I'm trying to plot the time evolution of a function f(x,t). The data is stored in a file which has the following format:
1st row:f(0,0) f(0,1) f(0,2) ....f(0,N)
2nd row:f(1,0) f(1,1) f(1,2) ....f(1,N)
Mth row:f(M,0) f(M,1) f(M,2) ....f(M,N)
where N is the no: of points of the simulation box and M is the number of timesteps.
I used basic_animation by Jake Vanderplas (https://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/) to start with, the original example works fine as long as i put blit=False.
Then i tried to replace x by :
x= np.arange(0,192)
and y by the contents of the file mentioned above.
If i do just plt.plot(x,y), it does plot f(x,t) at a given time t, but I want the animation of f(x,t) in time.
set_data should accept 2 1Darrays and I've checked that len(x)=len(y).
But I get the following error message:
'RuntimeError: xdata and ydata must be the same length'
This is the code (in the future i would like to plot multiple functions):
"""
Modified Matplotlib Animation Example
original example:
email: vanderplas#astro.washington.edu
website: http://jakevdp.github.com
license: BSD
Feel free to use and modify this, but keep the above information.
"""
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation
from itertools import islice
filename = 'DensityByPropagation__a_0_VHxcS_kick'
# First set up the figure, the axis, and the plot element we want to animate
fig = plt.figure()
ax = plt.axes(xlim=(0, 192), ylim=(-2, 2))
lineS, = ax.plot([], [], lw=2)
# initialization function: plot the background of each frame
def init():
lineS.set_data([], [])
return lineS,
# animation function. This is called sequentially
def animate(i):
w = np.linspace(0, 2, 1000)
z = np.sin(2 * np.pi * (w - 0.01 * i))
x= np.arange(0,192)
with open(filename) as fobj:
ketchup = islice(fobj, 0, None, 10)
for line in ketchup:
x,y = x,zip(*([float(y) for y in line.split("\t")] for line in fobj))
#plt.plot(x,y)
#plt.show()
#print len(x)
#print len(y)
#lineS.set_data(w,z)
lineS.set_data(x,y)
return lineS,
# call the animator. blit=True means only re-draw the parts that have changed.
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=200, interval=20, blit=False)
# save the animation as an mp4. This requires ffmpeg or mencoder to be
# installed. The extra_args ensure that the x264 codec is used, so that
# the video can be embedded in html5. You may need to adjust this for
# your system: for more information, see
# http://matplotlib.sourceforge.net/api/animation_api.html
anim.save('movieJoh.mp4', fps=30, extra_args=['-vcodec', 'libx264'])
plt.show()
I'm not sure what exactly is causing your error, but let me point something out, then I'll make a toy example that should help clarify what's happening.
These lines seem unnecessarily complicated.
with open(filename) as fobj:
ketchup = islice(fobj, 0, None, 10)
for line in ketchup:
x,y = x,zip(*([float(y) for y in line.split("\t")] for line in fobj))
If your data is in fact in the simple format you stated, i.e., values separated by spaces, np.loadtxt() would load all the values into an easy to manage array.
Example
Lets assume this is your data file (10 time steps, 2 points on plot at each step):
0 0 0 0 0 0 0 0 0 0
9 8 7 6 5 4 3 2 1 0
Now some code:
filename = 'data.txt'
# First set up the figure, the axis, and the plot element we want to animate
fig = plt.figure()
ax = plt.axes(xlim=(0, 1), ylim=(0, 9))
lineS, = ax.plot([], [], lw=2)
x = range(2) # the domain
Now we load the data in with np.loadtxt(), this creates a 2-d matrix with t in the columns and x in the rows. We then transpose it to make indexing each time step possible in animate().
# load the data from file
data = np.loadtxt(filename)
# transpose so we could easily index in the animate() function
data = np.transpose(data)
Now for animation functions. This part is really quite simple. animate(i) takes one argument - the frame number. Using the frame number, we extract the values of f(x,t=frameNumber) and set that as the data on the plot.
