cibrrig.videos

Attributes

_log

PROJECTION_KWARGS

TRAIL_KWARGS

HISTORY_KWARGS

AUX_KWARGS

CACHE_DIR

Functions

make_aux_raster_projection_with_stims(pop, intervals, ...)

Make a video of the projection with a raster and an auxiliary trace.

make_projection(pop, t0, duration, fn_out[, ...])

Make an animation of just the projection with temporal evolution.

make_rotating_projection(pop, t0, duration, fn_out[, ...])

Rotate a 3D projection without temporal evolution.

_trim_axes(ax, pop, t0, tf, dims)

Trim the limits of the projection plots

_plot_xy_plane(ax, **kwargs)

Plot a transparent XY plane on a 3D axes.

_plot_all_planes(ax, **kwargs)

Plot transparent XY, YZ, and XZ planes on a 3D axes.

Module Contents

cibrrig.videos._log[source]
cibrrig.videos.PROJECTION_KWARGS[source]
cibrrig.videos.TRAIL_KWARGS[source]
cibrrig.videos.HISTORY_KWARGS[source]
cibrrig.videos.AUX_KWARGS[source]
cibrrig.videos.make_aux_raster_projection_with_stims(pop, intervals, aux, aux_t, fn_out, stim_color, aux_label='', frame_step=0.01, duration=2, cmap='bone', vmax=0.5, baseline=10, fps=30, dpi=300, dims=[0, 1], lead_in=1, winsize=1, trail_length=0.05, figsize=(3, 8), azim_speed=0.1, elev_speed=0.1, rotation_delay=1, rotate=True, style='dark_background', projection_kwargs=PROJECTION_KWARGS, trail_kwargs=TRAIL_KWARGS, history_kwargs=HISTORY_KWARGS, aux_kwargs=AUX_KWARGS)[source]

Make a video of the projection with a raster and an auxiliary trace.

This function creates a video of the projection with a raster plot and an auxiliary trace. It allows for various customizations, including the duration, colormap, frame rate, and rotation settings. The video is saved to the specified output file.

Parameters:

  • pop (Population) – Population object containing the projection data.

  • intervals (np.ndarray) – Array of intervals (n x 2) for the stimulus periods.

  • aux (np.ndarray) – Auxiliary data to be plotted.

  • aux_t (np.ndarray) – Time vector for the auxiliary data.

  • fn_out (str or Path) – Output file path for the video.

  • stim_color (str) – Color for the stimulus periods.

  • aux_label (str, optional) – Label for the auxiliary trace. Defaults to “”.

  • frame_step (float, optional) – Time step between frames in seconds. Defaults to 0.01.

  • duration (float, optional) – Duration of the video in seconds. Defaults to 2.

  • cmap (str, optional) – Colormap for the projection. Defaults to “bone”.

  • vmax (float, optional) – Maximum value for the colormap normalization. Defaults to 0.5.

  • baseline (int, optional) – Baseline value for the projection. Defaults to 10.

  • fps (int, optional) – Frames per second for the video. Defaults to 30.

  • dpi (int, optional) – Dots per inch for the video. Defaults to 300.

  • dims (list, optional) – Dimensions of the data to be plotted. Defaults to [0, 1].

  • lead_in (float, optional) – Lead-in time before the start of the intervals. Defaults to 1.

  • winsize (float, optional) – Window size for the projection. Defaults to 1.

  • trail_length (float, optional) – Length of the trail in the projection. Defaults to 0.05.

  • figsize (tuple, optional) – Figure size for the video. Defaults to (3, 8).

  • azim_speed (float, optional) – Speed of azimuthal rotation. Defaults to 0.1.

  • elev_speed (float, optional) – Speed of elevation rotation. Defaults to 0.1.

  • rotation_delay (float, optional) – Delay before starting the rotation. Defaults to 1.

  • rotate (bool, optional) – Whether to rotate the 3D plot. Defaults to True.

  • style (str, optional) – Matplotlib style to use. Defaults to “dark_background”.

  • projection_kwargs (dict, optional) – Additional keyword arguments for the projection. Defaults to PROJECTION_KWARGS.

  • trail_kwargs (dict, optional) – Additional keyword arguments for the trail.Passed to plt.plot. Defaults to TRAIL_KWARGS.

  • history_kwargs (dict, optional) – Additional keyword arguments for the history. Passed to LineCollection. Defaults to HISTORY_KWARGS.

  • aux_kwargs (dict, optional) – Additional keyword arguments for the auxiliary trace. Passed to plt.plot. Defaults to AUX_KWARGS.

Returns:

None

cibrrig.videos.make_projection(pop, t0, duration, fn_out, stim_color='C1', intervals=None, cvar=None, cvar_label='', cmap='magma', dims=[0, 1], frame_step=0.01, fps=30, dpi=300, trail_length=0.05, figsize=(4, 4), style='dark_background', projection_kwargs=PROJECTION_KWARGS, history_kwargs=HISTORY_KWARGS, trail_kwargs=TRAIL_KWARGS, baseline=20, mode='line', rotate=True, rotation_delay=1, elev_speed=0.2, azim_speed=0.2, vmin=None, vmax=None)[source]

Make an animation of just the projection with temporal evolution.

Parameters:

  • pop (Population) – Population object containing the projection data.

  • t0 (float) – Start time of the projection.

  • duration (float) – Duration of the projection in seconds.

  • fn_out (str or Path) – Output file path for the animation.

  • stim_color (str, optional) – Color for the stimulus periods. Defaults to ‘C1’.

  • intervals (np.ndarray, optional) – Array of intervals (n x 2) for the stimulus periods. Defaults to None.

  • cvar (np.ndarray, optional) – Covariate data for coloring the history. Defaults to None.

