I am running an animated scatter in a process. Everything is working fine, except that an exception is throw when I want to exit everything.
import multiprocessing as mp
import time
from collections import deque
def start_colored_scores(nb_channels):
q = mp.Queue()
process = mp.Process(target=colored_scores,args=(q,nb_channels,4000))
process.start()
return process,q
def colored_scores(q,nb_channels,size):
import matplotlib.pyplot as plt
import matplotlib.animation as animation
fig, axes = plt.subplots(nrows=nb_channels,ncols=1,sharex=True,sharey=True)
plt.axis([-1.0,1.0,-1.0,1.0])
scats = [axe.scatter([0], [0], c="white", s=size) for axe in axes]
def animate(i):
scores = q.get()
if scores is None : # this is the external signal saying things should stop
plt.close()
return [axe.scatter([0], [0], c="white", s=size) for axe in axes]
scats = []
for score,axe in zip(scores,axes):
score = max(min(1,1-score),0)
scats.append(axe.scatter([0], [0], c=(1-score,0,score), s=size))
return scats
ani = animation.FuncAnimation(fig, animate, interval=1, blit=True)
plt.show()
For example, this is working fine:
_,q = start_colored_scores(2)
x = 0
right = 1
time_start = time.time()
while time.time()-time_start < 5:
if right==1 and x>1.0:
x = 1.0
right = -1
if right==-1 and x<0.0:
x = 0.0
right = 1
x+=right*0.02
q.put([x,1-x])
time.sleep(0.02)
q.put(None) # indicating I do not need plotting anymore
print "this is printed ... exception in the process ?"
The behavior is as I expect : scatters are displayed and animated for 5 seconds, then the program continues. The only issue is that an exception is thrown (I guess in the process) saying :
AttributeError: 'NoneType' object has no attribute 'tk'
Is there a way to do the exact same thing but avoiding the exception ? Or to catch this exception somewhere ?
You can catch that exception pretty easily:
def colored_scores(q,nb_channels,size):
import matplotlib.pyplot as plt
import matplotlib.animation as animation
fig, axes = plt.subplots(nrows=nb_channels,ncols=1,sharex=True,sharey=True)
plt.axis([-1.0,1.0,-1.0,1.0])
scats = [axe.scatter([0], [0], c="white", s=size) for axe in axes]
def animate(i):
scores = q.get()
if scores is None : # this is the external signal saying things should stop
plt.close()
return [axe.scatter([0], [0], c="white", s=size) for axe in axes]
scats = []
for score,axe in zip(scores,axes):
score = max(min(1,1-score),0)
scats.append(axe.scatter([0], [0], c=(1-score,0,score), s=size))
return scats
ani = animation.FuncAnimation(fig, animate, interval=1, blit=True)
try:
plt.show()
except AttributeError: # This will supress the exception
pass
However, once you get catch that one, you get a new one (at least on my system):
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1489, in __call__
return self.func(*args)
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 536, in callit
func(*args)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 141, in _on_timer
TimerBase._on_timer(self)
File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 1203, in _on_timer
ret = func(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 876, in _step
still_going = Animation._step(self, *args)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 735, in _step
self._draw_next_frame(framedata, self._blit)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 755, in _draw_next_frame
self._post_draw(framedata, blit)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 778, in _post_draw
self._blit_draw(self._drawn_artists, self._blit_cache)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 798, in _blit_draw
ax.figure.canvas.blit(ax.bbox)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 353, in blit
tkagg.blit(self._tkphoto, self.renderer._renderer, bbox=bbox, colormode=2)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/tkagg.py", line 20, in blit
tk.call("PyAggImagePhoto", photoimage, id(aggimage), colormode, id(bbox_array))
TclError: this isn't a Tk application
I can't find any way to supress that one. What you could do, is just terminate the subprocess, rather than try to send it a signal to shutdown:
proc,q = start_colored_scores(2)
x = 0
right = 1
time_start = time.time()
while time.time()-time_start < 5:
if right==1 and x>1.0:
x = 1.0
right = -1
if right==-1 and x<0.0:
x = 0.0
right = 1
x+=right*0.02
q.put([x,1-x])
time.sleep(0.02)
#q.put(None) # indicating I do not need plotting anymore
proc.terminate()
This is not as graceful as sending something through the queue (and doesn't allow for any additional clean-up in the sub-process, assuming you want it), but doesn't throw any exceptions.