# initialization function: plot the background of each frame
def init():
lineS.set_data([], [])
return lineS,
# animation function. This is called sequentially
def animate(i):
lineS.set_data(x, data[i])
return lineS,
# call the animator. blit=True means only re-draw the parts that have changed.
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=10, interval=100, blit=True)
plt.show()
This is the working code:
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation
# Input
filename = 'PeriodicDensity' # Filename
x = np.linspace(-7.5,7.5,192) # Domain
xLimits=[-7.5,7.5] # x limits
yLimits=[0,1] # y limits
framesToUse = range(1,9000,150)# The time-steps to plot
# load the data from file
data = np.loadtxt(filename)
# Set up the figure, the axis, and the plot element we want to animate
fig = plt.figure()
ax = plt.axes(xlim=xLimits,ylim=yLimits)
lineS, = ax.plot([], [], lw=2)
# Initialisation function
def init():
lineS.set_data([],[])
return lineS,
# Animation function (called sequentially)
def animate(i):
lineS.set_data(x,data[i])
return lineS,
# call the animator. blit=True means only re-draw the parts that have changed.
anim = animation.FuncAnimation(fig, animate, init_func=init,interval=1000, frames=framesToUse, blit=True)
# save the animation as an mp4. This requires ffmpeg or mencoder to be
# installed. The extra_args ensure that the x264 codec is used, so that
# the video can be embedded in html5. You may need to adjust this for
# your system: for more information, see
# http://matplotlib.sourceforge.net/api/animation_api.html
anim.save('movieDensity.mp4', fps=1, extra_args=['-vcodec', 'libx264'])
plt.show()
Related
I'm trying to plot data that is generated in runtime. In order to do so I'm using matplotlib.animation.FuncAnimation.
While the data is displayed correctly, the axis values are not updating accordingly to the values that are being displayed:
The x axis displays values from 0 to 10 eventhough I update them in every iteration in the update_line function (see code below).
DataSource contains the data vector and appends values at runtime, and also returns the indexes of the values being returned:
import numpy as np
class DataSource:
data = []
display = 10
# Append one random number and return last 10 values
def getData(self):
self.data.append(np.random.rand(1)[0])
if(len(self.data) <= self.display):
return self.data
else:
return self.data[-self.display:]
# Return the index of the last 10 values
def getIndexVector(self):
if(len(self.data) <= self.display):
return list(range(len(self.data)))
else:
return list(range(len(self.data)))[-self.display:]
I've obtained the plot_animation function from the matplotlib docs.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from datasource import DataSource
def update_line(num, source, line):
data = source.getData()
indexs = source.getIndexVector()
if indexs[0] != 0:
plt.xlim(indexs[0], indexs[-1])
dim=np.arange(indexs[0],indexs[-1],1)
plt.xticks(dim)
line.set_data(indexs,data)
return line,
def plot_animation():
fig1 = plt.figure()
source = DataSource()
l, = plt.plot([], [], 'r-')
plt.xlim(0, 10)
plt.ylim(0, 1)
plt.xlabel('x')
plt.title('test')
line_ani = animation.FuncAnimation(fig1, update_line, fargs=(source, l),
interval=150, blit=True)
# To save the animation, use the command: line_ani.save('lines.mp4')
plt.show()
if __name__ == "__main__":
plot_animation()
How can I update the x axis values in every iteration of the animation?
(I appreciate suggestions to improve the code if you see any mistakes, eventhough they might not be related to the question).
Here is a simple case of how you can achieve this.
