diff --git a/doc/calibration.qmd b/doc/calibration.qmd index dd82680..2253914 100644 --- a/doc/calibration.qmd +++ b/doc/calibration.qmd @@ -20,22 +20,22 @@ Lets look at the calibration and the first trial of the recording. import pathlib -import rlxnix as rlx -import plotly.graph_objects as go import numpy as np +import plotly.graph_objects as go +import rlxnix as rlx import scipy.signal as signal from plotly.subplots import make_subplots - -from util import trial_plot, plot_line_comparision - +from util import plot_line_comparision, trial_plot dataset_path = pathlib.Path("../oephys2nix/test/Test1/2025-10-08-aa-invivo-2-recording.nix") -relacs_path = pathlib.Path("../oephys2nix/test/Test1/2025-10-08-aa-invivo-2_relacs/2025-10-08-aa-invivo-2.nix") +relacs_path = pathlib.Path( + "../oephys2nix/test/Test1/2025-10-08-aa-invivo-2_relacs/2025-10-08-aa-invivo-2.nix" +) dataset = rlx.Dataset(str(dataset_path)) relacs = rlx.Dataset(str(relacs_path)) -#INFO: Select the first stimulus of the calibration repro +# INFO: Select the first stimulus of the calibration repro repro_d = dataset.repro_runs("CalibEfield_1")[0].stimuli[2] repro_r = relacs.repro_runs("CalibEfield_1")[0].stimuli[2] @@ -57,7 +57,7 @@ ttl, t = repro_d.trace_data("ttl-line") If you zoom in you can see a little delay between the different recording systems. It seems that open-ephys is before the relacs recording. ```{python} -#| echo: False +# | echo: False fig = trial_plot(repro_d, repro_r) fig.show() ``` @@ -68,11 +68,10 @@ print(f"Duration of the dataset {repro_d.duration}") print(f"Duration of the relacs {repro_r.duration}") # Resample the open-ephys data sinus_resampled = signal.resample(sinus, len(sinus_r)) - ``` ```{python} -#| echo: False +# | echo: False fig = plot_line_comparision(t_r, t, sinus_r, sinus, ["sinus-relacs", "sinus-oephys"]) fig.show() ``` @@ -83,19 +82,27 @@ oephys_lanes = [sinus, local_eod_oe, global_eod_oe, stimulus_oe] relacs_lanes = [sinus_r, local_eod_re, global_eod_re, stimulus_re] names_lanes = ["sinus", "local-eod", "global-eod", "stimulus"] lags_lanes = [] -for oephys_lane, relacs_lane, names_lane in zip(oephys_lanes, relacs_lanes, names_lanes, strict=True): - print(oephys_lane.shape) - print(relacs_lane.shape) - oephys_lane_resampled = signal.resample(oephys_lane, len(relacs_lane)) - correlation = signal.correlate(oephys_lane_resampled, relacs_lane, mode="full") - lags = signal.correlation_lags(oephys_lane_resampled.size, relacs_lane.size, mode="full") - lag = lags[np.argmax(correlation)] - lags_lanes.append(lag) - print(f"{names_lane} has a lag of {lag}") +for oephys_lane, relacs_lane, names_lane in zip( + oephys_lanes, relacs_lanes, names_lanes, strict=True +): + print(oephys_lane.shape) + print(relacs_lane.shape) + oephys_lane_resampled = signal.resample(oephys_lane, len(relacs_lane)) + correlation = signal.correlate(oephys_lane_resampled, relacs_lane, mode="full") + lags = signal.correlation_lags(oephys_lane_resampled.size, relacs_lane.size, mode="full") + lag = lags[np.argmax(correlation)] + lags_lanes.append(lag) + print(f"{names_lane} has a lag of {lag}") ``` ```{python} -#| echo: False -fig = plot_line_comparision(t_r, t_r, np.roll(sinus_r, lags_lanes[0]),sinus_resampled, ["sinus-relacs", "sinus-resampled-openepyhs"]) +# | echo: False +fig = plot_line_comparision( + t_r, + t_r, + np.roll(sinus_r, lags_lanes[0]), + sinus_resampled, + ["sinus-relacs", "sinus-resampled-openepyhs"], +) fig.show() ```