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Animate facet of states¤

exponax.viz.animate_state_1d_facet ¤

animate_state_1d_facet(
    trj: Float[Array, "B T C N"],
    *,
    vlim: tuple[float, float] = (-1.0, 1.0),
    labels: list[str] = None,
    titles: list[str] = None,
    domain_extent: float = None,
    dt: float = None,
    include_init: bool = False,
    grid: tuple[int, int] = (3, 3),
    figsize: tuple[float, float] = (10, 10),
    **kwargs
)

Animate a trajectory of faceted 1d states.

Requires the input to be a four-axis array with a leading batch axis, a time axis, a channel axis, and a spatial axis. If there is more than one dimension in the channel axis, this will be plotted in a different color. Hence, there are two ways to display multiple states: either via the batch axis (resulting in faceted subplots) or via the channel axis (resulting in different colors).

Periodic boundary conditions will be applied to the spatial axis (the state is wrapped around).

Arguments:

  • trj: The trajectory of states to animate. Must be a four-axis array with shape (n_batches, n_timesteps, n_channels, n_spatial). If the channel axis has more than one dimension, the different channels will be plotted in different colors.
  • vlim: The limits of the colorbar. Default is (-1, 1).
  • labels: The labels for each channel. Default is None.
  • titles: The titles for each subplot. Default is None.
  • domain_extent: The extent of the spatial domain. Default is None. This affects the x-axis limits of the plot.
  • grid: The grid of subplots. Default is (3, 3).
  • figsize: The size of the figure. Default is (10, 10).
  • **kwargs: Additional keyword arguments to pass to the plotting function.

Returns:

  • ani: The animation object.
Source code in exponax/viz/_animate_facet.py 
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def animate_state_1d_facet(
    trj: Float[Array, "B T C N"],
    *,
    vlim: tuple[float, float] = (-1.0, 1.0),
    labels: list[str] = None,
    titles: list[str] = None,
    domain_extent: float = None,
    dt: float = None,
    include_init: bool = False,
    grid: tuple[int, int] = (3, 3),
    figsize: tuple[float, float] = (10, 10),
    **kwargs,
):
    """
    Animate a trajectory of faceted 1d states.

    Requires the input to be a four-axis array with a leading batch axis, a time
    axis, a channel axis, and a spatial axis. If there is more than one
    dimension in the channel axis, this will be plotted in a different color.
    Hence, there are two ways to display multiple states: either via the batch
    axis (resulting in faceted subplots) or via the channel axis (resulting in
    different colors).

    Periodic boundary conditions will be applied to the spatial axis (the state
    is wrapped around).

    **Arguments**:

    - `trj`: The trajectory of states to animate. Must be a four-axis array with
        shape `(n_batches, n_timesteps, n_channels, n_spatial)`. If the channel
        axis has more than one dimension, the different channels will be plotted
        in different colors.
    - `vlim`: The limits of the colorbar. Default is `(-1, 1)`.
    - `labels`: The labels for each channel. Default is `None`.
    - `titles`: The titles for each subplot. Default is `None`.
    - `domain_extent`: The extent of the spatial domain. Default is `None`. This
        affects the x-axis limits of the plot.
    - `grid`: The grid of subplots. Default is `(3, 3)`.
    - `figsize`: The size of the figure. Default is `(10, 10)`.
    - `**kwargs`: Additional keyword arguments to pass to the plotting function.

    **Returns**:

    - `ani`: The animation object.
    """
    if trj.ndim != 4:
        raise ValueError("states must be a four-axis array.")