  • cvar_label (str, optional) – Label for the covariate data. Defaults to “”.

  • cmap (str, optional) – Colormap for the projection. Defaults to “magma”.

  • dims (list, optional) – Dimensions of the data to be plotted. Defaults to [0, 1].

  • frame_step (float, optional) – Time step between frames in seconds. Defaults to 0.01.

  • fps (int, optional) – Frames per second for the animation. Defaults to 30.

  • dpi (int, optional) – Dots per inch for the animation. Defaults to 300.

  • trail_length (float, optional) – Length of the trail in the projection. Defaults to 0.05.

  • figsize (tuple, optional) – Figure size for the animation. Defaults to (4, 4).

  • style (str, optional) – Matplotlib style to use. Defaults to “dark_background”.

  • projection_kwargs (dict, optional) – Additional keyword arguments for the projection. Defaults to PROJECTION_KWARGS.

  • history_kwargs (dict, optional) – Additional keyword arguments for the history. Passed to LineCollection. Defaults to HISTORY_KWARGS.

  • trail_kwargs (dict, optional) – Additional keyword arguments for the trail. Passed to plt.plot. Defaults to TRAIL_KWARGS.

  • baseline (int, optional) – Baseline value for the projection. Defaults to 20.

  • mode (str, optional) – Mode for the projection. Defaults to “line”.

  • rotate (bool, optional) – Whether to rotate the 3D plot. Defaults to True.

  • rotation_delay (float, optional) – Delay before starting the rotation. Defaults to 1.

  • elev_speed (float, optional) – Speed of elevation rotation. Defaults to 0.2.

  • azim_speed (float, optional) – Speed of azimuthal rotation. Defaults to 0.2.

  • vmin (float, optional) – Minimum value for the colormap normalization. Defaults to None.

  • vmax (float, optional) – Maximum value for the colormap normalization. Defaults to None.

Returns:

None

cibrrig.videos.make_rotating_projection(pop, t0, duration, fn_out, figsize=(4, 4), dims=[0, 1, 2], cvar=None, rotation_delay=1, elev_speed=0.1, azim_speed=0.1, mode='scatter', style='dark_background', cvar_label='', cmap='magma', vmin=None, vmax=None, frame_step=0.01, fps=30, dpi=300, n_frames=100, projection_kwargs=PROJECTION_KWARGS)[source]

Rotate a 3D projection without temporal evolution.

Parameters:

  • pop (Population) – Population object containing the projection data.

  • t0 (float) – Start time of the projection.

  • duration (float) – Duration of the projection in seconds.

  • fn_out (str or Path) – Output file path for the animation.

  • figsize (tuple, optional) – Figure size for the animation. Defaults to (4, 4).

  • dims (list, optional) – Dimensions of the data to be plotted. Defaults to [0, 1, 2].

  • cvar (np.ndarray, optional) – Covariate data for coloring the projection. Defaults to None.

  • rotation_delay (float, optional) – Delay before starting the rotation. Defaults to 1.

  • elev_speed (float, optional) – Speed of elevation rotation. Defaults to 0.1.

  • azim_speed (float, optional) – Speed of azimuthal rotation. Defaults to 0.1.

  • mode (str, optional) – Mode for the projection (‘line’ or ‘scatter’). Defaults to “scatter”.

  • style (str, optional) – Matplotlib style to use. Defaults to “dark_background”.

  • cvar_label (str, optional) – Label for the covariate data. Defaults to “”.

  • cmap (str, optional) – Colormap for the projection. Defaults to “magma”.

  • vmin (float, optional) – Minimum value for the colormap normalization. Defaults to None.

  • vmax (float, optional) – Maximum value for the colormap normalization. Defaults to None.

  • frame_step (float, optional) – Time step between frames in seconds. Defaults to 0.01.

  • fps (int, optional) – Frames per second for the animation. Defaults to 30.

  • dpi (int, optional) – Dots per inch for the animation. Defaults to 300.

  • n_frames (int, optional) – Number of frames for the animation. Defaults to 100.

  • projection_kwargs (dict, optional) – Additional keyword arguments for the projection. Defaults to PROJECTION_KWARGS.

Returns:

None

cibrrig.videos._trim_axes(ax, pop, t0, tf, dims)[source]

Trim the limits of the projection plots N.B. Might be uneeded now that the plot module does this already

Parameters:

  • ax (matplotlib.axes) – Axis to modify

  • pop (Population) – Population object

  • t0 (float) – start time of data that is plotted

  • tf (float) – end time of data that is plotted

  • dims (list) – Dimensions of the data that are plotted

Returns:

Modifiied axes

Return type:

ax (matplotlib.axes)

cibrrig.videos._plot_xy_plane(ax, **kwargs)[source]

Plot a transparent XY plane on a 3D axes.

This function plots a transparent XY plane on a 3D axes based on the current x and y limits of the axes. The plane is plotted with the specified keyword arguments.

Parameters:

  • ax (Axes3D) – The 3D axes on which to plot the XY plane.

  • **kwargs – Additional keyword arguments to pass to the plot_surface method.

Returns:

None

cibrrig.videos._plot_all_planes(ax, **kwargs)[source]

Plot transparent XY, YZ, and XZ planes on a 3D axes.

This function plots transparent XY, YZ, and XZ planes on a 3D axes based on the current x, y, and z limits of the axes. The planes are plotted with the specified keyword arguments.

Parameters:

  • ax (Axes3D) – The 3D axes on which to plot the planes.

  • **kwargs – Additional keyword arguments to pass to the plot_surface method.

Returns:

None

cibrrig.videos.CACHE_DIR = '/data/hps/assoc/private/medullary/data/alf_data_repo'[source]