animating a stem plot in matplotlib

Question

I'm trying to animate a stem plot in matplotlib and I can't find the necessary documentation to help me. I have a series of data files which each look like this:

1 0.345346
2 0.124325
3 0.534585

and I want plot each file as a separate frame.

According to this and this other tutorial, I should create a function which updates the data contained in each plot object (artist? I'm not sure about the terminology)

From the second link, this is the update function

def update(frame):
global P, C, S

# Every ring is made more transparent
C[:,3] = np.maximum(0, C[:,3] - 1.0/n)

# Each ring is made larger
S += (size_max - size_min) / n

# Reset ring specific ring (relative to frame number)
i = frame % 50
P[i] = np.random.uniform(0,1,2)
S[i] = size_min
C[i,3] = 1

# Update scatter object
scat.set_edgecolors(C)
scat.set_sizes(S)
scat.set_offsets(P)

# Return the modified object
return scat,

How can I adapt this kind of update function for a stem plot? The documentation for stem is horribly brief (in fact this is a recurring issue as I'm learning matplotlib), but the example code shows that the output of stem is a tuple markerline, stemlines, baseline rather than an artist object like for plt.plot or plt.imshow.

So when I write my update function for the animation, how can I update the data inside the stem plot?

Answer 1

When using the keyword use_line_collection=True (default behavior since Matplotlib 3.3) one can update the three elements

• markerline
• stemlines
• baseline

individualy. Here is the code for the sine wave example:

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation

fig, ax = plt.subplots()
x = np.linspace(0.1, 2*np.pi, 10)
y = np.cos(x)
bottom = 0
h_stem = ax.stem(x, y, bottom=bottom, use_line_collection=True, linefmt='-.')

def update(i):
    y = np.cos(x+i/10)

    # markerline
    h_stem[0].set_ydata(y)
    h_stem[0].set_xdata(x)  # not necessary for constant x 

    # stemlines
    h_stem[1].set_paths([np.array([[xx, bottom], 
                                   [xx, yy]]) for (xx, yy) in zip(x, y)])

    # baseline
    h_stem[2].set_xdata([np.min(x), np.max(x)])
    h_stem[2].set_ydata([bottom, bottom])  # not necessary for constant bottom

anim = FuncAnimation(fig, update, frames=range(10, 110, 10), interval=1)
anim.save('so.gif', dpi=80, writer='imagemagick')

Depending on what values (x, y, bottom) should be updated you can omit some parts of this update or reuse the current values. I wrote a more general function, where you can pass an arbitrary combination of these values:

def update_stem(h_stem, x=None, y=None, bottom=None):
    if x is None:
        x = h_stem[0].get_xdata()
    else:
        h_stem[0].set_xdata(x)
        h_stem[2].set_xdata([np.min(x), np.max(x)])

    if y is None:
        y = h_stem[0].get_ydata()
    else:
        h_stem[0].set_ydata(y)

    if bottom is None:
        bottom = h_stem[2].get_ydata()[0]
    else:
        h_stem[2].set_ydata([bottom, bottom])

    h_stem[1].set_paths([np.array([[xx, bottom], 
                                   [xx, yy]]) for (xx, yy) in zip(x, y)])

Answer 2

Here you go!

import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation

import numpy as np

fig, ax = plt.subplots()
x = np.linspace(0.1, 2*np.pi, 10)
markerline, stemlines, baseline = ax.stem(x, np.cos(x), '-.')

def update(i):
    ax.cla()
    markerline, stemlines, baseline = ax.stem(x, np.cos(x+i/10), '-.')
    ax.set_ylim((-1, 1))

anim = FuncAnimation(fig, update, frames=range(10, 110, 10), interval=500)
anim.save('so.gif', dpi=80, writer='imagemagick')

I think there can be better ways of achieving this- not requiring to clear the plot each time. However, this works!