    if include_init:
        temporal_grid = jnp.arange(trj.shape[1])
    else:
        temporal_grid = jnp.arange(1, trj.shape[1] + 1)

    if dt is not None:
        temporal_grid *= dt

    fig, ax_s = plt.subplots(*grid, figsize=figsize)

    num_subplots = trj.shape[0]

    if grid[0] * grid[1] == 1:
        ax_s = np.array([[ax_s]])
    for j, ax in enumerate(ax_s.flatten()):
        plot_state_1d(
            trj[j, 0],
            vlim=vlim,
            domain_extent=domain_extent,
            labels=labels,
            ax=ax,
            **kwargs,
        )
        if j >= num_subplots:
            ax.remove()
        else:
            if titles is not None:
                ax.set_title(titles[j])
    title = fig.suptitle(f"t = {temporal_grid[0]:.2f}")

    def animate(i):
        for j, ax in enumerate(ax_s.flatten()):
            ax.clear()
            plot_state_1d(
                trj[j, i],
                vlim=vlim,
                domain_extent=domain_extent,
                labels=labels,
                ax=ax,
                **kwargs,
            )
            if j >= num_subplots:
                ax.remove()
            else:
                if titles is not None:
                    ax.set_title(titles[j])
        title.set_text(f"t = {temporal_grid[i]:.2f}")

    ani = FuncAnimation(fig, animate, frames=trj.shape[1], interval=100, blit=False)

    return ani

exponax.viz.animate_state_2d_facet ¤

animate_state_2d_facet(
    trj: Union[
        Float[Array, "T C N N"], Float[Array, "B T 1 N N"]
    ],
    *,
    facet_over_channels: bool = True,
    vlim: tuple[float, float] = (-1.0, 1.0),
    cmap: str = "RdBu_r",
    domain_extent: float = None,
    dt: float = None,
    include_init: bool = False,
    grid: tuple[int, int] = (3, 3),
    figsize: tuple[float, float] = (10, 10),
    titles=None
)

Animate a facet of trajectories of 2d states.

Requires the input to be either a four-axis array or a five-axis array:

  • If facet_over_channels is True, the input must be a four-axis array with a leading time axis, a channel axis, and two spatial axes. Each faceted subplot displays a different channel.
  • If facet_over_channels is False, the input must be a five-axis array with a leading batch axis, a time axis, a channel axis, and two spatial axes. Each faceted subplot displays a different batch. Only the zeroth dimension in the channel axis is plotted.

Periodic boundary conditions will be applied to the spatial axes (the state is wrapped around).

Arguments:

  • trj: The trajectory of states to animate. Must be a four-axis array with shape (n_timesteps, n_channels, n_spatial, n_spatial) if facet_over_channels is True, or a five-axis array with shape (n_batches, n_timesteps, n_channels, n_spatial, n_spatial) if facet_over_channels is False.
  • facet_over_channels: Whether to facet over the channel axis or the batch axis. Default is True.
  • vlim: The limits of the colorbar. Default is (-1, 1).
  • cmap: The colormap to use. Default is "RdBu_r".
  • domain_extent: The extent of the spatial domain. Default is None. This affects the x-axis and y-axis limits of the plot.
  • dt: The time step between each frame. Default is None.
  • include_init: Whether to the state starts at an initial condition (t=0) or at the first frame in the trajectory. This affects is the the time range is [0, (T-1)dt] or [dt, Tdt]. Default is False.
  • grid: The grid of subplots. Default is (3, 3).
  • figsize: The size of the figure. Default is (10, 10).
  • titles: The titles for each subplot. Default is None.

Returns:

  • ani: The animation object.
Source code in exponax/viz/_animate_facet.py 
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def animate_state_2d_facet(
    trj: Union[Float[Array, "T C N N"], Float[Array, "B T 1 N N"]],
    *,
    facet_over_channels: bool = True,
    vlim: tuple[float, float] = (-1.0, 1.0),
    cmap: str = "RdBu_r",
    domain_extent: float = None,
    dt: float = None,
    include_init: bool = False,
    grid: tuple[int, int] = (3, 3),
    figsize: tuple[float, float] = (10, 10),
    titles=None,
):
    """
    Animate a facet of trajectories of 2d states.

    Requires the input to be either a four-axis array or a five-axis array:

    - If `facet_over_channels` is `True`, the input must be a four-axis array
        with a leading time axis, a channel axis, and two spatial axes. Each
        faceted subplot displays a different channel.
    - If `facet_over_channels` is `False`, the input must be a five-axis array
        with a leading batch axis, a time axis, a channel axis, and two spatial
        axes. Each faceted subplot displays a different batch. Only the zeroth
        dimension in the channel axis is plotted.