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import numpy as np
%matplotlib notebook
#data generator
data = np.random.random((100,))
#setup figure
fig = plt.figure(figsize=(5,4))
ax = fig.add_subplot(1,1,1)
#rolling window size
repeat_length = 25
ax.set_xlim([0,repeat_length])
ax.set_ylim([-2,2])
#set figure to be modified
im, = ax.plot([], [])
def func(n):
im.set_xdata(np.arange(n))
im.set_ydata(data[0:n])
if n>repeat_length:
lim = ax.set_xlim(n-repeat_length, n)
else:
lim = ax.set_xlim(0,repeat_length)
return im
ani = animation.FuncAnimation(fig, func, frames=data.shape[0], interval=30, blit=False)
plt.show()
#ani.save('animation.gif',writer='pillow', fps=30)
Solution
My problem was in the following line:
line_ani = animation.FuncAnimation(fig1, update_line, fargs=(source, l),
interval=150, blit=True)
What I had to do is change the blit parameter to False and the x axis started to move as desired.
I'm using the following code to produce an animation with matplotlib that is intended to visualize my experiments.
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import ArtistAnimation, PillowWriter
plt.rcParams['animation.html'] = 'jshtml'
def make_grid(X, description=None, labels=None, title_fmt="label: {}", cmap='gray', ncols=3, colors=None):
L = len(X)
nrows = -(-L // ncols)
frame_plot = []
for i in range(L):
plt.subplot(nrows, ncols, i + 1)
im = plt.imshow(X[i].squeeze(), cmap=cmap, interpolation='none')
if labels is not None:
color = 'k' if colors is None else colors[i]
plt.title(title_fmt.format(labels[i]), color=color)
plt.xticks([])
plt.yticks([])
frame_plot.append(im)
return frame_plot
def animate_step(X):
return X ** 2
n_splots = 6
X = np.random.random((n_splots,32,32,3))
Y = X
X_t = []
for i in range(10):
Y = animate_step(Y)
X_t.append((Y, i))
frames = []
for X, step in X_t:
frame = make_grid(X,
description="step={}".format(step),
labels=range(n_splots),
title_fmt="target: {}")
frames.append(frame)
anim = ArtistAnimation(plt.gcf(), frames,
interval=300, repeat_delay=8000, blit=True)
plt.close()
anim.save("test.gif", writer=PillowWriter())
anim
The result can be seen here:
https://i.stack.imgur.com/OaOsf.gif
It works fine so far, but I'm having trouble getting a shared xlabel to add a description for all of the 6 subplots in the animation. It is supposed to show what step the image is on, i.e. "step=5".
Since it is an animation, I cannot use xlabel or set_title (since it would be constant over the whole animation) and have to draw the text myself.
I've tried something along the lines of..
def make_grid(X, description=None, labels=None, title_fmt="label: {}", cmap='gray', ncols=3, colors=None):
L = len(X)
nrows = -(-L // ncols)
frame_plot = []
desc = plt.text(0.5, .04, description,
size=plt.rcparams["axes.titlesize"],
ha="center",
transform=plt.gca().transAxes
)
frame_plot.append(desc)
...
This, of course, won't work, because the axes are not yet created. I tried using the axis of another subplot(nrows, 1, nrows), but then the existing images are drawn over..
Does anyone have a solution to this?
Edit:
unclean, hacky solution for now:
Wait for the axes of the middle image of the last row to be created and use that for plotting the text.
In the for loop:
...
if i == int((nrows - 0.5) * ncols):
title = ax.text(0.25, -.3, description,
size=plt.rcParams["axes.titlesize"],
# ha="center",
transform=ax.transAxes
)
frame_plot.append(title)
...
To me, your case is easier to solve with FuncAnimation instead of ArtistAnimation, even if you already have access to the full list of data you want to show animated (see this thread for a discussion about the difference between the two functions).
Inspired from this FuncAnimation example, I wrote the code below that does what you needed (using the same code with ArtistAnimation and correct list of arguments does not work).
The main idea is to initialize all elements to be animated at the beginning, and to update them over the animation frames. This can be done for the text object (step_txt = fig.text(...)) in charge of displaying the current step, and for the images out from ax.imshow. You can then update whatever object you would like to see animated with this recipe.
Note that the technique works if you want the text to be an x_label or any text you choose to show. See the commented line in the code.
