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I'm trying to make moving stick figure 3D animation with matplotlib, using npy file made from VideoPose3D.
And I find this topic and use the same code, but it made this log.
"Module 'matplotlib.cm' has no 'jet' member"
I tried to resolve this problem and made the following code. But the next error occurred.
So please tell me why this happens and fix this code and show animation?
details : matplotlib==3.3.3, python3==3.6.9, numpy==1.19.5
npy file is here.
https://drive.google.com/file/d/1PJME78STVCPgKZdxpC3KOeP39SRJAx00/view?usp=sharing[][1]
import numpy as np
import pandas as pd
import matplotlib
import os
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.colors import cnames
from matplotlib import animation
from matplotlib import cm
arrayMarker3Dcoordinates = np.load('/home/shime/posesimulate/pose.npy')
arrayMarker3Dcoordinates.shape
size = arrayMarker3Dcoordinates.size
df = pd.DataFrame(arrayMarker3Dcoordinates.reshape(size//51, 17*3),
columns=['pelvisX', 'pelvisY', 'pelvisZ', 'R-troX', 'R-troY', 'R-troZ', 'R-kneeX', 'R-kneeY', 'R-kneeZ', 'R-ankleX', 'R-ankleY', 'R-ankleZ', 'L-troX', 'L-troY', 'L-troZ', 'L-kneeX', 'L-kneeY', 'L-kneeZ', 'L-ankleX', 'L-ankleY', 'L-ankleZ', 'centerX', 'centerY', 'centerZ', 'neckX', 'neckY', 'neckZ', 'noseX', 'noseY', 'noseZ', 'headX', 'headY', 'headZ', 'L-shoX', 'L-shoY', 'L-shoZ', 'L-elbX', 'L-elbY', 'L-elbZ', 'L-wristX', 'L-wristY', 'L-wristZ', 'R-shoX', 'R-shoY', 'R-shoZ', 'R-elbX', 'R-elbY', 'R-elbZ', 'R-wristX', 'R-wristY', 'R-wristZ'])
t_start = 0 # start frame
t_end = df.shape[0] #frame数
N_tag = df.shape[1] # nr of tags used (all)
N_trajectories = N_tag
# pseudo time-vector for first walking activity
t = np.linspace(0, t_end/30, df.shape[0])
# empty animation array (3D) 3*3のarray
x_t = np.zeros(shape=(int(N_tag), df.shape[0], 3))
for tag in range(17):
# store data in numpy 3D array: (tag,time-stamp,xyz-coordinates)
x_t[tag,:,:] = df.iloc[:, tag * 3:tag * 3 + 3]
# ===STICK-LINES========================================================================================
# xx = [x_t[1,:,0],x_t[2,:,0]]
# yy = [x_t[1,:,1],x_t[2,:,1]]
# zz = [x_t[1,:,2],x_t[2,:,2]]
# ======================================================================================================
# Set up figure & 3D axis for animation
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1], projection='3d')
ax.axis('on')
"""#this is original code
# choose a different color for each trajectory
colors = plt.cm.jet(np.linspace(0, 1, int(N_trajectories)))
#colors
# set up trajectory lines
lines = sum([ax.plot([], [], [], '-', c=c) for c in colors], [])
# set up points
pts = sum([ax.plot([], [], [], 'o', c=c) for c in colors], [])
"""
lines = sum([ax.plot([], [], [], '-', color='C3')for i in range(N_trajectories)], [])
pts = sum([ax.plot([], [], [], 'o', color='C3') for i in range(N_trajectories)], [])
# set up lines which create the stick figures
stick_defines = [
(0, 1),
(0, 4),
(4, 5),
(5, 6),
(0, 7),
(1, 2),
(2, 3),
(7, 8),
(8, 9),
(9, 10),
(8, 14),
(8, 11),
(11, 12),
(12, 13),
(14, 15),
(15, 16)
]
# 上で定義されたstick_definesにある点の間に線をひく "draw line between 2 points"
stick_lines = [ax.plot([], [], [], 'k-')[0] for _ in stick_defines]
# Automatically set axes limits
# prepare the axes limits
# ax.set_xlim(df_minmax.loc['x'].values)
# ax.set_ylim(df_minmax.loc['y'].values)
# ax.set_zlim(df_minmax.loc['z'].values)
# Setting the axes properties
# https://matplotlib.org/2.1.2/gallery/animation/simple_3danim.html
mid_x = 0
x_range = 1
ax.set_xlim3d(mid_x - x_range, mid_x + x_range)
ax.set_xlabel('X')
mid_y =0
y_range = 1
ax.set_ylim3d(mid_y - x_range, mid_y + x_range)
ax.set_ylabel('Y')
mid_z = 0.5
z_range = 1
ax.set_zlim3d(mid_z - z_range, 1.5)
ax.set_zlabel('Z')
ax.set_title('markers in 3D')
# set point-of-view: specified by (altitude degrees, azimuth degrees)
ax.view_init(20,45)
# initialization function: plot the background of each frame
def init():
for line, pt in zip(lines, pts): # lines, ptsのリストから，同時にi番目のデータを取得する．linesからline, pts からpt "at the same time,get number i date, line from lines, pt from pts"
# trajectory lines
line.set_data([], [])
line.set_3d_properties([], [])
# points
pt.set_data([], [])
pt.set_3d_properties([], [])
return lines + pts + stick_lines
# animation function. This will be called sequentially with the frame number
def animate(i):
# 1 * i means show every frame, 2*i means one frame show one frame no-show
i = (1 * i) % x_t.shape[1]
for pt, xi in zip(pts, x_t):
x, y, z = xi[:i].T # note ordering of points to line up with true exogenous registration (x,z,y)
pt.set_data(x[-1:], y[-1:])
pt.set_3d_properties(z[-1:])
for stick_line, (sp, ep) in zip(stick_lines, stick_defines):
stick_line._verts3d = x_t[[sp, ep], i,:].T.tolist()
# ax.view_init(30, 0.3 * i)
ax.view_init(20,60+i*2)
fig.canvas.draw()
