Develop Reference

edgecolors='None' causes error on animated 3d scatterplot

I'm trying to make a 3d scatterplot with fading points over time, similar to this question. However, when I apply the colormap to the data, then the face of the marker changes color but the edge remains solid.
I've tried using the edgecolors='None', edgecolor='none' kwargs, the marker='o' kwarg as per this example, and the edgecolor='face' kwarg. I've also tried using post creation methods such as scat3D.set_edgecolor("None") etc. The first attempts throw an error, and the latter have no effect.
Error from setting kwargs:
Traceback (most recent call last):
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 230, in saving
yield self
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 1156, in save
writer.grab_frame(**savefig_kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 384, in grab_frame
dpi=self.dpi, **savefig_kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/figure.py", line 2180, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backends/backend_qt5agg.py", line 88, in print_figure
super().print_figure(*args, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 2082, in print_figure
**kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 442, in print_raw
FigureCanvasAgg.draw(self)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 388, in draw
self.figure.draw(self.renderer)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/figure.py", line 1709, in draw
renderer, self, artists, self.suppressComposite)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/image.py", line 135, in _draw_list_compositing_images
a.draw(renderer)
File "/home/max/.local/lib/python3.6/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 292, in draw
reverse=True)):
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 291, in <lambda>
key=lambda col: col.do_3d_projection(renderer),
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 545, in do_3d_projection
ecs = (_zalpha(self._edgecolor3d, vzs) if self._depthshade else
File "/home/max/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 847, in _zalpha
rgba = np.broadcast_to(mcolors.to_rgba_array(colors), (len(zs), 4))
File "<__array_function__ internals>", line 6, in broadcast_to
File "/home/max/.local/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 182, in broadcast_to
return _broadcast_to(array, shape, subok=subok, readonly=True)
File "/home/max/.local/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 127, in _broadcast_to
op_flags=['readonly'], itershape=shape, order='C')
ValueError: operands could not be broadcast together with remapped shapes [original->remapped]: (0,4) and requested shape (100,4)
(There's a during the handling the above exception another occured error after that, but my post was flagged as spam so I didn't include it)
Here's the code without the error (adding a kwarg listed above causes the error):
import matplotlib.pyplot as plt
import numpy as np
import matplotlib.animation as animation
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.patches as mpatches
total = 10
num_whatever = 100
to_plot = [np.random.rand(num_whatever, 3) for i in range(total)]
colors = np.linspace(0, 1, num_whatever)
fig = plt.figure()
ax3d = Axes3D(fig)
scat3D = ax3d.scatter([],[],[], s=10, cmap="Blues", vmin=0, vmax=1)
scat3D.set_cmap("Blues") # cmap argument above is ignored, so set it manually
ttl = ax3d.text2D(0.05, 0.95, "", transform=ax3d.transAxes)
def update_plot(i):
print( i, to_plot[i].shape)
ttl.set_text('PCA on 3 components at step = {}'.format(i*20))
scat3D._offsets3d = np.transpose(to_plot[i])
scat3D.set_array(colors)
return scat3D,
def init():
scat3D.set_offsets([[],[],[]])
plt.style.use('ggplot')
ani = animation.FuncAnimation(fig, update_plot, init_func=init,
blit=False, interval=300, frames=range(total))
ani.save("ani.gif", writer="imagemagick")
plt.show()
Here's the plot with the marker edges not hidden:
Plot
You can see that the faded points still have the marker edges not colormapped. I would expect that setting edgecolor would be unnecessary in the first place, since the 2d animation clearly doesn't need it. But why would adding that kwarg cause me to get a operands could not be broadcast togeather error? I don't have any array with shape (0, 4), so it's not clear where this is coming from.

The problem is that if c (as the color argument) is not specified, it is not a priori clear if a colormapping should happen or not. This leads to some internal confusion about which arguments to obey to. But we can specify c as an empty list to get around that.
import matplotlib.pyplot as plt
import numpy as np
import matplotlib.animation as animation
from mpl_toolkits.mplot3d import Axes3D
total = 10
num_whatever = 100
to_plot = [np.random.rand(num_whatever, 3) for i in range(total)]
colors = np.linspace(0, 1, num_whatever)
fig = plt.figure()
ax3d = Axes3D(fig)
scat3D = ax3d.scatter([], [], [], s=10, c=[], cmap="Blues", vmin=0, vmax=1,
depthshade=False)
ttl = ax3d.text2D(0.05, 0.95, "", transform=ax3d.transAxes)
def update_plot(i):
print( i, to_plot[i].shape)
ttl.set_text('PCA on 3 components at step = {}'.format(i*20))
scat3D._offsets3d = np.transpose(to_plot[i])
scat3D.set_array(colors)
return scat3D,
def init():
scat3D.set_offsets([[],[],[]])
plt.style.use('ggplot')
ani = animation.FuncAnimation(fig, update_plot, init_func=init,
blit=False, interval=300, frames=range(total))
ani.save("ani.gif", writer="imagemagick")
plt.show()

