dicts[0].keys():
- list_of_parameter_lists = [dict[key] for dict in expanded_dicts]
- final_dict[key] = sum(list_of_parameter_lists, [])
- traj.f_explore(final_dict)
- env.run(spatial_network_with_entropy_maximisation)
- env.disable_logging()
- if __name__ == "__main__":
- main()
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