Related
import matplotlib.image as mpimg
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.widgets import Button
from matplotlib.widgets import Slider
fig = plt.figure()
image_list = ['downloads/20120831_194836_aia.lev1_euv_12s_4k.jpg', 'downloads/20120831_194936_aia.lev1_euv_12s_4k.jpg', 'downloads/20120831_195036_aia.lev1_euv_12s_4k.jpg']
list = []
for raw_image in image_list:
image1 = mpimg.imread(raw_image)
real_image1 = plt.imshow(image1)
list.append([real_image1])
def update_plot(t):
print(t)
return list[t]
anim = animation.FuncAnimation(fig, update_plot, repeat = True, interval=1, blit=False,
repeat_delay=200)
plt.show()
I am trying to create a func animation with the 3 jpg images in the list. After the program runs the 3 images 1 time, it gives me an error. When I print 't', it never resets to 0.
Error:
Traceback (most recent call last):
File "/Users/jamisenma/opt/anaconda3/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 1194, in _on_timer
ret = func(*args, **kwargs)
File "/Users/jamisenma/opt/anaconda3/lib/python3.7/site-packages/matplotlib/animation.py", line 1447, in _step
still_going = Animation._step(self, *args)
File "/Users/jamisenma/opt/anaconda3/lib/python3.7/site-packages/matplotlib/animation.py", line 1173, in _step
self._draw_next_frame(framedata, self._blit)
File "/Users/jamisenma/opt/anaconda3/lib/python3.7/site-packages/matplotlib/animation.py", line 1192, in _draw_next_frame
self._draw_frame(framedata)
File "/Users/jamisenma/opt/anaconda3/lib/python3.7/site-packages/matplotlib/animation.py", line 1755, in _draw_frame
self._drawn_artists = self._func(framedata, *self._args)
File "/Users/jamisenma/Library/Application Support/JetBrains/PyCharmCE2020.1/scratches/scratch_59.py", line 19, in update_plot
return list[t]
IndexError: list index out of range
Does anyone know what the issue is?
Solved it. I had to add frames = len(list) as a parameter of FuncAnimation
You failed to provide into the expected MRE, and didn't do the expected initial debugging work. Therefore, I can't be sure.
However, my greatest suspicion is at the return from update_plot, which is using an argument you failed to show us -- and using that as subscript into a global sequence that shadows a pre-defined type.
Try debugging with this simple technique:
def update_plot(t):
print("ENTER update_plot; t =", t, "\n list =", list)
print(t)
return list[t]
I expect that, just before your point of failure, you will see that t >= len(list).
General hint: do not give a variable the same name as a built-in or predefined name. In particular, change list.
I have been trying to animate a polar plot in which I have a one degree wide wedge sweep all the way around the plot in a circle. I tried using the code below, but for some reason, it gives me the error AttributeError: 'NoneType' object has no attribute 'canvas'. I was trying to initialize the wedge as a rectangle patch that starts off on the right side of the plot and increases in x (angle), so I thought I should update the x-coordinate in the animate function, but for some reason, whenever I return patch (the rectangle) from animation, it gives me an error. Any tips? Thanks!
