2021-01-13 • Connection test plot functions
Contents
2021-01-13 • Connection test plot functions¶
Integrated plot functions from recent notebooks (plotting overlaid STAs, height-, p-value-, and rel height distributions, and ROC curve) in codebase. This notebook showcases them, including a new four-coloured classification matrix plot.
Setup¶
from voltage_to_wiring_sim.notebook_init import *
Preloading: numpy, numba, matplotlib.pyplot, seaborn.
Importing from submodules … ✔
Imported `np`, `mpl`, `plt`, `sns`, `pd`
Imported codebase (`voltage_to_wiring_sim`) as `v`
Imported `*` from `v.support.units`
Setup autoreload
v.print_reproducibility_info()
This cell was last run by tfiers on yoga
on Fri 15 Jan 2021, at 22:20 (UTC+0100).
Last git commit (Fri 15 Jan 2021, 22:07).
Uncommited changes to:
M codebase/voltage_to_wiring_sim/sim/izhikevich_neuron.py
M notebooks/2021-01-13__conntest_in_codebase.ipynb
M notebooks/2021-01-13__multiple_ROC.ipynb
from voltage_to_wiring_sim.N_to_1_experiment import N_to_1_SimParams, simulate, plot_sim_slice
from voltage_to_wiring_sim.sim.neuron_params import cortical_RS
Base parameters¶
sim_params = N_to_1_SimParams(
sim_duration = 5 * minute,
timestep = 0.1 * ms,
num_spike_trains = 30,
p_connected = 0.5,
spike_rate = 20 * Hz,
Δg_syn = 0.8 * nS,
τ_syn = 7 * ms,
neuron_params = cortical_RS,
imaging_spike_SNR = 4,
);
sim_data = simulate(sim_params);
plot_sim_slice(sim_data, t_start=3 * second, duration=1 * second);
ax = v.sim.izhikevich_neuron.show_output_spike_stats(sim_data.izh_output);
Output spike rate (1 / median ISI): 10.8 Hz
test_data, test_summaries = v.N_to_1_experiment.test_connections(sim_data);
Testing connections: 100%|██████████| 30/30 [00:07<00:00, 4.04it/s]
v.N_to_1_experiment.plot_conntest(test_data, test_summaries, sim_data)
classifs = v.conntest.classification.sweep_threshold(test_summaries, sim_data.is_connected);
v.N_to_1_experiment.plot_classifications_with_ROC(classifs)
Reproducibility¶
v.print_reproducibility_info(verbose=True)
This cell was last run by tfiers on yoga
on Fri 15 Jan 2021, at 15:58 (UTC+0100).
Last git commit (Fri 15 Jan 2021, 15:34).
Uncommited changes to:
M codebase/voltage_to_wiring_sim/support/reproducibility.py
M notebooks/2021-01-13__multiple_ROC.ipynb
Platform:
Windows-10
CPython 3.8.6 (C:\conda\python.exe)
Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
Dependencies of voltage_to_wiring_sim and their installed versions:
numpy 1.19.5
matplotlib 3.3.3
numba 0.52.0
seaborn 0.11.1
scipy 1.6.0
scikit-learn 0.24.0
preload 2.2
nptyping 1.4.0
tqdm 4.56.0
!conda list
# packages in environment at C:\conda:
#
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