return lines + pts + stick_lines
# instantiate the animator.
anim = animation.FuncAnimation(fig, animate, init_func=init, frames=t_end, interval=100, repeat = False, blit=True)
# save GIF animation
# anim.save('3Dplotanimation.gif', writer='pillow', fps=10)
plt.show()
And log is this.
/usr/bin/python3 /home/shime/posesimulate/simulate.py
Traceback (most recent call last):
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/backends/backend_gtk3.py", line 258, in size_allocate
FigureCanvasBase.resize_event(self)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 1767, in resize_event
self.callbacks.process(s, event)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/cbook/__init__.py", line 229, in process
self.exception_handler(exc)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/cbook/__init__.py", line 81, in _exception_printer
raise exc
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/cbook/__init__.py", line 224, in process
func(*args, **kwargs)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 1259, in _on_resize
self._init_draw()
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 1706, in _init_draw
self._drawn_artists = self._init_func()
File "/home/shime/posesimulate/simulate.py", line 109, in init
line.set_3d_properties([], [])
File "/home/shime/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 143, in set_3d_properties
zs = np.broadcast_to(zs, xs.shape)
AttributeError: 'list' object has no attribute 'shape'
Traceback (most recent call last):
File "/home/shime/posesimulate/simulate.py", line 139, in <module>
plt.show()
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/pyplot.py", line 353, in show
return _backend_mod.show(*args, **kwargs)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 3524, in show
manager.show() # Emits a warning for non-interactive backend.
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/backends/backend_gtk3.py", line 446, in show
self.canvas.draw()
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/backends/backend_gtk3agg.py", line 70, in draw
backend_agg.FigureCanvasAgg.draw(self)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 407, in draw
self.figure.draw(self.renderer)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/figure.py", line 1870, in draw
self.canvas.draw_event(renderer)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 1759, in draw_event
self.callbacks.process(s, event)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/cbook/__init__.py", line 229, in process
self.exception_handler(exc)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/cbook/__init__.py", line 81, in _exception_printer
raise exc
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/cbook/__init__.py", line 224, in process
func(*args, **kwargs)
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 959, in _start
self._init_draw()
File "/home/shime/.local/lib/python3.6/site-packages/matplotlib/animation.py", line 1706, in _init_draw
self._drawn_artists = self._init_func()
File "/home/shime/posesimulate/simulate.py", line 109, in init
line.set_3d_properties([], [])
File "/home/shime/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 143, in set_3d_properties
zs = np.broadcast_to(zs, xs.shape)
AttributeError: 'list' object has no attribute 'shape'
My writing is probably difficult to read. I'm sorry. As ever, any help is much appreciated.
Inside the init function, simply replace line.set_3d_properties([], []) with line.set_3d_properties([])
I have the following code snippet to illustrate the issue:
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
import time
import random
# Mock categories
categories = ["cat1", "cat2", "cat3", "cat4"]
counter = 0
# Plot
x_data = []
y_data = []
plt.ion()
fig = plt.figure()
subplt = fig.add_subplot(312)
subplt_line, = subplt.plot(x_data, y_data, 'b.')
while True:
time.sleep(0.1) # simulate some delay that occurs in the actual application
x_data.append(counter)
subplt_line.set_xdata(x_data)
counter += 1
# y_data.append(random.randrange(1, 15)) # This works fine (except the scaling)
y_data.append(random.choice(categories)) # This will end in an exception
subplt_line.set_ydata(y_data)
# Update the plot
fig.canvas.draw()
fig.canvas.flush_events()
It will end in an exception like this:
Traceback (most recent call last):
File "test.py", line 36, in <module>
fig.canvas.draw()
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py", line 12, in draw
super(FigureCanvasTkAgg, self).draw()
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 437, in draw
self.figure.draw(self.renderer)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/figure.py", line 1493, in draw
renderer, self, artists, self.suppressComposite)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/image.py", line 141, in _draw_list_compositing_images
a.draw(renderer)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 2635, in draw
mimage._draw_list_compositing_images(renderer, self, artists)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/image.py", line 141, in _draw_list_compositing_images
a.draw(renderer)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/lines.py", line 738, in draw
self.recache()
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/lines.py", line 656, in recache
yconv = self.convert_yunits(self._yorig)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/artist.py", line 200, in convert_yunits
return ax.yaxis.convert_units(y)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/axis.py", line 1526, in convert_units
ret = self.converter.convert(x, self.units, self)
File "/anaconda3/envs/xxx/lib/python2.7/site-packages/matplotlib/category.py", line 65, in convert
unit.update(values)
AttributeError: 'NoneType' object has no attribute 'update'
I seems like the combination of categorcal y data and the interactivity is causing this. When using numerical values it works fine, and when using the non-interactive feature it works well even with the categorical axis.
