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add cvode argument to apply_multiple_stimuli #191

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Jul 8, 2024
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add cvode argument to apply_multiple_stimuli #191

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8 changes: 6 additions & 2 deletions bluecellulab/analysis/inject_sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ def run_stimulus(
stimulus: Stimulus,
section: str,
segment: float,
cvode: bool = True,
) -> Recording:
"""Creates a cell and stimulates it with a given stimulus.

Expand All @@ -45,6 +46,7 @@ def run_stimulus(
stimulus: The input stimulus to inject into the cell.
section: Name of the section of cell where the stimulus is to be injected.
segment: The segment of the section where the stimulus is to be injected.
cvode: True to use variable time-steps. False for fixed time-steps.

Returns:
The voltage-time recording at the specified location.
Expand All @@ -61,7 +63,7 @@ def run_stimulus(
current_vector = neuron.h.Vector()
current_vector.record(iclamp._ref_i)
simulation = Simulation(cell)
simulation.run(stimulus.stimulus_time)
simulation.run(stimulus.stimulus_time, cvode=cvode)
current = np.array(current_vector.to_python())
voltage = cell.get_voltage_recording(neuron_section, segment)
time = cell.get_time()
Expand All @@ -78,6 +80,7 @@ def apply_multiple_stimuli(
section_name: str | None = None,
segment: float = 0.5,
n_processes: int | None = None,
cvode: bool = True,
) -> StimulusRecordings:
"""Apply multiple stimuli to the cell on isolated processes.

Expand All @@ -91,6 +94,7 @@ def apply_multiple_stimuli(
If None, the stimuli are applied at the soma[0] of the cell.
segment: The segment of the section where the stimuli are applied.
n_processes: The number of processes to use for running the stimuli.
cvode: True to use variable time-steps. False for fixed time-steps.

Returns:
A dictionary where the keys are the names of the stimuli and the values
Expand Down Expand Up @@ -140,7 +144,7 @@ def apply_multiple_stimuli(
else:
raise ValueError("Unknown stimulus name.")

task_args.append((cell.template_params, stimulus, section_name, segment))
task_args.append((cell.template_params, stimulus, section_name, segment, cvode))

with IsolatedProcess(processes=n_processes) as pool:
# Map expects a function and a list of argument tuples
Expand Down