Xarray: Animate DataArrays

[tomchor]

Hi, this is my first a feature request here. I've been using xarray for a while but it always comes somewhat short when I'm trying to do animations. It always ends up being a big hassle.

Is there a good way to provide some functionality to make animations easier? I really like the way xarray sets up the plots by default, but I always end up re-writing it when setting up an animation, which I always feel like is kind of a shame.

Cheers

[max-sixty]

Sounds interesting and thanks for your first issue.

What's an example of an animation?

[tomchor]

Unfortunately I don't have any example with DataArray right now. Since I never could take advantage of DataArray's plotting capabilities for animations, I always did animations using pure Numpy. However, I'm talking about the standard matplotlib animations. Here's an example taken from here:

```import numpy as np
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import matplotlib.animation as animation

def update_line(num, data, line):
line.set_data(data[..., :num])
return line,

Set up formatting for the movie files

Writer = animation.writers['ffmpeg']
writer = Writer(fps=15, metadata=dict(artist='Me'), bitrate=1800)

fig1 = plt.figure()

data = np.random.rand(2, 25)
l, = plt.plot([], [], 'r-')
plt.xlim(0, 1)
plt.ylim(0, 1)
plt.xlabel('x')
plt.title('test')
line_ani = animation.FuncAnimation(fig1, update_line, 25, fargs=(data, l),
interval=50, blit=True)
line_ani.save('lines.mp4', writer=writer)
```

If you have some directions on a smart way to bring xarray into the picture, maybe I can try to come up with an example that might evolve into a contribution.

[benbovy]

@tomchor Note that holoviews supports xarray objects.

You can find an example of an animation made using holoviews and xarray here:
http://nbviewer.jupyter.org/gist/benbovy/e9d4f3d3be076de24b8842dae109d6e7

[tomchor]

I didn't know holoviews existed, thanks for pointing that out to me. The fact that it can't create an animation file (as far as I could tell so far) does mean I can't use it, though. So I'll still try to pursue the matplotlib animation option, although maybe for most users holoviews+xarray might already be enough (I don't know).

[philippjfr]

The fact that it can't create an animation file (as far as I could tell so far) does mean I can't use it, though

You can create animation files using the matplotlib backend in holoviews, as a simple example:

import xarray as xr
import holoviews as hv
hv.extension('matplotlib')

air = xr.tutorial.load_dataset('air_temperature')
ds = hv.Dataset(air.isel(time=range(100)))
images = ds.to(hv.Image, ['lon', 'lat']).options(fig_inches=(10, 5), colorbar=True, cmap='viridis')

To display it in the notebook:

%%output holomap='mp4'
images

To save it to file:

renderer = hv.renderer('matplotlib')
renderer.save(images, 'hv_anim', 'mp4')

[tomchor]

@philippjfr Thanks for the comment. I hand't found anything like that. For me, %%output isn't a recognized magic command, and the renderer.save command fails for me with a tkinter-related error (can't invoke "wm" command), so I really couldn't see anything yet. But I believe I'll be able to solve that eventually.

[philippjfr]

I hand't found anything like that.

Yes, the Plotting with Matplotlib section in the user guide should cover it but it appears to be broken in the last website build.

For me, %%output isn't a recognized magic command

That will only work in the notebook after you have run hv.extension('matplotlib').

fails for me with a tkinter-related error (can't invoke "wm" command), so I really couldn't see anything yet.

You might have to switch to a different matplotlib GUI toolkit or forego one entirely and use agg, either by declaring it in your matplotlib.rc or by setting the backend before importing holoviews, e.g.:

import matplotlib
matplotlib.use('Agg')

[benbovy]

In the example above I had to change this line:

images = ds.to(hv.Image, ['lon', 'lat']).options(fig_inches=(10, 5), colorbar=True, cmap='viridis')

to

images = ds.to(hv.Image, ['lon', 'lat']).options('Image', fig_inches=(10, 5), colorbar=True, cmap='viridis')

in order to avoid

ValueError: HoloMap type not found, could not apply options.

(Holoviews version 1.10.0a2)

[philippjfr]

@benbovy Yes that's right, my apologies, I always work with the bleeding edge and forget what was merged before the last release. What I posted will be valid in 1.10.0, due to be released next week.

[tomchor]

@philippjfr Even with the alteration I still get a HoloMap type not found (using HV 1.9.5) error. I can still see the animation, though. And switching to 'Agg' did allow me to save the animation in mp4, which is good. All workarounds aside, this works pretty well. Thanks a lot to all.

[tommylees112]

@philippjfr

How do you change the fps in the code that you posted above

Thanks for your help!

[philippjfr]

Small update in the syntax, which also happens to make it easier to set fps:

import xarray as xr
import holoviews as hv
hv.extension('matplotlib')

air = xr.tutorial.open_dataset('air_temperature').load()
ds = hv.Dataset(air.isel(time=range(100)))
images = ds.to(hv.Image, ['lon', 'lat']).options(fig_inches=(10, 5), colorbar=True, cmap='viridis')
hv.save(images, 'hv_anim.mp4', fps=4)