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.patches import Rectangle
fig = plt.figure()
ax = fig.add_subplot(111, projection='polar')
_, rlim = ax.get_ylim()
patch = Rectangle((0,0), np.radians(1), rlim)
def init():
ax.add_patch(patch)
return patch,
def animate(i):
patch.set_xy((np.radians(i), 0))
return patch,
ani = animation.FuncAnimation(fig, animate, frames=360, interval=30, blit=True)
plt.show()
Error:
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib64/python3.6/tkinter/__init__.py", line 1705, in __call__
return self.func(*args)
File "/usr/lib64/python3.6/tkinter/__init__.py", line 749, in callit
func(*args)
File "/usr/lib64/python3.6/site-packages/matplotlib/backends/_backend_tk.py", line 114, in _on_timer
TimerBase._on_timer(self)
File "/usr/lib64/python3.6/site-packages/matplotlib/backend_bases.py", line 1187, in _on_timer
ret = func(*args, **kwargs)
File "/usr/lib64/python3.6/site-packages/matplotlib/animation.py", line 1449, in _step
still_going = Animation._step(self, *args)
File "/usr/lib64/python3.6/site-packages/matplotlib/animation.py", line 1169, in _step
self._draw_next_frame(framedata, self._blit)
File "/usr/lib64/python3.6/site-packages/matplotlib/animation.py", line 1189, in _draw_next_frame
self._post_draw(framedata, blit)
File "/usr/lib64/python3.6/site-packages/matplotlib/animation.py", line 1212, in _post_draw
self._blit_draw(self._drawn_artists, self._blit_cache)
File "/usr/lib64/python3.6/site-packages/matplotlib/animation.py", line 1229, in _blit_draw
bg_cache[a.axes] = a.figure.canvas.copy_from_bbox(a.axes.bbox)
AttributeError: 'NoneType' object has no attribute 'canvas'
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.
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()
having issues with the FuncAnimantion function in matplotlib. Code is as follows:
import time
from matplotlib import pyplot as plt
from matplotlib import animation
from ppbase import *
plt.ion()
#This is just essentially a stream of data
Paramater = PbaProObject("address of object")
fig = plt.figure()
ax = plt.axes(xlim=(0,2), ylim=(-90, 90))
line, = ax.plot([], [], lw=2)
def init():
line.set_data([], [])
return line,
def animate(Parameter):
x = time.time()
y = Parameter.ValueStr
line.set_data(x, y)
return line,
anim = animation.FuncAnimation(fig, animate(Parameter), init_func=init,
frames=200, interval=2, blit=True)
plt.show()
And the error is:
Traceback (most recent call last):
File "C:\Anaconda\lib\site-packages\matplotlib\backend_bases.py", line 1203, in _on_timer
ret = func(*args, **kwargs)
File "C:\Anaconda\lib\site-packages\matplotlib\animation.py", line 876, in _step
still_going = Animation._step(self, *args)
File "C:\Anaconda\lib\site-packages\matplotlib\animation.py", line 735, in _step self._draw_frame(framedata)
File "C:\Anaconda\lib\site-packages\matplotlib\animation.py", line 754, in _draw_next_frame self._draw_frame(framedata, self._blit)
File "C:\Anaconda\lib\site-packages\matplotlib\animation.py", line 1049, in _draw_frame self._drawn_artists = self._func(framedata, *self._args)
TypeError: 'tuple' object is not callable
Been reading around all morning and it seems commonly plt.plot is overwritten by a tuple, so I checked for that but don't think I have done it anywhere. I've also turned blit to false but that didn't help either. I do also want to interactively update the x-axis, I had line:
ax = plt.axes(xlim((x-10), (x+10)), ylim=(-90, 90))
in the animate function but took that out to see if it made any difference.
I think mostly the problems stem from not really understanding tuples too well. Also my understanding of the FuncAnimation function is that it calls the animate() each time it updates the plot - hence why I though that I could use it to update the axis' also. But this may not be the case.
Any help appreciated.
You need to pass in the function object not the result of the calling the function and you can pass a generator to frames (this might only work on 1.4.0+).
# turn your Parameter object into a generator
def param_gen(p):
yield p.ValueStr
def animate(p):
# get the data the is currently on the graph
old_x = line.get_xdata()
old_y = line.get_ydata()
# add the new data to the end of the old data
x = np.r_[old_x, time.time()]
y = np.r_[old_y, p]
# update the data in the line
line.set_data(x, y)
# return the line2D object so the blitting code knows what to redraw
return line,
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=param_gen(Parameter), interval=2, blit=True)
I also fixed a problem with your animation function and you should use 4 space indents, not 2.