#!/Users/seydoux/anaconda3/envs/jupyter/bin/python
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation, PillowWriter
# parameters
n_frames = 10
n_splots = 6
n_cols = 3
n_rows = n_splots // n_cols
def update_data(x):
return x ** 2
# create all snapshots
snapshots = [np.random.rand(n_splots, 32, 32, 3)]
for _ in range(n_frames):
snapshots.append(update_data(snapshots[-1]))
# initialize figure and static elements
fig, axes = plt.subplots(2, 3)
axes = axes.ravel() # so we can access all axes with a single index
for i, ax in enumerate(axes):
ax.set_xticks([])
ax.set_yticks([])
ax.set_title("target: {}".format(i))
# initialize elements to be animated
step_txt = fig.text(0.5, 0.95, "step: 0", ha="center", weight="bold")
# step_txt = axes[4].set_xlabel("step: 0") # also works with x_label
imgs = list()
for a, s in zip(axes, snapshots[0]):
imgs.append(a.imshow(s, interpolation="none", cmap="gray"))
# animation function
def animate(i):
# update images
for img, s in zip(imgs, snapshots[i]):
img.set_data(s)
# update text
step_txt.set_text("step: {}".format(i))
# etc
anim = FuncAnimation(fig, animate, frames=n_frames, interval=300)
anim.save("test.gif", writer=PillowWriter())
Here is the output I got from the above code:
The following gif is created with gnuplot and Fortran. However, now I want to do the same using only Python (animation form matplotlib mainly).
I can generate a gif with Python but I don't know how to generate something like the righthand side gif (you plot also the last 100 points), the evolution in phase space.
Any help will be apreciated,
Thanks
Gnuplot code for the gif:
set term gif size 1000,600 animate delay 1000 loop 0
set output "animacio.gif"
cd 'C:\Users\Usuario\Desktop'
datafile ="P7-1718-b-res.dat"
do for[i=1:5000:10]{
set multiplot
set size 0.5,0.8
set origin 0.0,0.0
set title "Evolució de l'angle girat i velocitat angular (t)"
set xrange[0:50]
set yrange[-pi:pi]
set xlabel "t (s)"
set ylabel "Angle girat, v_{ang}"
set key below
plot datafile index 9 every ::1::i with line linewidth 4 t"Posició angular" ,datafile index 9 every ::1::i u 1:3 with line linewidth 4 t"V_{ang}"
set origin 0.5,0
set size 0.5,0.8
set title "Evolució en l'espai de fases"
set yrange[-pi:pi]
set xrange[-pi:pi]
set xlabel "Angle girat(rad)"
set ylabel "Velocitat angular(rad/s)"
set key below
if (i>101) {
plot datafile index 9 every::i::i u 2:3 t"" ps 3,datafile index 9 every::i-100::i u 2:3 w l t"" }
else {
plot datafile index 9 every::i::i u 2:3 t"" ps 3}
unset multiplot
}
And assume your data have three rows (time,position,angular velocity) at index 9.
As you mentioned, you can use Matplotlib animation to make it work.
I have done something "similar" to your data, but of course, as I haven't got the data file, it is not equal. The code is the following one:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
w = 1.
t = np.linspace(0,10,200)
x = np.cos(w*t)
v = -w*np.cos(w*t)
fig, ax = plt.subplots(1,2)
line_1, = ax[0].plot([], [], 'b-', lw=2)
line_2, = ax[0].plot([], [], 'r-', lw=2)
ax[0].set_xlim([0,50])
ax[0].set_ylim([-np.pi,np.pi])
line_3, = ax[1].plot([], [], 'g-', lw=2)
star_3, = ax[1].plot([], [], 'g*')
ax[1].set_xlim([-np.pi,np.pi])
ax[1].set_ylim([-np.pi,np.pi])
def animate(i):
line_1.set_data(t[:i],x[:i]) # update the data
line_2.set_data(t[:i],v[:i])
nLast = 20
idFrom = i-nLast if(i-nLast >= 0) else 0
line_3.set_data(np.cos(t[idFrom:i+1]),np.sin(t[idFrom:i+1]))
star_3.set_data(np.cos(t[i]),np.sin(t[i]))