    Periodic boundary conditions will be applied to the spatial axes (the state
    is wrapped around).

    **Arguments**:

    - `trj`: The trajectory of states to animate. Must be a four-axis array with
        shape `(n_timesteps, n_channels, n_spatial, n_spatial)` if
        `facet_over_channels` is `True`, or a five-axis array with shape
        `(n_batches, n_timesteps, n_channels, n_spatial, n_spatial)` if
        `facet_over_channels` is `False`.
    - `facet_over_channels`: Whether to facet over the channel axis or the batch
        axis. Default is `True`.
    - `vlim`: The limits of the colorbar. Default is `(-1, 1)`.
    - `cmap`: The colormap to use. Default is `"RdBu_r"`.
    - `domain_extent`: The extent of the spatial domain. Default is `None`. This
        affects the x-axis and y-axis limits of the plot.
    - `dt`: The time step between each frame. Default is `None`.
    - `include_init`: Whether to the state starts at an initial condition (t=0)
        or at the first frame in the trajectory. This affects is the the time
        range is [0, (T-1)dt] or [dt, Tdt]. Default is `False`.
    - `grid`: The grid of subplots. Default is `(3, 3)`.
    - `figsize`: The size of the figure. Default is `(10, 10)`.
    - `titles`: The titles for each subplot. Default is `None`.

    **Returns**:

    - `ani`: The animation object.
    """
    if facet_over_channels:
        if trj.ndim != 4:
            raise ValueError("trj must be a four-axis array.")
    else:
        if trj.ndim != 5:
            raise ValueError("trj must be a five-axis array.")

    if facet_over_channels:
        trj = jnp.swapaxes(trj, 0, 1)
        trj = trj[:, :, None]

    if include_init:
        temporal_grid = jnp.arange(trj.shape[1])
    else:
        temporal_grid = jnp.arange(1, trj.shape[1] + 1)

    if dt is not None:
        temporal_grid *= dt

    fig, ax_s = plt.subplots(*grid, sharex=True, sharey=True, figsize=figsize)

    if grid[0] * grid[1] == 1:
        ax_s = np.array([[ax_s]])
    for j, ax in enumerate(ax_s.flatten()):
        plot_state_2d(
            trj[j, 0],
            vlim=vlim,
            cmap=cmap,
            ax=ax,
            domain_extent=domain_extent,
        )
        if titles is not None:
            ax.set_title(titles[j])
    title = fig.suptitle(f"t = {temporal_grid[0]:.2f}")

    def animate(i):
        for j, ax in enumerate(ax_s.flatten()):
            ax.clear()
            plot_state_2d(
                trj[j, i],
                vlim=vlim,
                cmap=cmap,
                ax=ax,
            )
            if titles is not None:
                ax.set_title(titles[j])
        title.set_text(f"t = {temporal_grid[i]:.2f}")

    plt.close(fig)

    ani = FuncAnimation(fig, animate, frames=trj.shape[1], interval=100, blit=False)

    return ani

exponax.viz.animate_state_3d_facet ¤

animate_state_3d_facet(
    trj: Union[
        Float[Array, "T C N N N"],
        Float[Array, "B T 1 N N N"],
    ],
    *,
    facet_over_channels: bool = True,
    vlim: tuple[float, float] = (-1.0, 1.0),
    grid: tuple[int, int] = (3, 3),
    figsize: tuple[float, float] = (10, 10),
    titles=None,
    domain_extent: float = None,
    dt: float = None,
    include_init: bool = False,
    bg_color: Union[
        Literal["black"],
        Literal["white"],
        tuple[jnp.int8, jnp.int8, jnp.int8, jnp.int8],
    ] = "white",
    resolution: int = 384,
    cmap: str = "RdBu_r",
    transfer_function: callable = zigzag_alpha,
    distance_scale: float = 10.0,
    gamma_correction: float = 2.4,
    chunk_size: int = 64,
    **kwargs
)

Animate a facet of trajectories of 3d states as volume renderings.

