On-the-fly Animation in IJulia Notebooks

Specific Domains Visualization
1

I recently revisited how to do on-the-fly visualisation in an IJulia notebook, i.e., plotting results while the computation is still running. This was discussed a while back in Google groups link

I’ve tried the same scheme with Plots.jl with Plotly backend, and I am thrilled that this still works. (Julia 0.5.1pre). Below is the code for anybody interested.

But my key issue back then and still now is: why does it need to be so complicated? I.e. why can I not simply write

x = linspace(0, 2*pi, 100) |> collect 
dt, nsteps = 0.03, 300
for n = 1:nsteps
    plot(x, sin(x - dt*n))
end

Is there a fundamental barrier? I would really appreciate this functionality not just for my own research but also for teaching with Julia. (I can’t promise but I might even be able to find some funding to get it implemented.)

Here is the promised code now:

CELL 1

using Reactive, Interact, Plots
Plots.plotlyjs()

function myplot(data)    
    Plots.plot(data[1], data[2], xlims=(0, 2*pi), ylims=(-1.2,1.2))
end

x = linspace(0, 2*pi, 100) |> collect 
myinput = Signal((x, sin(x)))
lift(myplot, my input)

CELL 2

dt, nsteps = 0.03, 300
for n = 1:nsteps
    push!(myinput, (x, sin(x - n*dt)))
end
2

I don’t understand… What “doesn’t work”? You probably just need to show
the plot inside your loop. See the docs (specifically the page on “output”)

3

Hi cortner, I would use Plots.jl for anything fancy, but I sometimes use this solution for quick and dirty “animations”

using PyPlot
x = linspace(0, 2*pi, 100) |> collect 
dt, nsteps = 0.03, 30
fig = figure()
for n = 1:nsteps
    plot(x, sin(x - dt*n), animated=true)
    sleep(0.3)
    IJulia.clear_output(true)
    display(fig)
    clf()
end
2 Likes
4

@tbreloff Thank you for pointing that out; embarrassingly I didn’t actually see this (I was only following the discussion groups to see whether somebody brings it up)

I now tried both default(show=true) and display(plt) and neither worked for me. With PyPlot nothing happens at all, while with Plotly it will overwrite the existing plot instead of replacing it. Probably there will be a way to fix either - I’ll go read you docs in detail. (But if somebody has seen this and knows the fix I’d love to hear it)

EDIT: if I use GR, then the kernel either crashes or I see nothing?

5

@cstjean Thank you - this seems to work. Good to know there is such a simple solution.

The only problem with IJulia.clear_output(true) is that it creates very strong flickering, so not very useful for presentations.

6

The following example works on macOS, Linux and Windows:

using GR
inline()
x = linspace(0, 2*pi, 100)
dt, nsteps = 0.03, 30
for n = 1:nsteps
    plot(x, sin(x - dt*n))
end

Can also be used in iTerm2 or Atom (inline("iterm"), inline("atom") resp.).

If you observe some flickering (in non-GUI mode), simple enable double buffering …

ENV["GKS_DOUBLE_BUF"]="true"
```

... before importing ``GR``.

Using ``gr()`` via ``Plots`` should also work.
7

@jheinen Copy pasting your code into my notebook, I get no output at all. I am beginning to wonder whether there is something wrong with my installation . . .

8

Sounds fishy. Update, build, and restart?

9

Sorry. There is sth going wrong. Right now, it only works when creating a movie on the fly. That’s probably not what you want …

I’ll check that.

using GR
inline("mov")
x = linspace(0, 2*pi, 100)
dt, nsteps = 0.03, 30
for n = 1:nsteps
    plot(x, sin(x - dt*n))
end
GR.show()
10

GKS: /home/kjwiik/.julia/v0.5/GR/src/…/deps/gr/lib/./movplugin.so: undefined symbol: gks_movplugin

11

This problem is solved with the actual GR release …

Pkg.update()
ENV["GRDIR"]=""
Pkg.build("GR")

… should update GR to 0.18.0 and download the GR run-time (0.22.0).

12

Thanks, now there are no errors but the movie is empty…

1161×405 13.9 KB

13

I get the same result

14

The following code, which modifies @cstjean’s suggestion works perfectly:

using Plots
Plots.plotlyjs()
x = linspace(0, 2*pi, 100) |> collect 
dt, nsteps = 0.03, 100
for n = 1:nsteps
    IJulia.clear_output(true)
    Plots.plot(x, sin(x - n*dt))  |> display
end

Replacing Plotly backend with GR works equally well. With PyPlot is just slow and flickers.

Thank you all for the help - I am very happy that this works.

15

there is just one nagging little issue left: the notebook freezes during the animation (i.e. I can’t scroll, type or do anything else) Is this avoidable and if so where could I raise it as an issue?

16

This should not be necessary. There must be some issue with the IJulia integration?

17

So this is the code that works fine ith GR:

using GR
inline()
x = linspace(0, 2*pi, 100) |> collect 
dt, nsteps = 0.03, 100
for n = 1:nsteps
    IJulia.clear_output(true)
    plot(x, sin(x - n*dt))  |> display
end

There should be some GR option (in the next release) to avoid the IJulia.clear_output() call.

BTW: It seems to me, that the PlotlyJS solution is somehow buffered and not plotting in real-time.

1 Like
18

@mkborregaard What should not be necessary?

19

the clear_output() call

1 Like
20

Did GR create a file gks.mov in your working directory? If so, can you play it using ffplay or vlc. If not, what system (OS, version) are you using?

Does the version I posted 1h ago work?