Another issue is be the automatic scaling of the y axis. New values added via set_y_data() dot seem to trigger this.
The plot will visualize analysis done on an endless stream of data and is used like a dashboard - therefore the plot should update with each iteration of the loop.
I couldn't run your code using the while loop, but I would suggest using FuncAnimation to create self-updating graphs anyway (there are plenty of examples on SO and online).
I believe your problem is with the initialization of the Line2D object. When you're passing any empty y-array, matplotlib seem to assume you're going to use numerical and not categorical values. Initializing the line with a string as a y-value seem to do the trick. You'll have to adjust the code so that the first point created makes sense for your data, but that should only be a minor annoyance.
For the scaling of the axis, matplotlib adds each category to a new integer value, so you need only to count how many categories you have in your data to know what is the extent of the axes.
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.animation as animation
import random
# Mock categories
categories = ["cat1", "cat2", "cat3", "cat4"]
counter = 0
# Plot
x_data = [0]
y_data = ['cat1']
fig = plt.figure()
subplt = fig.add_subplot(312)
subplt_line, = subplt.plot(x_data, y_data, 'b.-')
debug_text = fig.text(0, 1, "TEXT", va='top') # for debugging
def init():
subplt_line.set_data([0],['cat1'])
def animate(num, ax):
new_x, new_y = num, random.choice(categories)
debug_text.set_text('{:d} {:s}'.format(num, new_y))
x, y = subplt_line.get_data()
x = np.append(x, new_x)
y = np.append(y, new_y)
subplt_line.set_data(x,y)
ax.set_xlim(min(x),max(x))
ax.set_ylim(0,len(np.unique(y))-1)
return subplt_line,debug_text
ani = animation.FuncAnimation(fig, animate, fargs=[subplt], init_func=init, frames=20, blit=False, repeat=False)
plt.show()
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.
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!)
This question already has answers here:
matplotlib imshow(): how to animate?
(2 answers)
Closed 6 years ago.
Can you please help me figuring out what the problem is here? I don't know what is going wrong. Single plots from img can be plotted just fine, but the animation module gives an error. The Traceback says:
Traceback (most recent call last):
File "/home/ckropla/workspace/TAMM/Sandkasten.py", line 33, in <module>
ani = animation.ArtistAnimation(fig, img, interval=20, blit=True,repeat_delay=0)
File "/home/ckropla/.pythonbrew/pythons/Python-3.3.1/lib/python3.3/site-packages/matplotlib/animation.py", line 818, in __init__
TimedAnimation.__init__(self, fig, *args, **kwargs)
File "/home/ckropla/.pythonbrew/pythons/Python-3.3.1/lib/python3.3/site-packages/matplotlib/animation.py", line 762, in __init__
*args, **kwargs)
File "/home/ckropla/.pythonbrew/pythons/Python-3.3.1/lib/python3.3/site-packages/matplotlib/animation.py", line 481, in __init__
self._init_draw()
File "/home/ckropla/.pythonbrew/pythons/Python-3.3.1/lib/python3.3/site-packages/matplotlib/animation.py", line 824, in _init_draw
for artist in f:
TypeError: 'AxesImage' object is not iterable
Code:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
def FUNCTION(p,r,t):
k_0,dx,c = p
x,y = r
z = np.exp(1j*(k_0[0]*np.meshgrid(x,y)[0]+k_0[1]*np.meshgrid(x,y)[1]-c*t))*np.exp(-((np.sqrt(np.meshgrid(x,y)[0]**2+np.meshgrid(x,y)[1]**2)-c*t)/(2*dx))**2 )*(2/np.pi/dx**2)**(1/4)
z = abs(z)
#k,F = FFT((x-c*t),y)
return(x,y,z)
#Parameter
N = 500
n = 20
x = np.linspace(-10,10,N)
y = np.linspace(-10,10,N)
t = np.linspace(0,30,n)
r=[x,y]
k_0 = [1,1]
dx = 1
c = 1
p = [k_0,dx,c]
fig = plt.figure("Moving Wavepackage")
Z = []
img = []
for i in range(n):
Z.append(FUNCTION(p,r,t[i])[2])
img.append(plt.imshow(Z[i]))
ani = animation.ArtistAnimation(fig, img, interval=20, blit=True,repeat_delay=0)
plt.show()
Each element in img needs to be a sequence of artists, not a single artist. If you change img.append(plt.imshow(Z[i])) to img.append([plt.imshow(Z[i])]) then your code works fine.