Requires the input to be either a five-axis array or a six-axis array:

  • If facet_over_channels is True, the input must be a five-axis array with a leading time axis, a channel axis, and three spatial axes. Each faceted subplot displays a different channel.
  • If facet_over_channels is False, the input must be a six-axis array with a leading batch axis, a time axis, a channel axis, and three spatial axes. Each faceted subplot displays a different batch. Only the zeroth dimension in the channel axis is plotted.

Arguments:

  • trj: The trajectory of states to animate. Must be a five-axis array with shape (n_timesteps, n_channels, n_spatial, n_spatial, n_spatial) if facet_over_channels is True, or a six-axis array with shape (n_batches, n_timesteps, n_channels, n_spatial, n_spatial, n_spatial) if facet_over_channels is False.
  • facet_over_channels: Whether to facet over the channel axis or the batch axis. Default is True.
  • vlim: The limits of the colorbar. Default is (-1, 1).
  • grid: The grid of subplots. Default is (3, 3).
  • figsize: The size of the figure. Default is (10, 10).
  • titles: The titles for each subplot. Default is None.
  • domain_extent: The extent of the spatial domain. Default is None. This affects the x-axis and y-axis limits of the plot.
  • dt: The time step between each frame. Default is None.
  • include_init: Whether to the state starts at an initial condition (t=0) or at the first frame in the trajectory. This affects is the the time range is [0, (T-1)dt] or [dt, Tdt]. Default is False.
  • bg_color: The background color. Either "black", "white", or a tuple of RGBA values. Default is "white".
  • resolution: The resolution of the output image (affects render time). Default is 384.
  • cmap: The colormap to use. Default is "RdBu_r".
  • transfer_function: The transfer function to use, i.e., how values within the vlim range are mapped to alpha values. Default is zigzag_alpha.
  • distance_scale: The distance scale of the volume renderer. Default is 10.0.
  • gamma_correction: The gamma correction to apply to the image. Default is 2.4.
  • chunk_size: The number of images to render at once. Default is 64.

Returns:

  • ani: The animation object.

Note:

  • This function requires the vape volume renderer package.
Source code in exponax/viz/_animate_facet.py 
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def animate_state_3d_facet(
    trj: Union[Float[Array, "T C N N N"], Float[Array, "B T 1 N N N"]],
    *,
    facet_over_channels: bool = True,
    vlim: tuple[float, float] = (-1.0, 1.0),
    grid: tuple[int, int] = (3, 3),
    figsize: tuple[float, float] = (10, 10),
    titles=None,
    domain_extent: float = None,
    dt: float = None,
    include_init: bool = False,
    bg_color: Union[
        Literal["black"],
        Literal["white"],
        tuple[jnp.int8, jnp.int8, jnp.int8, jnp.int8],
    ] = "white",
    resolution: int = 384,
    cmap: str = "RdBu_r",
    transfer_function: callable = zigzag_alpha,
    distance_scale: float = 10.0,
    gamma_correction: float = 2.4,
    chunk_size: int = 64,
    **kwargs,
):
    """
    Animate a facet of trajectories of 3d states as volume renderings.

    Requires the input to be either a five-axis array or a six-axis array:

    - If `facet_over_channels` is `True`, the input must be a five-axis array
        with a leading time axis, a channel axis, and three spatial axes. Each
        faceted subplot displays a different channel.
    - If `facet_over_channels` is `False`, the input must be a six-axis array
        with a leading batch axis, a time axis, a channel axis, and three spatial
        axes. Each faceted subplot displays a different batch. Only the zeroth
        dimension in the channel axis is plotted.

