Plotting Serial data in Python how to pause matplotlib figure?

Question

Basically I want to pause the live plot that I have setup here:

import serial
import numpy as np
from matplotlib import pyplot as plt
ser = serial.Serial('/dev/tty.usbmodemfa131', 9600)


#Setting up the animated plot
plt.ion() # set plot to animated
fig = plt.figure()

ydata = [0] * 100
ax1=plt.axes()  

# make plot
line, = plt.plot(ydata)
plt.ylim([24,29])

#Starting data collection
while True:
    rawData = ser.readline().rstrip()
    x = len(rawData)
    #print(floatData)
    if len(rawData) <= 6:
        try:
            data = float(rawData)
            if data <= 100:
                ydata.append(data)
                del ydata[0]
                line.set_xdata(np.arange(len(ydata)))
                line.set_ydata(ydata)  # update the data
                plt.draw() # update the plot
        except ValueError:
            print "Not a float"

I am wanting to pause the plot in the figure but I can't figure out how to work with the figure at all as the data is streaming.

Answer 1

So a good solution to your problem would be to use a thread to run the plotting window and have control performed through the main thread. This could be implemented like so:

import serial
import numpy as np
from matplotlib import pyplot as plt
from threading import Thread,Event
import time

#A simple ring buffer to keep the plotting data in
class RingBuffer(object):
    def __init__(self,size):
        self.size = size
        self._size = 2*size
        self._buffer = np.zeros(self._size)
        self._idx = 0

    def insert(self,val):
        idx = self._idx%self.size
        self._buffer[idx] = val
        self._buffer[idx+self.size] = val
        self._idx+=1
        if self._idx > self.size:
            self._idx-=self.size

    def get(self):
        start_idx = (self._idx)%self.size
        end_idx = start_idx+self.size
        return self._buffer[start_idx:end_idx]

#A thread to handle plotting and reading data from the serial port
class Plotter(Thread):
    def __init__(self,stream,stop,pause):
        Thread.__init__(self)
        self.stream = stream
        self.fig = plt.figure()
        self.ax = plt.axes()
        self.size = 100
        self.xdata = np.arange(self.size)
        self.ydata = RingBuffer(self.size)
        self.line, = self.ax.plot(self.ydata.get())
        plt.ylim([24,29])                                                  
        self.stop = stop
    self.pause = pause

    #The main loop of the thread, invoked with .start()
    def run(self):
        while not self.stop.is_set():
            if self.pause.is_set():
                continue
            raw_data = self.stream.readline().rstrip()                     
            if len(raw_data) <= 6:
                try:
                    data = float(raw_data)
                except ValueError:
                    print "Not a float"
                else:
                    if data <= 100:
                        self.ydata.insert(data)
                        self.line.set_xdata(self.xdata)
                        self.line.set_ydata(self.ydata.get())
                        plt.draw()

            #sleep statement to reduce processor load 
        time.sleep(1) 

#this is implemented to facilitate use through something like Ipython easily
class Controller(object):
    def __init__(self):

        #These events control execution of the thread main loop
        self.stop = Event()
        self.pause = Event()
        self.stream = serial.Serial('/dev/tty.usbmodemfa131', 9600)
        self.plotter_thread = Plotter(self.stream,self.stop,self.pause)
        self.plotter_thread.start()

def main():
    con = Controller()

    #Loop over terminal input
    #possible commands are stop, pause and unpause
    while True:
        command = raw_input("cmd >>>")
        if command == "stop":
            con.stop.set()
            con.plotter_thread.join()
            break
        elif command == "pause":
            con.pause.set()
        elif command == "unpause":
            con.pause.clear()
        else:
            print "unrecognised command"

if __name__ == "__main__":
    main()

This should give you a command line interface like:

cmd >>>

Where any of the following statements should control the plotter

cmd >>>pause
cmd >>>unpause
cmd >>>stop