return line_1,line_2,line_3,star_3
# Init only required for blitting to give a clean slate.
def init():
line_1.set_data([], [])
line_2.set_data([], [])
line_3.set_data([], [])
star_3.set_data([], [])
return line_1,line_2,line_3,star_3
anim = animation.FuncAnimation(fig, animate, np.arange(1, len(t)), init_func=init, interval=100, blit=True)
#anim.save('Plot_last_nLast.mp4', fps=15)
#anim.save('Plot_last_nLast.gif', dpi=80, writer='imagemagick')
plt.show()
You can save the animation in a GIF (required Imagemagick) or as a MP4 movie if you have ffmpeg to use it as writer of the animation.
But that's another issue
I am trying to create an animation that plots GPS data from a run. I have code that plots the points and creates the animation. In order to have the old point deleted and the new plotted with each frame I am using scat.set_offsets(x[i],y[i]) to plot the points. The trouble I am running into is that I want the color of the point to reflect the speed at that position. The code below works but I cannot figure out the color updating. I have tried using scat.alpha() but it switches the color once and never updates again. I want to use, jet, for example, and have 0 mph be blue and the fastest time to be red.
The running log has the first two columns as lon/lat and the third is velocity. Some data:
Longitude Latitude GPS Speed(km/h)
-88.19895578 43.19975045 0
-88.19894667 43.19976286 0
-88.19893236 43.19977277 0
-88.19872605 43.19969481 9.9
-88.19871956 43.19967161 10.799999
-88.19872339 43.19962663 11.7
-88.19873801 43.19959561 11.7
-88.19879232 43.19958254 9.9
-88.19876674 43.1995382 9.9
-88.19876797 43.19948614 7.2
The code is below. Thanks for the help!
"""
Matplotlib Animation of Accelerometer Vectors
author: Ryan Croke
website: http://TheHolyMath.com
"""
import numpy as np
import networkx as nx
from matplotlib import pyplot as plt
from matplotlib import animation
from matplotlib import cm
import csv
import json
import smopy
import re
### DATA ###
# Read shape file
g = nx.read_shp("tl_2014_us_state/tl_2014_us_state.shp")
# plot points of acceleration and deceleration
f = open('runninglog.csv')
cr = csv.reader(f)
# Make arrays for processing
latitude = []
longitude = []
velocity = []
# Velocity is in m/s - convert to miles/hour
# 1m/s = 2.236 mph
for row in cr:
# Need to test for headers - pass anything with letters
if any(c.isalpha() for c in row[0]) == True:
pass
else:
longitude.append(float(row[0]))
if any(c.isalpha() for c in row[1]) == True:
pass
else:
latitude.append(float(row[1]))
if any(c.isalpha() for c in row[2]) == True:
pass
else:
velocity.append(round(float(row[2])*2.236,2))
# Numer of plots
P = int(len(latitude))
# In the USA longitude is decreasing from west to east, latitude is increasing from south to north
# lower left will be max(lon) and min(lat)
pos1 = (float(min(latitude)),float(max(longitude)))
pos2 = (float(max(latitude)),float(min(longitude)))
### Animation ###
# First set up the figure, the axis, and the plot element we want to animate
map = smopy.Map(pos1, pos2, z=15)
# Smoopy allows you to create a matplotlib image using a t0_pixels command
x = []
y = []
# Create array's for lat/lon in pixel image
for i in xrange(len(latitude)):
x1, y1 = map.to_pixels(latitude[i],longitude[i])
x.append(x1)
y.append(y1)
# animation of a scatter plot using x, y from above
#------------------------------------------------------------------------------
fig = plt.figure()
ax = map.show_mpl(figsize=(8, 6))
scat = ax.scatter([],[],s=60)
# initialization function: plot the background of each frame
def init():
scat.set_offsets([])
#scat.set_facecolor([])
return scat,
# animation function. This is called sequentially
def animate(i):
scat.set_offsets([x[i], y[i]])
#scat.set_edgecolors('red')
#scat.set_facecolor()