Animating 3D scatter plot using Python mplotlib via serial data

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()

Python matplotlib: Error while saving scatter plot in svg format

I am trying to create a scatter plot with the color for each point based on the value in y-dimension and the tooltip for each point based on the value of x-axis. I was in need of creating tooltips for each point on mouseover event, which I was able to achieve. I would like to save this plot to a svg file with events so that the svg file can be viewed in a browser with tooltip.
I get the following error when I try to save it,
Traceback (most recent call last):
File "./altered_tooltip.py", line 160, in <module>
example.plot()
File "./altered_tooltip.py", line 70, in plot
pl.savefig(f, format="svg")
File "/usr/lib/pymodules/python2.7/matplotlib/pyplot.py", line 561, in savefig
return fig.savefig(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1421, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 2220, in print_figure
**kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 1978, in print_svg
return svg.print_svg(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_svg.py", line 1157, in print_svg
return self._print_svg(filename, svgwriter, fh_to_close, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_svg.py", line 1185, in _print_svg
self.figure.draw(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 1034, in draw
func(*args)
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/axes.py", line 2086, in draw
a.draw(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/collections.py", line 718, in draw
return Collection.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/collections.py", line 250, in draw
renderer.open_group(self.__class__.__name__, self.get_gid())
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_svg.py", line 516, in open_group
self.writer.start('g', id=gid)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_svg.py", line 141, in start
v = escape_attrib(v)
File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_svg.py", line 80, in escape_attrib
s = s.replace(u"&", u"&")
AttributeError: 'list' object has no attribute 'replace'
The code that I am running is
from numpy import *
import pylab as pl
import matplotlib.colors as mcolors
import xml.etree.ElementTree as ET
from StringIO import StringIO
ET.register_namespace("","http://www.w3.org/2000/svg")
class wxToolTipExample(object):
def __init__(self, plot_data):
self.figure = pl.figure()
self.axis = pl.axes()
self.ax = self.figure.add_subplot(111)
self.tooltip.SetTip() calls
self.dataX = plot_data[:,0]
self.dataY = plot_data[:,1]
self.annotes = []
self.pathCol = None #to hold the scatter object
def plot(self):
for idx in arange(self.dataX.size):
# create a tuple of co-ordinates
tup = (self.dataX[idx], self.dataY[idx])
# create annotation with tooltip
annotation = self.axis.annotate("Column %s" % int(self.dataX[idx]),
xy=tup, xycoords='data',
xytext=(+10, +30), textcoords='offset points',
#horizontalalignment="right",
arrowprops=dict(arrowstyle="->",
connectionstyle="arc3,rad=0.2"),
#bbox=dict(boxstyle="round", facecolor="w",
# edgecolor="0.0", alpha=0.0)
)
# by default, disable the annotation visibility
annotation.set_visible(False)
# append the annotation object and co-ords tuple to the list
self.annotes.append([tup, annotation])
self.figure.canvas.mpl_connect('motion_notify_event', self._onMotion)
c_map = self.WGrYR()
self.pathCol = self.axis.scatter(self.dataX, self.dataY, c=self.dataY, marker='s', s=40, cmap=c_map)
# Set id for the annotations
for i, t in enumerate(self.axis.texts):
t.set_gid('tooltip_%d'%i)
# Set id for the points on the scatter plot
points = ['point_{0}'.format(ii) for ii in arange(1, self.dataX.size+1)]
self.pathCol.set_gid(points)
f = StringIO()
#pl.show()
pl.savefig(f, format="svg")
"""
# Create XML tree from the SVG file.
tree, xmlid = ET.XMLID(f.getvalue())
tree.set('onload', 'init(evt)')
# Hide the tooltips
for i, t in enumerate(self.axis.texts):
ele = xmlid['tooltip_%d'%i]
ele.set('visibility','hidden')
# assign mouseover and mouseout events
for p in points:
ele = xmlid[p]
ele.set('onmouseover', "ShowTooltip(this)")
ele.set('onmouseout', "HideTooltip(this)")
script = self.getSvgScript()
# Insert the script at the top of the file and save it.
tree.insert(0, ET.XML(script))
ET.ElementTree(tree).write('svg_tooltip.svg')
"""
def getSvgScript(self):
return """
<script type="text/ecmascript">
<![CDATA[
function init(evt) {
if ( window.svgDocument == null ) {
svgDocument = evt.target.ownerDocument;
}
}
function ShowTooltip(obj) {
var cur = obj.id.slice(-1);
var tip = svgDocument.getElementById('tooltip_' + cur);
tip.setAttribute('visibility',"visible")
}
function HideTooltip(obj) {
var cur = obj.id.slice(-1);
var tip = svgDocument.getElementById('tooltip_' + cur);
tip.setAttribute('visibility',"hidden")
}
]]>
</script>
"""
def _onMotion(self, event):
visibility_changed = False
for point, annotation in self.annotes:
if event.xdata != None and event.ydata != None: # mouse is inside the axes
should_be_visible = abs(point[0]-event.xdata) < 0.2 and abs(point[1]-event.ydata) < 0.05
if should_be_visible != annotation.get_visible():
visibility_changed = True
annotation.set_visible(should_be_visible)
if visibility_changed:
pl.draw()
def WGrYR(self):
c = mcolors.ColorConverter().to_rgb
seq = [c('white'), c('grey'), 0.33, c('grey'), c('yellow'), 0.66, c('yellow'), c('red')]
seq = [(None,) * 3, 0.0] + list(seq) + [1.0, (None,) * 3]
cdict = {'red': [], 'green': [], 'blue': []}
for i, item in enumerate(seq):
if isinstance(item, float):
r1, g1, b1 = seq[i - 1]
r2, g2, b2 = seq[i + 1]
cdict['red'].append([item, r1, r2])
cdict['green'].append([item, g1, g2])
cdict['blue'].append([item, b1, b2])
#print cdict
return mcolors.LinearSegmentedColormap('Custom_WGrYR', cdict)
ET.register_namespace("","http://www.w3.org/2000/svg")
# test column heat for nodes
n_cols = 5
plot_data = zeros((n_cols,2))
# generate column numbers and random heat values to test
plot_data[:,0] = asarray(arange(1, n_cols+1))#.reshape(n_cols,1)
plot_data[:,1] = random.rand(n_cols,1).reshape(n_cols,)
example = wxToolTipExample(plot_data)
example.plot()
Where am I going wrong?

