Tag Archives: matplotlib

Matplotlib legends for mean and confidence interval plots

When plotting means and confidence intervals, sometimes the mean lines are hard to see and it’s nice to have included in your legend the color of the confidence interval shading. It turns out this is a bit of a chore in Matplotlib, but building off of their online examples you can get something that looks pretty alright:

mean_and_CI

So here’s code for getting the above plot, with an option for solid or dashed lines. The sky is the limit!

import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from matplotlib.colors import colorConverter as cc
import numpy as np

def plot_mean_and_CI(mean, lb, ub, color_mean=None, color_shading=None):
    # plot the shaded range of the confidence intervals
    plt.fill_between(range(mean.shape[0]), ub, lb,
                     color=color_shading, alpha=.5)
    # plot the mean on top
    plt.plot(mean, color_mean)

# generate 3 sets of random means and confidence intervals to plot
mean0 = np.random.random(50)
ub0 = mean0 + np.random.random(50) + .5
lb0 = mean0 - np.random.random(50) - .5

mean1 = np.random.random(50) + 2
ub1 = mean1 + np.random.random(50) + .5
lb1 = mean1 - np.random.random(50) - .5

mean2 = np.random.random(50) -1
ub2 = mean2 + np.random.random(50) + .5
lb2 = mean2 - np.random.random(50) - .5

# plot the data
fig = plt.figure(1, figsize=(7, 2.5))
plot_mean_and_CI(mean0, ub0, lb0, color_mean='k', color_shading='k')
plot_mean_and_CI(mean1, ub1, lb1, color_mean='b', color_shading='b')
plot_mean_and_CI(mean2, ub2, lb2, color_mean='g--', color_shading='g')

class LegendObject(object):
    def __init__(self, facecolor='red', edgecolor='white', dashed=False):
        self.facecolor = facecolor
        self.edgecolor = edgecolor
        self.dashed = dashed

    def legend_artist(self, legend, orig_handle, fontsize, handlebox):
        x0, y0 = handlebox.xdescent, handlebox.ydescent
        width, height = handlebox.width, handlebox.height
        patch = mpatches.Rectangle(
            # create a rectangle that is filled with color
            [x0, y0], width, height, facecolor=self.facecolor,
            # and whose edges are the faded color
            edgecolor=self.edgecolor, lw=3)
        handlebox.add_artist(patch)

        # if we're creating the legend for a dashed line,
        # manually add the dash in to our rectangle
        if self.dashed:
            patch1 = mpatches.Rectangle(
                [x0 + 2*width/5, y0], width/5, height, facecolor=self.edgecolor,
                transform=handlebox.get_transform())
            handlebox.add_artist(patch1)

        return patch

bg = np.array([1, 1, 1])  # background of the legend is white
colors = ['black', 'blue', 'green']
# with alpha = .5, the faded color is the average of the background and color
colors_faded = [(np.array(cc.to_rgb(color)) + bg) / 2.0 for color in colors]

plt.legend([0, 1, 2], ['Data 0', 'Data 1', 'Data 2'],
           handler_map={
               0: LegendObject(colors[0], colors_faded[0]),
               1: LegendObject(colors[1], colors_faded[1]),
               2: LegendObject(colors[2], colors_faded[2], dashed=True),
            })

plt.title('Example mean and confidence interval plot')
plt.tight_layout()
plt.grid()
plt.show()

Side note, really enjoying the default formatting in Matplotlib 2+.

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Arm simulation visualization with Matplotlib

One of the downsides of switching to Python from Matlab is that it can be a pain to plot some kinds of things, and I’ve found animations to be one those things. In previous posts I’ve done the visualization of my arm simulations through Pyglet, but I recently started playing around with Matplotlib’s animation function, and the results are pretty smooth. The process is also relatively painless and quick to get up and running, so I thought I would throw up some Matplotlib code for visualizing my previously described 2 link arm MapleSim simulation.

So, let’s look at the code:

#Written by Travis DeWolf (Sept, 2013)
#Based on code by Jake Vanderplas - http://jakevdp.github.com

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import py2LinkArm

class TwoLinkArm:
    """
    :param list u: the torque applied to each joints
    """
    def __init__(self, u = [.1, 0]): 
        self.u = np.asarray(u, dtype='float') # control signal
        self.state = np.zeros(3) # vector for current state
        self.L1=0.37 # length of arm link 1 in m
        self.L2=0.27 # length of arm link 2 in m
        self.time_elapsed = 0

        self.sim = py2LinkArm.pySim()
        self.sim.reset(self.state)
    
    def position(self):
        """Compute x,y position of the hand"""

        x = np.cumsum([0,
                       self.L1 * np.cos(self.state[1]),
                       self.L2 * np.cos(self.state[2])])
        y = np.cumsum([0,
                       self.L1 * np.sin(self.state[1]),
                       self.L2 * np.sin(self.state[2])])
        return (x, y)

    def step(self, dt):
        """Simulate the system and update the state"""
        for i in range(1500):
            self.sim.step(self.state, self.u)
        self.time_elapsed = self.state[0]

#------------------------------------------------------------
# set up initial state and global variables
arm = TwoLinkArm()
dt = 1./30 # 30 fps

#------------------------------------------------------------
# set up figure and animation
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111, aspect='equal', autoscale_on=False,
                     xlim=(-1, 1), ylim=(-1, 1))
ax.grid()

line, = ax.plot([], [], 'o-', lw=4, mew=5)
time_text = ax.text(0.02, 0.95, '', transform=ax.transAxes)

def init():
    """initialize animation"""
    line.set_data([], [])
    time_text.set_text('')
    return line, time_text

def animate(i):
    """perform animation step"""
    global arm, dt
    arm.step(dt)
    
    line.set_data(*arm.position())
    time_text.set_text('time = %.2f' % arm.time_elapsed)
    return line, time_text

# frames=None for matplotlib 1.3
ani = animation.FuncAnimation(fig, animate, frames=None,
                              interval=25, blit=True, 
                              init_func=init)

# uncomment the following line to save the video in mp4 format.
# requires either mencoder or ffmpeg to be installed
#ani.save('2linkarm.mp4', fps=15, 
#         extra_args=['-vcodec', 'libx264'])

plt.show()

There’s not all too much to it, which is nice. I’ve created a class TwoLinkArm that wraps the actual arm simulator, stores the current state of the arm, and has a step function that gets called to move the system forward in time. Then, I created a line and stored a reference to it; this is what is going to be updated in the simulation. I then need functions that specify how the line will be initialized and updated. The init function doesn’t do anything except set the line and text data to nothing, and then the animate function calls the arm simulation’s step function and updates the line and text data.

For more details about it there’s this blog post which steps through the process a bit more. For simple arm simulations the above is all I need though, so I’ll leave it there for now!

Here’s an animation of the resulting sim visualization, I’ve removed a lot of the frames to keep the size down. It’s smoother when running the actual code, which can be found up on my github.

Hurray better visualization!

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