Create gif

[vlachina]

Hi,

I am using OS Monterey and I am trying to install Imagemagick to use to create gifs in tyssue.

I have installed it via installing home-brew first (/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)") and then installed Imagemagick via " brew install imagemagick ".

The installation was successful but tyssue still displays an error - Converting didn't work, make sure imagemagick is available on your system.

Could you please help?

Kind regards,
Veronika

[glyg]

Hi Veronika thanks for using tyssue!

Can you try to type convert -h in a terminal to see if the program is indeed available?

alternatively you can try to use the function defined bellow, that just generates the pngs, and then create the gif manually with another software (like ffmpeg or maybe ImageJ, or even Blender).

def create_frames(
    history,
    output,
    num_frames=None,
    interval=None,
    draw_func=None,
    margin=5,
    **draw_kwds,
):
    """Creates a set of png frames of the recorded history.
   
    Parameters
    ----------
    history : a :class:`tyssue.History` object
    output : path to the output directory
    num_frames : int, the number of frames in the gif
    interval : tuples, define begin and end frame of the gif
    draw_func : a drawing function
         this function must take a `sheet` object as first argument
         and return a `fig, ax` pair. Defaults to quick_edge_draw
         (aka sheet_view with quick mode)
    margin : int, the graph margins in percents, default 5
         if margin is -1, let the draw function decide
    **draw_kwds are passed to the drawing function
    """
    if draw_func is None:
        if draw_kwds.get("mode") in ("quick", None):
            draw_func = quick_edge_draw
        else:
            draw_func = sheet_view

    graph_dir = pathlib.Path(output)
    graph_dir.mkdir(parents=True, exist_ok=True)

    x, y = coords = draw_kwds.get("coords", history.sheet.coords[:2])
    sheet0 = history.retrieve(0)
    bounds = sheet0.vert_df[coords].describe().loc[["min", "max"]]
    delta = (bounds.loc["max"] - bounds.loc["min"]).max()
    margin = delta * margin / 100
    xlim = bounds.loc["min", x] - margin, bounds.loc["max", x] + margin
    ylim = bounds.loc["min", y] - margin, bounds.loc["max", y] + margin

    if interval is None:
        start, stop = None, None
    else:
        start, stop = interval[0], interval[1]

    for i, (t, sheet) in enumerate(history.browse(start, stop, num_frames)):
        try:
            fig, ax = draw_func(sheet, **draw_kwds)
        except Exception as e:
            print("Droped frame {i}")

        if isinstance(ax, plt.Axes) and margin >= 0:
            ax.set(xlim=xlim, ylim=ylim)
        fig.savefig(graph_dir / f"movie_{i:04d}.png")
        plt.close(fig)

It would be good to split that function anyway