Animating 3D scatter plot using Python mplotlib via serial data

Question

I am trying to animate a 3D scatter plot using mplotlib in Python. I am able to graph the data and redraw every time, but this results in a frame rate of less than 1 FPS, and I need to scale to upwards of 30 FPS. When I run my code:

import serial
import numpy
import matplotlib.pyplot as plt #import matplotlib library
from mpl_toolkits.mplot3d import Axes3D
from drawnow import *
import matplotlib.animation
import time

ser = serial.Serial('COM7',9600,timeout=5)
ser.flushInput()
time.sleep(5)
ser.write(bytes(b's1000'))

x=list()
y=list()
z=list()

#plt.ion()
fig = plt.figure(figsize=(16,12))
ax = fig.add_subplot(111, projection="3d")
graph = ax.scatter(x,y,z, c='r',marker='o')
ax.set_xlim3d(-255, 255)
ax.set_ylim3d(-255, 255)
ax.set_zlim3d(-255, 255)

def generate():
    while True:
        try:
            ser_bytes = ser.readline()
            data = str(ser_bytes[0:len(ser_bytes)-2].decode("utf-8"))
            xyz = data.split(", ")
            dx = float(xyz[0])
            dy = float(xyz[1])
            dz = float(xyz[2].replace(";",""))
            x.append(dx);
            y.append(dy);
            z.append(dz);
            graph._offset3d(x,y,z, c='r',marker='o')

        except:
            print("Keyboard Interrupt")
            ser.close()
            break
    return graph,

ani = matplotlib.animation.FuncAnimation(fig, generate(), interval=1, blit=True)
plt.show()

I get the following error:

Traceback (most recent call last):
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\cbook\__init__.py", line 388, in process
    proxy(*args, **kwargs)
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\cbook\__init__.py", line 228, in __call__
    return mtd(*args, **kwargs)
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\animation.py", line 1026, in _start
    self._init_draw()
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\animation.py", line 1750, in _init_draw
    self._draw_frame(next(self.new_frame_seq()))
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\animation.py", line 1772, in _draw_frame
    self._drawn_artists = self._func(framedata, *self._args)
TypeError: 'tuple' object is not callable
Traceback (most recent call last):
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\cbook\__init__.py", line 388, in process
    proxy(*args, **kwargs)
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\cbook\__init__.py", line 228, in __call__
    return mtd(*args, **kwargs)
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\animation.py", line 1308, in _handle_resize
    self._init_draw()
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\animation.py", line 1750, in _init_draw
    self._draw_frame(next(self.new_frame_seq()))
  File "C:\Users\bunti\AppData\Local\Programs\Python\Python36-32\lib\site-packages\matplotlib\animation.py", line 1772, in _draw_frame
    self._drawn_artists = self._func(framedata, *self._args)
TypeError: 'tuple' object is not callable

I am receiving x, y, z coordinates from a lidar module connected to an Arduino, which sends the coordinates over serial to the Python script.

when posting an error message, please post the **full** stacktrace so one can see where the error happens. Also, it would help if you would provide a [Minimal, Complete, and Verifiable example](https://stackoverflow.com/help/mcve). In you case, that would be code that does not rely on receiving data through the serial port — Diziet Asahi, May 15 '18 at 13:37

score 2 · Accepted Answer · answered May 16 '18 at 14:37

A possible problem with your code is that the animation function (generate) is not supposed to run in an infinite loop. Furthermore, you are supposed to pass a reference to that function to FuncAnimate, but instead you are calling the function (i.e. you need to omit the parentheses in FuncAnimation(..., generate, ...)

The second problem is that you are treating graph._offset3d as if it was a function, when it is merely a tuple of lists. You should assign a new tuple to it, instead of trying to call the function (which I believe is what the error message alludes to).

I simplified your code and the following works fine:

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


def update_lines(num):
    dx, dy, dz = np.random.random((3,)) * 255 * 2 - 255  # replace this line with code to get data from serial line
    text.set_text("{:d}: [{:.0f},{:.0f},{:.0f}]".format(num, dx, dy, dz))  # for debugging
    x.append(dx)
    y.append(dy)
    z.append(dz)
    graph._offsets3d = (x, y, z)
    return graph,


x = [0]
y = [0]
z = [0]

fig = plt.figure(figsize=(5, 5))
ax = fig.add_subplot(111, projection="3d")
graph = ax.scatter(x, y, z, color='orange')
text = fig.text(0, 1, "TEXT", va='top')  # for debugging

ax.set_xlim3d(-255, 255)
ax.set_ylim3d(-255, 255)
ax.set_zlim3d(-255, 255)

# Creating the Animation object
ani = animation.FuncAnimation(fig, update_lines, frames=200, interval=50, blit=False)
plt.show()

Animating 3D scatter plot using Python mplotlib via serial data

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