Quickstart

Verified against jaxfne==0.3.42 (pip install "jaxfne==0.3.42").

Configure, construct, simulate

import jaxfne as jtfne

cfg = jtfne.Configuration()
cfg = cfg.runtime(seed=7, dtype="float32", duration_ms=1000.0, dt_ms=0.1)
cfg = cfg.column("single_neuron", layers=["L2/3"], n=1)
cfg = cfg.cell_types({"E": 1.0})
cfg = cfg.connectivity()
cfg = cfg.set_emitter("izhikevich", "cortical_eig")
cfg = cfg.probes(["MUA-proxy", "source-proxy", "LFP-proxy"])

model = jtfne.construct(cfg)
signals = jtfne.simulate(model, duration_ms=1000.0, dt_ms=0.1, seed=7)
print(signals.V_m.shape, signals.spikes.sum())

Tune

objectives = jtfne.rate_targets(
    groups={"first_half": range(24), "second_half": range(24, 48)},
    targets_hz={"first_half": 5.0, "second_half": 10.0},
)
optimizer = jtfne.agsdr(
    parameters={"drive_scale_a": (0.35, 2.25), "drive_scale_b": (0.35, 2.25)},
    generations=8,
    population_size=6,
    seed=42,
)
result = model.tune(objectives=objectives, optimizer=optimizer)
print(result.summary)

Validate

python -m compileall -q jaxfne tests examples
PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 PYTHONPATH=. python -m pytest tests/ -q --tb=line