emodelrunner.GUI_utils.simulator¶

Class containing simulation for the GUI.

Functions

`get_holding_data`(holdings, stimulus_data, ...)	Extract holding data from StepProtocol json dict and add amplitude to a holding list.
`get_pos_and_color`(sec, seg_pos, syn_type)	Returns the position and the synaptic type (0 for inhib.
`get_step_data`(steps, step, default_step)	Extract step data from StepProtocol json dict and add amplitude to a step list.
`section_coordinate_3d`(sec, seg_pos)	Returns the 3d coordinates of a point in a section.

Classes

NeuronSimulation([config_path])

Class containing BPO cell, simulation & protocol.

class emodelrunner.GUI_utils.simulator.NeuronSimulation(config_path='config/config_allsteps.ini')[source]¶

Bases: object

Class containing BPO cell, simulation & protocol.

config¶

dictionary containing configuration data

Type:: dict

cell_path¶

path to cell repo. should be “.”

Type:: str

total_duration¶

duration of cell simulation (ms)

Type:: float

steps¶

default step stimuli (nA)

Type:: list of floats

hypamps¶

default holding stimuli (nA)

Type:: list of floats

step_stim¶

selected step stimulus (nA)

Type:: float

hypamp¶

selected holding stimulus (nA)

Type:: float

step_delay¶

delay before applying step stimulus (ms)

Type:: float

step_duration¶

duration of step stimulus (ms)

Type:: float

hold_step_delay¶

delay of holding stimulus (ms)

Type:: float

hold_step_duration¶

duration of holding stimulus (ms)

Type:: float

available_pre_mtypes¶

all synapses pre_mtypes {mtypeidx: mtype_name, …}

Type:: dict

pre_mtypes¶

selected pre_mtypes to run [mtypeidx, …]

Type:: list of int

netstim_params¶

netstim parameters for synapses of each mtype {mtypeidx:[start, interval, number, noise]}

Type:: dict

syn_start¶

default time (ms) at which the synapse starts firing

Type:: int

syn_interval¶

default interval (ms) between two synapse firing

Type:: int

syn_nmb_of_spikes¶

default number of synapse firing

Type:: int

syn_noise¶

default synapse noise

Type:: int

protocol¶

BluePyOpt-based Protocol

Type:: ephys.protocols.SweepProtocol

cell¶

BluePyOpt-based cell

Type:: CellModelCustom

release_params¶

optimised cell parameters to fill in the cell’s free parameters

Type:: dict

sim¶

BluePyOpt simulator can access neuron data from it

Type:: ephys.simulators.NrnSimulator

syn_display_data¶

synapse data (position and type) for display syn_display_data[pre_mtype] = [x,y,z,type], type=0 if inhib, type=1 if excit

Type:: dict

create_cell_custom()[source]¶

Create a cell.

Returns:: cell model
Return type:: emodelrunner.cell.CellModelCustom

destroy()[source]¶: Destroy cell & protocol.

get_syn_stim()[source]¶

Create synapse stimuli.

Returns:: synapse stimuli
Return type:: emodelrunner.synapses.stimuli.NrnNetStimStimulusCustom

get_voltage()[source]¶

Returns voltage response.

Returns:

a tuple containing

ndarray: the time response
ndarray: the voltage response

instantiate()[source]¶: Instantiate cell, simulation & protocol.

load_available_pre_mtypes()[source]¶

Load the list of pre mtype cells to which are connected the synapses.

Returns:: mtypes of cells connected to the synapses
Return type:: dict

load_cell_sim()[source]¶: Load BPO cell & simulation.

load_protocol(protocol_name='protocol')[source]¶

Load BPO protocol.

Parameters:: protocol_name (str) – protocol name to use in BluePyOpt classes. Does not have an effect on the simulation

load_protocol_params(total_duration=3000, step_delay=700, step_duration=2000, hold_step_delay=0, hold_step_duration=3000, default_step=0, default_holding=0)[source]¶

Load default protocol params.

Parameters:

total_duration (float) – default value for duration of cell simulation (ms) if no StepProtocol is found
step_delay (float) – default value for delay before applying step stimulus (ms) if no StepProtocol is found
step_duration (float) – default value for duration of step stimulus (ms) if no StepProtocol is found
hold_step_delay (float) – default value for delay of holding stimulus (ms) if no StepProtocol is found
hold_step_duration (float) – default value for duration of holding stimulus (ms) if no StepProtocol is found
default_step (float) – default value for custom step amplitude (nA)
default_holding (float) – default value for custom holding amplitude (nA)

load_synapse_display_data()[source]¶: Load dict containing x,y,z of each synapse & inhib/excit.

load_synapse_params(syn_start=0, syn_interval=0, syn_nmb_of_spikes=0, syn_noise=0)[source]¶

Load default synapse params.

Parameters:

syn_start (int) – default time (ms) at which the synapse starts firing
syn_interval (int) – default interval (ms) between two synapse firing
syn_nmb_of_spikes (int) – default number of synapse firing
syn_noise (int) – default synapse noise

emodelrunner.GUI_utils.simulator.get_holding_data(holdings, stimulus_data, total_duration, default_holding)[source]¶

Extract holding data from StepProtocol json dict and add amplitude to a holding list.

Parameters:

holdings (list) – list of holding amplitudes (nA) to be updated
stimulus_data (dict) – stimulus dict from protocol json file containing holding data
total_duration (float) – total duration of the step (ms)
default_holding (float) – default value for the custom holding entry

Returns:

a tuple containing

float: delay of the holding stimulus (ms)
float: duration of the holding stimulus (ms)

emodelrunner.GUI_utils.simulator.get_pos_and_color(sec, seg_pos, syn_type)[source]¶

Returns the position and the synaptic type (0 for inhib. or 1 for excit.).

Parameters:

sec – neuron section
seg_pos (float) – postion of the segment os the section (should be between 0 and 1)
syn_type (int) – synaptic type. excitatory if >=100, inhibitory if <100

Returns:

first 3 numbers are the position, fourth is the synaptic type, None if pos not found

Return type:

list

emodelrunner.GUI_utils.simulator.get_step_data(steps, step, default_step)[source]¶

Extract step data from StepProtocol json dict and add amplitude to a step list.

Parameters:

steps (list) – list of step amplitudes (nA) to be updated
step (dict or list of dicts) – step from which to extract step data
default_step (float) – default value for the custom step entry (nA)

Returns:

a tuple containing

float: total duration of the step (ms)
float: delay of the step (ms)
float: duration of the step (ms)

emodelrunner.GUI_utils.simulator.section_coordinate_3d(sec, seg_pos)[source]¶

Returns the 3d coordinates of a point in a section.

Parameters:

sec – neuron section
seg_pos (float) – postion of the segment os the section (should be between 0 and 1)

Returns:

3d coordinates of a point in a section, or None if not found

Return type:

list