How to update text in matplotlib with serial data from Arduino? - matplotlib

Question

I am attempting to create an animated plot that updates in real time with the data from my serial port. Data is streamed in by an Arduino in an 8x8 array. The data are temperatures from an IR camera. I am able to create an instance of a figure but I cannot get the text to update with the serial stream data.
I tried to set 'plt.show(block=False)' so that the script would continue, but this makes the figure empty completely and scales it into a small window with a loading cursor that just continues to load.
I only want the text to update with the array data, as well as the colors from the new normalized data.
How can I get the text to update with the serial data in matplotlib?
Thanks!
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import serial
import time
tempdata = serial.Serial("COM3",9600)
tempdata.timeout = 100
strn = []
rows = ["A", "B", "C", "D",
"E", "F", "G","H"]
columns = ["1", "2", "3", "4",
"5", "6", "7","8"]
print("AMG8833 8x8 Infrared Camera")
time.sleep(0.75)
print("Connected to: " + tempdata.portstr)
time.sleep(0.75)
print("Initializing Camera...")
tempsArray = np.empty((8,8))
while True: #Makes a continuous loop to read values from Arduino
fig, ax = plt.subplots()
im = ax.imshow(tempsArray,cmap='plasma')
tempdata.flush()
strn = tempdata.read_until(']') #reads the value from the serial port as a string
tempsString = np.asarray(strn)
tempsFloat = np.fromstring(tempsString, dtype=float, sep= ', ')
# Axes ticks
ax.set_xticks(np.arange(len(columns)))
ax.set_yticks(np.arange(len(rows)))
# Axes labels
ax.set_xticklabels(columns)
ax.set_yticklabels(rows)
# Rotate the tick labels and set their alignment.
plt.setp(ax.get_xticklabels(), rotation=45, ha="right",
rotation_mode="anchor")
tempsArray.flat=tempsFloat
im.set_array(tempsArray)
ax.set_title("")
fig.tight_layout()
#Loop over data dimensions and create text annotations.
for i in range(len(rows)):
for j in range(len(columns)):
text = ax.text(j, i, tempsArray[i, j],
ha="center", va="center", color="w")
plt.show()
Heat Map

Answer 1

This dynamic updating can be achieved with matplotlib's interactive mode. The answer to your question is very similar to this one: basically you need to enable interactive mode with ion() and then update the plot without calling the show() (or correlated) function.
Also, the plot and subplots are to be created only once, before the input loop.
This is the modified example:
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import serial
import time
tempdata = serial.Serial("COM3",9600)
tempdata.timeout = 100
strn = []
rows = ["A", "B", "C", "D",
"E", "F", "G","H"]
columns = ["1", "2", "3", "4",
"5", "6", "7","8"]
print("AMG8833 8x8 Infrared Camera")
time.sleep(0.75)
print("Connected to: " + tempdata.portstr)
time.sleep(0.75)
print("Initializing Camera...")
tempsArray = np.empty((8,8))
plt.ion()
fig, ax = plt.subplots()
# The subplot colors do not change after the first time
# if initialized with an empty matrix
im = ax.imshow(np.random.rand(8,8),cmap='plasma')
# Axes ticks
ax.set_xticks(np.arange(len(columns)))
ax.set_yticks(np.arange(len(rows)))
# Axes labels
ax.set_xticklabels(columns)
ax.set_yticklabels(rows)
# Rotate the tick labels and set their alignment.
plt.setp(ax.get_xticklabels(), rotation=45, ha="right",
rotation_mode="anchor")
ax.set_title("")
fig.tight_layout()
text = []
while True: #Makes a continuous loop to read values from Arduino
tempdata.flush()
strn = tempdata.read_until(']') #reads the value from the serial port as a string
tempsString = np.asarray(strn)
tempsFloat = np.fromstring(tempsString, dtype=float, sep= ', ')
tempsArray.flat=tempsFloat
im.set_array(tempsArray)
#Delete previous annotations
for ann in text:
ann.remove()
text = []
#Loop over data dimensions and create text annotations.
for i in range(len(rows)):
for j in range(len(columns)):
text.append(ax.text(j, i, tempsArray[i, j],
ha="center", va="center", color="w"))
# allow some delay to render the image
plt.pause(0.1)
plt.ioff()
Note: this code worked for me, but since I don't have an Arduino right now I tested it with a randomly generated sequence of frames (np.random.rand(8,8,10)), so I might have overlooked some detail. Let me know how it works.