dynamics

plot.dynamics

General-purpose plotting for Dynamics objects.

A single entry point plot_dynamics (also exposed as Dynamics.plot) that selects between several kind of representations: time series, 1D/2D/3D phase portraits, and 2D vector fields. Dimensions can be state-variable names, derived-variable names, or arbitrary sympy-parseable expressions over them. Labels are rendered as LaTeX via sympy.latex. Styling and colormaps come from bsplot.

Functions

Name	Description
animate_dynamics	Animate a :class:Dynamics by sweeping one parameter through values.
plot_dynamics	Plot a Dynamics in several ways.
plot_dynamics_layout	Backwards-compatible shim — delegates to tvbo.plot.dynamics_layout.plot_dynamics_layout.
plot_experiment_layout	Backwards-compatible shim — delegates to tvbo.plot.experiment_layout.plot_experiment_layout.

animate_dynamics

plot.dynamics.animate_dynamics(
    dynamics,
    parameter,
    values,
    *dims,
    kind='vectorfield',
    interval=80,
    figsize=(5, 4.5),
    title_fmt='{name} = {value:.3f}',
    **kwargs,
)

Animate a :class:Dynamics by sweeping one parameter through values.

For each frame the parameter is set, the chosen kind of plot is drawn on the same axes (cleared between frames), and a title shows the current value. Returns a :class:matplotlib.animation.FuncAnimation that you can display with anim.to_jshtml() (Quarto / notebooks) or save with anim.save("foo.mp4").

Parameters

dynamics : Dynamics parameter : str Name of the parameter to sweep (must be in dynamics.parameters). values : sequence of float Parameter values, one per frame. *dims, kind, **kwargs Forwarded to :func:plot_dynamics. interval : int Delay between frames in ms. figsize : (float, float) title_fmt : str Format string with {name} and {value} placeholders.

plot_dynamics

plot.dynamics.plot_dynamics(
    dynamics,
    *dims,
    kind='auto',
    duration=2000,
    dt=0.1,
    n_trials=1,
    u_0=None,
    color_by=None,
    cmap='viridis',
    transient=0.0,
    ax=None,
    show_ic=True,
    lw=0.8,
    alpha=0.8,
    grid_n=20,
    stream=True,
    stream_density=1.2,
    stream_arrowsize=1.0,
    quiver_scale=None,
    quiver_width=None,
    n_trajectories=0,
    show_nullclines=True,
    show_fixed_points=True,
    trajectory_color='red',
)

Plot a Dynamics in several ways.

Parameters

dynamics : Dynamics *dims : str 1-3 dimensions: state-variable name, derived-variable name, or any sympy-parseable expression over them. Defaults: first SV (timeseries), first 2 SVs (phase / vectorfield / phaseplane). kind : {“auto”, “timeseries”, “phase”, “vectorfield”, “phaseplane”} - timeseries: stacked time series, one panel per dim. - phase: 1D/2D/3D phase portrait. - vectorfield: 2D vector field (stream- or quiver-plot). - phaseplane: vector field + nullclines + (optional) sample trajectories + auto-detected fixed points. - auto: timeseries for 1 dim, phase for 2-3 dims. duration, dt : float Integration parameters in ms. n_trials : int Number of trajectories. > 1 resamples ICs from each SV’s distribution. u_0 : array-like, optional Explicit IC(s); shape (n_sv,) or (n_trials, n_sv). color_by : str, optional Variable / expression to color trajectories by (phase). Defaults to trial index for multi-trial plots, time for single-trial 2D/3D. cmap : str Matplotlib / bsplot colormap name. transient : float Discard this many ms from the start of each trajectory. ax : matplotlib.axes.Axes, optional show_ic : bool lw, alpha : float grid_n : int Grid resolution for kind="vectorfield" / "phaseplane". stream : bool Stream- vs quiver-plot for vectorfield / phaseplane. stream_density, stream_arrowsize : float Matplotlib streamplot controls used when stream=True. quiver_scale, quiver_width : float, optional Matplotlib quiver sizing controls used when stream=False. n_trajectories : int Number of sample trajectories overlaid on a phase plane (random ICs). show_nullclines, show_fixed_points : bool Toggles for kind="phaseplane". trajectory_color : str Color of overlaid sample trajectories on a kind="phaseplane" plot. Defaults to "red" for clear contrast against the streamline / nullcline overlay.

Returns

matplotlib.figure.Figure

plot_dynamics_layout

plot.dynamics.plot_dynamics_layout(
    dynamics,
    layout=None,
    panels=None,
    figsize=None,
    subplot_kwargs=None,
    fig=None,
    axes=None,
)

Backwards-compatible shim — delegates to tvbo.plot.dynamics_layout.plot_dynamics_layout.

plot_experiment_layout

plot.dynamics.plot_experiment_layout(
    experiment,
    layout=None,
    panels=None,
    figsize=None,
    subplot_kwargs=None,
    run_kwargs=None,
    fig=None,
    axes=None,
)

Backwards-compatible shim — delegates to tvbo.plot.experiment_layout.plot_experiment_layout.