My problem is following:
I'm taking a data from files and want to make an animation of four plots at the same time: two colourbars and two lines.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as anim
import sys
begin = float(sys.argv[1])
end = float(sys.argv[2])
dataCl = np.loadtxt("file1.txt")
dataSS = np.loadtxt("file2.txt")
datajSR = np.loadtxt("file3.txt")
ibegin = 0
iend = 0
for i in range(len(dataCl[:,0])):
if np.abs(dataCl[i,0] - begin) < 1e-9:
ibegin = i
iend = i
while abs(dataCl[i,0] - end) >= 1e-9:
iend = iend + 1
i = i + 1
break
fig = plt.figure()
f, axarr = plt.subplots(2, 2)
temp = np.zeros((10,10))
Qs = axarr[0,0].imshow(temp,cmap = plt.cm.OrRd)
El = axarr[0,1].imshow(temp,cmap = plt.cm.OrRd)
SS, = axarr[1,0].plot([],[])
jSR, = axarr[1,1].plot([],[])
def init():
Qs.set_array(temp)
El.set_array(temp)
SS.set_data([],[])
jSR.set_data([],[])
return Qs,El,SS,jSR,
def animate(i):
a = 0
b = 0
dataQ = np.zeros((10,10))
dataE = np.zeros((10,10))
for j in range(100):
if b >= 10:
a = a + 1
b = 0
dataQ[a][b] = dataCl[i,2*j + 1]
dataE[a][b] = dataCl[i,2*(j+1)]
b = b + 1
Qs.set_array(dataQ)
El.set_array(dataE)
SS.set_data(dataSS[ibegin:ibegin+i,0],dataSS[ibegin:ibegin+i,1])
jSR.set_data(datajSR[ibegin:ibegin+i,0],datajSR[ibegin:ibegin+i,1])
return Qs,El,SS,jSR,
ani = anim.FuncAnimation(fig, animate, init_func = init, frames = iend-ibegin,interval=25, blit=True)
plt.show()
After running it shows these messages:
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1413, in __call__
return self.func(*args)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 236, in resize
self.show()
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 239, in draw
FigureCanvasAgg.draw(self)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 421, in draw
self.figure.draw(self.renderer)
File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 904, in draw
self.canvas.draw_event(renderer)
File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 1544, in draw_event
self.callbacks.process(s, event)
File "/usr/lib/pymodules/python2.7/matplotlib/cbook.py", line 262, in process
proxy(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/cbook.py", line 192, in __call__
return mtd(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 273, in _end_redraw
self._post_draw(None, self._blit)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 220, in _post_draw
self._blit_draw(self._drawn_artists, self._blit_cache)
File "/usr/lib/pymodules/python2.7/matplotlib/animation.py", line 235, in _blit_draw
a.axes.draw_artist(a)
File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 2008, in draw_artist
assert self._cachedRenderer is not None
AssertionError
I cannot find a mistake in my code ;(
The error message might be backend and platform specific. As the error message seems to point to the blitting mechanism, you might want to try setting blit=False in FuncAnimation. Also, you might try some other backend to see if the problem persists. (Knowing your platform and matplotlib version might also help.)
Update: If setting blit=False, trying another backend, and updating matplotlib does not help, then a few suggestions:
Try to see manually if you code works with the initial data (init(); animate(0); fig.savefig("/tmp/test.png")) - if it throws an error, there is a static plotting problem to fix.
Now you initialize the plot twice (first in the code, then in init), you can take one away (e.g. do not define init_func)
Initializing the plots with [],[] leaves the scale uninitialized. You should probably use set_ylim, set_xlim with the plots and vmin, vmax keywords with the imshow images when you initialize them. (This could possibly have something to do with the exception you get!)