Your code looks like a work in progress that hasn't been completely cleaned up. (I had to comment out self.tooltip.SetTip() calls to get it to run.) But here is the cause of your immediate issue with the exception you note, and how I found it:
On my machine, I edited backend_svg.py function start() to add a print(extra) and then I run your code. As a result of your lines:
points = ['point_{0}'.format(ii) for ii in arange(1, self.dataX.size+1)]
self.pathCol.set_gid(points)
the matplotlib backend attempts to create an SVG <g> node with the ID: ['point_1', 'point_2', 'point_3', 'point_4', 'point_5']. This is a list, rather than a valid string, so s.replace() fails.
Ultimately you must change your code so that set_gid() only receives string parameters. The simplest way to do that is to change the two lines above to simply:
self.pathCol.set_gid('point_1')
but then you don't get IDs for individual points in the generated SVG. You could also remove the self.pathCol.set_gid line altogether (pathCol it will be rendered to SVG as <g id="PathCollection_1"> and points will also not have IDs).
It appears that it is not simple to assign SVG IDs to individual points/vertices contained within a pathCollection. If you need to do that, you might need to come up with another way to plot them -- if I understand the problem correctly, you'd need to plot individual points rather than a path.

AssertionError in matplotlib animation

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!)

Axis limits causing error when attempting to save figure

I've got a problem with saving figures with matplotlib and the pgf-backend.
If I have a plot in which the axis limits (e.g. X: [20,70]; Y: [0,-50]) are much lower than the datapoints with the highest X- and Y-values (lowest datapoint: [0,0]; highest datapoint: [150000,-200000]) there's always the following error:
File "<>", line 816, in exportGraphs2
File "C:\Python26\lib\site-packages\matplotlib\pyplot.py", line 561, in savefig
return fig.savefig(*args, **kwargs)
File "C:\Python26\lib\site-packages\matplotlib\figure.py", line 1421, in savefig
self.canvas.print_figure(*args, **kwargs)
File "C:\Python26\lib\site-packages\matplotlib\backend_bases.py", line 2220, in print_figure
**kwargs)
File "C:\Python26\lib\site-packages\matplotlib\backends\backend_pgf.py", line 882, in print_pdf
self._print_pdf_to_fh(fh, *args, **kwargs)
File "C:\Python26\lib\site-packages\matplotlib\backends\backend_pgf.py", line 858, in _print_pdf_to_fh
check_output(cmdargs, stderr=subprocess.STDOUT, cwd=tmpdir)
File "C:\Python26\lib\site-packages\matplotlib\compat\subprocess.py", line 69, in _check_output
raise subprocess.CalledProcessError(retcode, cmd, output=output)
TypeError
:
__init__() got an unexpected keyword argument 'output'
However, if the axis limits are larger or slightly smaller than the largest values of the datapoints everything works fine.
Does anyone have an idea what the problem might be?
