Utils Module

This module contains utility functions for setup, NMODL file handling, current generation, plotting, and type definitions.

Current Generation

create_ramp_current(n_pools, t_points, ...)	Create a matrix of ramp currents for multiple pools.
create_step_current(n_pools, t_points, ...)	Create a matrix of step currents for multiple pools.
create_sinusoidal_current(n_pools, t_points, ...)	Create a matrix of sinusoidal currents for multiple pools.
create_sawtooth_current(n_pools, t_points, ...)	Create a matrix of sawtooth currents for multiple pools.
create_trapezoid_current(n_pools, t_points, ...)	Create a matrix of trapezoidal currents for multiple pools.

NEURON Utilities

inject_currents_into_populations(...)	Injects input currents into the specified populations.
inject_currents_and_simulate_spike_trains(...)	Injects input currents into populations and returns recorded spike trains.

Continuous Saver

ContinuousSaver(save_path[, ...])

Manages continuous saving of simulation data in chunks to prevent memory overflow.

convert_chunks_to_neo(save_path[, ...])

Load chunks and convert to NEO Block format (compatible with SimulationRunner output).

Plotting & Visualization

plot_raster_spikes(results, axs, populations)	Plot spike raster plots for neural populations, one per axis.
plot_membrane_potentials(results, axs[, ...])	Plot membrane potential traces for selected cells across populations.
plot_muscle_dynamics(results, joint_angle, ...)	Plot muscle dynamics from Hill model.
plot_antagonist_muscle_comparison(results, ...)	Plot comparison of antagonist muscle dynamics.
plot_spindle_dynamics(results, axs[, ...])	Plot spindle model dynamics.
plot_gto_dynamics(results, axs[, ...])	Plot Golgi tendon organ (GTO) dynamics.

Type Definitions

Quantity Types

Quantity__s	Physical quantity type for time in seconds.
Quantity__ms	Physical quantity type for time in milliseconds.
Quantity__rad	Physical quantity type for angles in radians.
Quantity__deg	Physical quantity type for angles in degrees.
Quantity__mV	Physical quantity type for electrical potential in millivolts.
Quantity__uV	Physical quantity type for electrical potential in microvolts.
Quantity__nA	Physical quantity type for electrical current in nanoamperes.
Quantity__uS	Physical quantity type for electrical conductance in microsiemens.
Quantity__S_per_m	Physical quantity type for conductivity in siemens per meter.
Quantity__Hz	Physical quantity type for frequency in hertz.
Quantity__pps	Physical quantity type for firing rate in pulses per second.
Quantity__mm	Physical quantity type for length in millimeters.
Quantity__m	Physical quantity type for length in meters.
Quantity__mm2	Physical quantity type for area in square millimeters.
Quantity__per_mm2	Physical quantity type for density per square millimeter.
Quantity__m_per_s	Physical quantity type for velocity in meters per second.
Quantity__mm_per_s	Physical quantity type for velocity in millimeters per second.

Neo Data Types

CURRENT__AnalogSignal	Neo AnalogSignal for input currents in nanoamperes with time in seconds.
FORCE__AnalogSignal	Neo AnalogSignal for force measurements in newtons or dimensionless units.
SPIKE_TRAIN__Block	Neo Block containing spike train data organized by motor unit pools.
SURFACE_MUAP__Block	Neo Block containing surface motor unit action potentials (MUAPs).
SURFACE_EMG__Block	Neo Block containing surface EMG signals.
INTRAMUSCULAR_MUAP__Block	Neo Block containing intramuscular motor unit action potentials (MUAPs).
INTRAMUSCULAR_EMG__Block	Neo Block containing intramuscular EMG signals.

Matrix & Array Types

CORTICAL_INPUT__MATRIX	2D floating-point array for cortical input patterns.
RECRUITMENT_THRESHOLDS__ARRAY	1D array of recruitment threshold values for motor units.
JOINT_ANGLE__ARRAY	1D array representing joint angle trajectory over time.
MOMENT_ARM__MATRIX	2D array of moment arms as a function of joint angle.