return scat,
# call the animator. blit=True means only re-draw the parts that have changed.
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=P, interval=40, repeat=False, blit=True)
# save the animation as an mp4. This requires ffmpeg or mencoder to be
# installed. The extra_args ensure that the x264 codec is used, so that
# the video can be embedded in html5. You may need to adjust this for
# your system: for more information, see
# http://matplotlib.sourceforge.net/api/animation_api.html
anim.save('Around_the_block_animation.mp4', fps=30, extra_args=['-vcodec', 'libx264'])
plt.show()
I'm trying to animate two subplots, each with multiple lines. I am using Matplotlib, and I am using the FuncAnimation, which is used by many of the animation examples.
Using animation:
If I try to animate it, I only get the result of the first frame:
Without using animation:
If I manually call my update_lines function, it works fine.
Code:
Below is the full code (uncommenting the 3 indicated lines in main() works, but I would like to see it update in real-time, hence trying to use the animation).
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
def make_subplots():
def setup_axes(axes):
for ax in axes:
ax.set_xbound(0, 100) # bound will change as needed.
ax.set_ylim(0, 1) # limit won't change automatically.
def make_lines(axes):
labels = ('a', 'b', 'c')
lines = []
for ax in axes:
ax_lines = []
for label in labels:
x, y = [0], [0]
line, = ax.plot(x, y, label=label) # comma for unpacking.
ax_lines.append((line, x, y))
lines.append(ax_lines)
return lines
fig, axes = plt.subplots(2, 1, sharex=True, sharey=True)
lines = make_lines(axes)
setup_axes(axes)
return fig, axes, lines
def make_data():
for i in xrange(100):
print 'make_data():', i
data = dict()
for label in ('a', 'b', 'c'):
from random import random
data[label] = random()
yield (i + 1, data)
def update_lines(data, lines):
print 'update_lines():', data, lines
updated_lines = []
for ax_lines in lines:
for line, x, y in ax_lines:
label = line.get_label()
x.append(data[0])
y.append(data[1][label])
line.set_data(x, y)
updated_lines.append(line)
def main():
fig, axes, lines = make_subplots()
# Uncomment these 3 lines, and it works!
# new_data = make_data()
# for data in new_data:
# update_lines(data, lines)
FuncAnimation(fig=fig,
func=update_lines,
frames=make_data,
fargs=(lines,),
interval=10,
blit=False)
plt.show()
if __name__ == '__main__':
main()
(Undocumented?) Hooks
So, I was digging around the source-code of matplotlib.animation.Animation, and I noticed these lines in the __init__() function:
# Clear the initial frame
self._init_draw()
# Instead of starting the event source now, we connect to the figure's
# draw_event, so that we only start once the figure has been drawn.
self._first_draw_id = fig.canvas.mpl_connect('draw_event', self._start)
Sounds familiar...
This looks right so far. The self._init_draw() call draws my first frame immediately. Then the animation-object hooks into the figure-object and waits for the figure to be shown before attempting to draw any more frames for the animation.
Eureka!
The keyword is: animation-object. Since I wasn't planning on using the animation instance later (for example, to draw a movie), I didn't assign it to a variable. In fact, I was being yelled at by pyflakes because Local variable '...' is assigned to but never used.
But because all of the functionality relies on the hook, when the canvas is finally shown I presume Python's garbage collection has removed the Animation instance---since it was never assigned to a variable---and therefore the animation can never be started.
The fix
Simply assign the instance FuncAnimation instance to a variable, and everything works as expected!
anim = FuncAnimation(fig=fig,
func=update_lines,
frames=make_data,
fargs=(lines,),
interval=10,
blit=False)