Edit:
Here is a part of my code. Since it's quite complex due to reading data from QTIPlot it's just a short snippet.
import matplotlib as mpl
import sys
sys.path.append("..")
mpl.use('pgf')
latex_preamble = {"text.usetex": True,
"pgf.rcfonts": False,
"pgf.preamble": [r"\usepackage{cmbright}",
r"\usepackage{siunitx}",
r"\usepackage{fontspec}",
r"\setmainfont{Calibri}",
r"\usepackage[utf8x]{inputenc}",
r"\usepackage{textgreek}"]}
mpl.rcParams.update(latex_preamble)
import matplotlib.pyplot as plt
mpl.rcParams.update({'font.size': 24})
x = [186691.98079420399, 94747.037718184903, 43238.854190494698, 19067.6709222838, 8804.8960840724703, 4616.3273881164196, 2784.39307777148, 1924.44569810138, 1421.6244001381001, 1044.0988528353901, 738.32026028954704, 499.78345554987698, 325.91902800532, 208.07599600125701, 136.48397798235101, 97.188999849599597, 77.189874321047498, 66.814364230185305, 61.930218121218097, 58.897007608510897, 57.004014967900098, 55.406903357827098, 54.041568494235101, 52.802043730081699, 51.759023715688997, 50.777510655714799, 49.815484593681198, 48.961058456802903, 48.191611656054903, 47.4882902162026, 46.848714837688902, 46.190288085990197, 45.3774348340838, 44.4693505256935, 43.434754403205901, 42.220754480990998, 40.854413497723201, 39.357546952524302, 37.878908712040399, 36.491255819384499, 35.284755433638502, 34.2610953105862, 33.420298363499299, 32.766550165311301, 32.298722787726398, 31.9724893134679, 31.733745041689001, 31.560804411243499, 31.4680666775029]
y = [-225457.06785031699, -151654.317412915, -93620.558383412499, -53880.168115145199, -30116.624926982, -16905.4587130902, -9712.6193383353802, -5810.69026270625, -3678.9706880631902, -2475.8794835536701, -1751.8371788254599, -1253.7787633139801, -901.12220338703003, -643.67630154638596, -454.56954062206199, -318.51086928594498, -223.35257106637999, -156.97451642102101, -112.89935316650001, -82.655897872917393, -61.638224025861199, -46.766272864377299, -36.093957934023599, -28.313379974280299, -22.4321281711178, -17.961980555220599, -14.556781594439601, -11.97682273137, -10.061208825108, -8.6707057874908102, -7.6773295770935901, -7.0721051618041599, -6.7628705905120299, -6.6605343376401303, -6.69407747810377, -6.8113923612978997, -6.8702914807042204, -6.8388590566887899, -6.5692275645203999, -6.1065237236783396, -5.5035760007258503, -4.79953162532468, -4.0671542575787001, -3.3690652676737902, -2.7612664707248298, -2.2359507233406499, -1.77482078896039, -1.44286837047643, -1.1560624817337399]
fig, ax1 = plt.subplots(figsize=(16,12))
p, = ax1.plot(x, y) # really, x and y would be arrays of doubles which are read from QTIPlot
ax1.set_xlabel(unicode("Z'"))
ax1.set_ylabel(unicode("Z''"))
ax1.set_xlim(20,70)
ax1.set_ylim(0,-50)
ax1.set_aspect('equal', adjustable='box')
ax1.tick_params(axis='y', direction = 'out')
ax1.tick_params(axis='x', direction = 'out')
ax1.yaxis.tick_left()
ax1.xaxis.tick_bottom()
plt.savefig("figure.pdf")