    **Arguments**:

    - `trj`: The trajectory of states to animate. Must be a five-axis array with
        shape `(n_timesteps, n_channels, n_spatial, n_spatial, n_spatial)` if
        `facet_over_channels` is `True`, or a six-axis array with shape
        `(n_batches, n_timesteps, n_channels, n_spatial, n_spatial, n_spatial)`
        if `facet_over_channels` is `False`.
    - `facet_over_channels`: Whether to facet over the channel axis or the batch
        axis. Default is `True`.
    - `vlim`: The limits of the colorbar. Default is `(-1, 1)`.
    - `grid`: The grid of subplots. Default is `(3, 3)`.
    - `figsize`: The size of the figure. Default is `(10, 10)`.
    - `titles`: The titles for each subplot. Default is `None`.
    - `domain_extent`: The extent of the spatial domain. Default is `None`. This
        affects the x-axis and y-axis limits of the plot.
    - `dt`: The time step between each frame. Default is `None`.
    - `include_init`: Whether to the state starts at an initial condition (t=0)
        or at the first frame in the trajectory. This affects is the the time
        range is [0, (T-1)dt] or [dt, Tdt]. Default is `False`.
    - `bg_color`: The background color. Either `"black"`, `"white"`, or a tuple
        of RGBA values. Default is `"white"`.
    - `resolution`: The resolution of the output image (affects render time).
        Default is `384`.
    - `cmap`: The colormap to use. Default is `"RdBu_r"`.
    - `transfer_function`: The transfer function to use, i.e., how values within
        the `vlim` range are mapped to alpha values. Default is `zigzag_alpha`.
    - `distance_scale`: The distance scale of the volume renderer. Default is
        `10.0`.
    - `gamma_correction`: The gamma correction to apply to the image. Default is
        `2.4`.
    - `chunk_size`: The number of images to render at once. Default is `64`.

    **Returns**:

    - `ani`: The animation object.

    **Note:**

    - This function requires the `vape` volume renderer package.
    """
    if facet_over_channels:
        if trj.ndim != 5:
            raise ValueError("trj must be a five-axis array.")
    else:
        if trj.ndim != 6:
            raise ValueError("trj must be a six-axis array.")

    if facet_over_channels:
        trj = jnp.swapaxes(trj, 0, 1)
        trj = trj[:, :, None]

    trj_wrapped = jax.vmap(jax.vmap(wrap_bc))(trj)

    imgs = []
    for facet_entry_trj in trj_wrapped:
        facet_entry_trj_no_channel = facet_entry_trj[:, 0]
        imgs.append(
            volume_render_state_3d(
                facet_entry_trj_no_channel,
                vlim=vlim,
                bg_color=bg_color,
                resolution=resolution,
                cmap=cmap,
                transfer_function=transfer_function,
                distance_scale=distance_scale,
                gamma_correction=gamma_correction,
                chunk_size=chunk_size,
                **kwargs,
            )
        )

    # shape = (B, T, resolution, resolution, 3)
    imgs = jnp.stack(imgs)

    if include_init:
        temporal_grid = jnp.arange(trj.shape[1])
    else:
        temporal_grid = jnp.arange(1, trj.shape[1] + 1)

    if dt is not None:
        temporal_grid *= dt

    fig, ax_s = plt.subplots(*grid, figsize=figsize)

    # num_subplots = trj.shape[0]

    if grid[0] * grid[1] == 1:
        ax_s = np.array([[ax_s]])
    for j, ax in enumerate(ax_s.flatten()):
        ax.imshow(imgs[j, 0])
        ax.axis("off")
        # if j >= num_subplots:
        #     ax.remove()
        # else:
        if titles is not None:
            ax.set_title(titles[j])
    title = fig.suptitle(f"t = {temporal_grid[0]:.2f}")

    def animate(i):
        for j, ax in enumerate(ax_s.flatten()):
            ax.clear()
            ax.imshow(imgs[j, i])
            ax.axis("off")
            if titles is not None:
                ax.set_title(titles[j])
        title.set_text(f"t = {temporal_grid[i]:.2f}")

    ani = FuncAnimation(fig, animate, frames=trj.shape[1], interval=100, blit=False)

    plt.close(fig)

    return ani