Re: [Matplotlib-users] 3d animated scatter plot

[Benjamin R. <ben...@ou...>]

On Sun, Nov 11, 2012 at 1:42 PM, Andrew Dawson <da...@at...> wrote:

> Hi
>
> I'm trying to plot the trajectory of a particle in 3d using mplot3d. I
> tried to follow the example of an animated 3d plot on the matplotlib
> website but I'm having trouble with the updating of the data point being
> plotted at each frame. Does anyone know how to do this?
>
> So far I have:
>
> import numpy as np
> import matplotlib.pyplot as plt
> from mpl_toolkits.mplot3d.axes3d import Axes3D
> from matplotlib.animation import FuncAnimation
>
>
> def update_plot(num, data, sc):
>     sc.set_array(data[num])
>     return sc
>
>
> def main():
>     numframes = 2
>     data = np.random.rand(10, 3)# a (time, position) array
>
>     fig = plt.figure()
>     ax = fig.add_subplot(111, projection='3d')
>
>     ix, iy, iz = data[0]
>     sc = ax.scatter(ix, iy, iz, c='k')
>
>     ani = FuncAnimation(fig, update_plot, frames=numframes,
>             fargs=(data,sc))
>     plt.show()
>
>
> if __name__ == '__main__':
>     main()
>
>
> This just changes the color of the initial marker. I also tried to use
> sc.set_3d_properties but it is not clear to me what the arguments should be
> here, I kept getting an error... If anyone has done this before I'd love to
> see an example.
>
> Thanks,
> Andrew
>
>

Andrew,

For scatter objects (which are PatchCollection), the get/set_data() refers
to the scalar mappable part of things, which is why the color kept
changing.  It does not seem to be an easy way to adjust the position data
for a Patch3DCollection (or a Line3DCollection for that matter...).  I
would suggest filing a feature request about that on github.  In coming up
with an example for your use-case, I have come across a couple of minor
bugs in mplot3d that I am going to need to resolve as well.  In the
meantime, I think the following version of the code:

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d.axes3d import Axes3D
from matplotlib.animation import FuncAnimation


def update_plot(num, data, sc):
    print sc._offsets3d
    sc._offsets3d = data[num]
    return sc


def main():
    numframes = 10
    data = np.random.rand(numframes, 3, 1)# a (time, position) array

    fig = plt.figure()
    ax = fig.add_subplot(111, projection='3d')

    ix, iy, iz = data[0]
    sc = ax.scatter(ix, iy, iz, c='k')
    ani = FuncAnimation(fig, update_plot, frames=numframes,
            fargs=(data,sc))
    plt.show()


if __name__ == '__main__':
    main()

Essentially, there is no nice way to set the 3d position data, and the
easiest way is to just go to the internal _offsets3d variable.  Second,
there seems to be an issue with array/scalar data in Patch3DCollection that
I had to make the random number generation be 3D, rather than 2D as you
originally had it.

Cheers!
Ben Root