ibllib.plots.figures

Module that produces figures, usually for the extraction pipeline

Functions

dlc_qc_plot	Creates DLC QC plot.
ephys_bad_channels
raw_destripe	param raw: raw ephys data, Ns x Nc, x-axis: time (s), y-axis: channel
remove_axis_outline	Function to remove outline of empty axis
set_axis_label_size	Function to normalise size of all axis labels

Classes

ApPlots	Plots AP RMS plots
BadChannelsAp	Plots raw electrophysiology AP band task = BadChannelsAp(pid, one=one=one)
BehaviourPlots	Behavioural plots
HistologySlices	Plots coronal and sagittal slice showing electrode locations
LfpPlots	Plots LFP spectrum and LFP RMS plots
SpikeSorting	Plots raw electrophysiology AP band

set_axis_label_size(ax, labels=14, ticklabels=12, title=14, cmap=False)

Function to normalise size of all axis labels

Parameters:

• ax –

• labels –

• ticklabels –

• title –

• cmap –

Returns:

remove_axis_outline(ax)

Function to remove outline of empty axis

Parameters:

ax –

Returns:

class BehaviourPlots(eid, session_path=None, one=None, **kwargs)

Bases: ReportSnapshot

Behavioural plots

signature = {'input_files': [('*trials.table.pqt', 'alf', True)], 'output_files': [('psychometric_curve.png', 'snapshot/behaviour', True), ('chronometric_curve.png', 'snapshot/behaviour', True), ('reaction_time_with_trials.png', 'snapshot/behaviour', True)]}

class HistologySlices(pid, session_path=None, one=None, brain_regions=None, brain_atlas=None, **kwargs)

Bases: ReportSnapshotProbe

Plots coronal and sagittal slice showing electrode locations

get_probe_signature()

class LfpPlots(pid, session_path=None, one=None, brain_regions=None, brain_atlas=None, **kwargs)

Bases: ReportSnapshotProbe

Plots LFP spectrum and LFP RMS plots

get_probe_signature()

class ApPlots(pid, session_path=None, one=None, brain_regions=None, brain_atlas=None, **kwargs)

Bases: ReportSnapshotProbe

Plots AP RMS plots

get_probe_signature()

class SpikeSorting(pid, session_path=None, one=None, brain_regions=None, brain_atlas=None, **kwargs)

Bases: ReportSnapshotProbe

Plots raw electrophysiology AP band

Parameters:

• session_path – session path

• probe_id – str, UUID of the probe insertion for which to create the plot

• **kwargs –

  keyword arguments passed to tasks.Task

get_probe_signature()

get_signatures(**kwargs)

This is the default but should be overwritten for each task :return:

class BadChannelsAp(pid, session_path=None, one=None, brain_regions=None, brain_atlas=None, **kwargs)

Bases: ReportSnapshotProbe

Plots raw electrophysiology AP band task = BadChannelsAp(pid, one=one=one)

Parameters:

• session_path – session path

• probe_id – str, UUID of the probe insertion for which to create the plot

• **kwargs –

  keyword arguments passed to tasks.Task

get_probe_signature()

ephys_bad_channels(raw, fs, channel_labels, channel_features, h=None, channels=None, title='ephys_bad_channels', save_dir=None, destripe=False, eqcs=None, br=None, pid_info=None, plot_backend='matplotlib')

raw_destripe(raw, fs, t0, i_plt, n_plt, fig=None, axs=None, savedir=None, detect_badch=True, SAMPLE_SKIP=200, DISPLAY_TIME=0.05, N_CHAN=384, MIN_X=-0.00011, MAX_X=0.00011)

Parameters:

• raw – raw ephys data, Ns x Nc, x-axis: time (s), y-axis: channel

• fs – sampling freq (Hz) of the raw ephys data

• t0 – time (s) of ephys sample beginning from session start

• i_plt – increment of plot to display image one (start from 0, has to be < n_plt)

• n_plt – total number of subplot on figure

• fig – figure handle

• axs – axis handle

• savedir – filename, including directory, to save figure to

• detect_badch – boolean, to detect or not bad channels

• SAMPLE_SKIP – number of samples to skip at origin of ephsy sample for display

• DISPLAY_TIME – time (s) to display

• N_CHAN – number of expected channels on the probe

• MIN_X – max voltage for color range

• MAX_X – min voltage for color range

Returns:

fig, axs

dlc_qc_plot(session_path, one=None, device_collection='raw_video_data', cameras=('left', 'right', 'body'), trials_collection='alf')

Creates DLC QC plot. Data is searched first locally, then on Alyx. Panels that lack required data are skipped.

Required data to create all panels

‘raw_video_data/_iblrig_bodyCamera.raw.mp4’, ‘raw_video_data/_iblrig_leftCamera.raw.mp4’, ‘raw_video_data/_iblrig_rightCamera.raw.mp4’, ‘alf/_ibl_bodyCamera.dlc.pqt’, ‘alf/_ibl_leftCamera.dlc.pqt’, ‘alf/_ibl_rightCamera.dlc.pqt’, ‘alf/_ibl_bodyCamera.times.npy’, ‘alf/_ibl_leftCamera.times.npy’, ‘alf/_ibl_rightCamera.times.npy’, ‘alf/_ibl_leftCamera.features.pqt’, ‘alf/_ibl_rightCamera.features.pqt’, ‘alf/rightROIMotionEnergy.position.npy’, ‘alf/leftROIMotionEnergy.position.npy’, ‘alf/bodyROIMotionEnergy.position.npy’, ‘alf/_ibl_trials.choice.npy’, ‘alf/_ibl_trials.feedbackType.npy’, ‘alf/_ibl_trials.feedback_times.npy’, ‘alf/_ibl_trials.stimOn_times.npy’, ‘alf/_ibl_wheel.position.npy’, ‘alf/_ibl_wheel.timestamps.npy’, ‘alf/licks.times.npy’,

Params session_path:

Path to session data on disk

Params one:

ONE instance, if None is given, default ONE is instantiated

Returns:

Matplotlib figure