live plotting using pyserial and matplotlib - matplotlib

Question

I can capture data from serial device via pyserial, at this time I can only export data to text file, the text file has format like below, it's have 3 columns
>21 21 0
>
>41 41 0.5
>
>73 73 1
>
....
>2053 2053 5
>
>2084 2084 5.5
>
>2125 2125 6
Now I want to use matplotlib to generate live graph has 2 figure (x,y) x,y are second and third column, first comlumn,'>', and lines don't have data can be remove
thank folks!
============================
Update : today, after follow these guides from
http://www.blendedtechnologies.com/realtime-plot-of-arduino-serial-data-using-python/231
http://eli.thegreenplace.net/2008/08/01/matplotlib-with-wxpython-guis
pyserial - How to read the last line sent from a serial device
now I can live plot with threading but eliben said that this Guis only plot single value each time, that lead to me the very big limitation, beacause my purpose is plotting 2 or 3 column, here is the code was modified from blendedtechnologies
Here is serial handler :
from threading import Thread
import time
import serial
last_received = ''
def receiving(ser):
global last_received
buffer = ''
while True:
buffer = buffer + ser.read(ser.inWaiting())
if '\n' in buffer:
lines = buffer.split('\n') # Guaranteed to have at least 2 entries
last_received = lines[-2]
#If the Arduino sends lots of empty lines, you'll lose the
#last filled line, so you could make the above statement conditional
#like so: if lines[-2]: last_received = lines[-2]
buffer = lines[-1]
class SerialData(object):
def __init__(self, init=50):
try:
self.ser = ser = serial.Serial(
port='/dev/ttyS0',
baudrate=9600,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=0.1,
xonxoff=0,
rtscts=0,
interCharTimeout=None
)
except serial.serialutil.SerialException:
#no serial connection
self.ser = None
else:
Thread(target=receiving, args=(self.ser,)).start()
def next(self):
if not self.ser:
return 100 #return anything so we can test when Arduino isn't connected
#return a float value or try a few times until we get one
for i in range(40):
raw_line = last_received[1:].split(' ').pop(0)
try:
return float(raw_line.strip())
except ValueError:
print 'bogus data',raw_line
time.sleep(.005)
return 0.
def __del__(self):
if self.ser:
self.ser.close()
if __name__=='__main__':
s = SerialData()
for i in range(500):
time.sleep(.015)
print s.next()
For me I modified this segment so it can grab my 1st column data
for i in range(40):
raw_line = last_received[1:].split(' ').pop(0)
try:
return float(raw_line.strip())
except ValueError:
print 'bogus data',raw_line
time.sleep(.005)
return 0.
and generate graph base on these function on the GUI file
from Arduino_Monitor import SerialData as DataGen
def __init__(self):
wx.Frame.__init__(self, None, -1, self.title)
self.datagen = DataGen()
self.data = [self.datagen.next()]
................................................
def init_plot(self):
self.dpi = 100
self.fig = Figure((3.0, 3.0), dpi=self.dpi)
self.axes = self.fig.add_subplot(111)
self.axes.set_axis_bgcolor('black')
self.axes.set_title('Arduino Serial Data', size=12)
pylab.setp(self.axes.get_xticklabels(), fontsize=8)
pylab.setp(self.axes.get_yticklabels(), fontsize=8)
# plot the data as a line series, and save the reference
# to the plotted line series
#
self.plot_data = self.axes.plot(
self.data,
linewidth=1,
color=(1, 1, 0),
)[0]
So my next question is how to realtime grab at least 2 column and passing 2 columns'data to the GUIs that it can generate graph with 2 axis.
self.plot_data.set_xdata(np.arange(len(self.data))) #my 3rd column data
self.plot_data.set_ydata(np.array(self.data)) #my 2nd column data

Answer 1

Well, this reads your string and converts the numbers to floats. I assume you'll be able to adapt this as needed.
import numpy as np
import pylab as plt
str = '''>21 21 0
>
>41 41 0.5
>
>73 73 1
>
>2053 2053 5
>
>2084 2084 5.5
>
>2125 2125 6'''
nums = np.array([[float(n) for n in sub[1:].split(' ') if len(n)>0] for sub in str.splitlines() if len(sub)>1])
fig = plt.figure(0)
ax = plt.subplot(2,1,1)
ax.plot(nums[:,0], nums[:,1], 'k.')
ax = plt.subplot(2,1,2)
ax.plot(nums[:,0], nums[:,2], 'r+')
plt.show()

Answer 2

Here you have an Eli Bendersky's example of how plotting data arriving from a serial port

Answer 3

some time back I had the same problem. I wasted a lot of writing same ting over and over again. so I wrote a python package for it.
https://github.com/girish946/plot-cat
you just have to write the logic for obtaining the data from serial port.
the example is here: https://github.com/girish946/plot-cat/blob/master/examples/test-ser.py