[Matplotlib-users] Rabinovich...
Hello, My latest fractal music video, made with MatPlotLib. Enjoy! --Prahas https://www.youtube.com/watch?v=kh6ZLvpWr5kfeature=youtu.be -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] matplotlib.backends.backend_gtk3cairo memory leak
Hi, I seem to have a memory leak while generating a 'live' plot display. This wasn't the case for GTK2, but the example below is consuming ~800k/second (Matplotlib 1.4.3, PyGI aio-3.14.0_rev18, Windows 7 x64, python 3.4.3). I have checked the garbage collector but it doesn't show anything interesting (no massive incrementing count of uncollected items). Anyway, I would be very grateful if somebody could confirm and/or fix this (or tell me what I'm doing wrong).Many thanksDavidCode below: from gi.repository import Gtk, Gdk, GLibfrom matplotlib.figure import Figure# Tell matplotlib to use a GTK canvas for drawing#from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as FigureCanvasfrom matplotlib.backends.backend_gtk3cairo import FigureCanvasGTK3Cairo as FigureCanvas# Application Classclass pyMatPlotLibTest(object):def update_gui(self):y = [self.index] * 1024self.index += 1if self.index 1024: self.index = 0 Gdk.threads_enter()self.line.set_ydata(y) self.axes.set_title(%d % self.index)self.canvas.draw() Gdk.threads_leave()return Truedef __init__(self): self.index = 0self.x = range(1024)# Initialise the threads system and allow threads to work with GTKGLib.threads_init() # Draw scopeself.figure = Figure(dpi=100)self.canvas = FigureCanvas(self.figure) # a Gtk.DrawingArea #self.widget.alignment_ScopeDisplay.add(self.canvas)# Draw initial scopeself.axes = self.figure.add_subplot(111)self.line, = self.axes.plot(self.x, [0]* 1024)self.axes.set_title(None) self.axes.set_xbound(0.0, 1024)self.axes.set_ybound(-16, 1040) self.window_main = Gtk.Window(title=pyMatPlotLibTest) self.window_main.connect(destroy, lambda x: Gtk.main_quit()) self.window_main.add(self.canvas)self.window_main.show_all() # Ticker for the update of the input state monitoring Gdk.threads_add_timeout(priority = GLib.PRIORITY_DEFAULT_IDLE, interval = 10, # msecfunction = self.update_gui)Gtk.main()if __name__ == __main__:gui = pyMatPlotLibTest() -- View this message in context: http://matplotlib.1069221.n5.nabble.com/matplotlib-backends-backend-gtk3cairo-memory-leak-tp45614.html Sent from the matplotlib - users mailing list archive at Nabble.com.-- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matplotlib.backends.backend_gtk3cairo memory leak
I removed all calls to threads and swapped Gdk.threads_add_timeout to Glib.timeout_add (See attached. However if I comment the call to self.canvas.draw(), the python memory utilisation sits at 30.8Mb. from gi.repository import Gtk, Gdk, GLib from matplotlib.figure import Figure # Tell matplotlib to use a GTK canvas for drawing #from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as FigureCanvas from matplotlib.backends.backend_gtk3cairo import FigureCanvasGTK3Cairo as FigureCanvas # Application Class class pyMatPlotLibTest(object): def update_gui(self): y = [self.index] * 1024 self.index += 1 if self.index 1024: self.index = 0 #Gdk.threads_enter() self.line.set_ydata(y) self.axes.set_title(%d % self.index) self.canvas.draw() #Gdk.threads_leave() return True def __init__(self): self.index = 0 self.x = range(1024) # Initialise the threads system and allow threads to work with GTK #GLib.threads_init() # Draw scope self.figure = Figure(dpi=100) self.canvas = FigureCanvas(self.figure) # a Gtk.DrawingArea #self.widget.alignment_ScopeDisplay.add(self.canvas) # Draw initial scope self.axes = self.figure.add_subplot(111) self.line, = self.axes.plot(self.x, [0]* 1024) self.axes.set_title(None) self.axes.set_xbound(0.0, 1024) self.axes.set_ybound(-16, 1040) self.window_main = Gtk.Window(title=pyMatPlotLibTest) self.window_main.connect(destroy, lambda x: Gtk.main_quit()) self.window_main.add(self.canvas) self.window_main.show_all() # Ticker for the update of the input state monitoring GLib.timeout_add(10, self.update_gui) #Gdk.threads_add_timeout(priority = GLib.PRIORITY_DEFAULT_IDLE, #interval = 10, # msec #function = self.update_gui) Gtk.main() if __name__ == __main__: gui = pyMatPlotLibTest() From: ben.v.r...@gmail.com [mailto:ben.v.r...@gmail.com] On Behalf Of Benjamin Root Sent: 26 May 2015 14:53 To: David Hughes Cc: Matplotlib Users Subject: Re: [Matplotlib-users] matplotlib.backends.backend_gtk3cairo memory leak I take it that it doesn't happen using the GTK3Agg backend? What about the threading portion? Does it happen if you take the threading out? Ben Root On Tue, May 26, 2015 at 8:23 AM, David dhug...@rapiscansystems.commailto:dhug...@rapiscansystems.com wrote: Hi, I seem to have a memory leak while generating a 'live' plot display. This wasn't the case for GTK2, but the example below is consuming ~800k/second (Matplotlib 1.4.3, PyGI aio-3.14.0_rev18, Windows 7 x64, python 3.4.3). I have checked the garbage collector but it doesn't show anything interesting (no massive incrementing count of uncollected items). Anyway, I would be very grateful if somebody could confirm and/or fix this (or tell me what I'm doing wrong). Many thanks David Code below: from gi.repository import Gtk, Gdk, GLib from matplotlib.figure import Figure # Tell matplotlib to use a GTK canvas for drawing #from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as FigureCanvas from matplotlib.backends.backend_gtk3cairo import FigureCanvasGTK3Cairo as FigureCanvas # Application Class class pyMatPlotLibTest(object): def update_gui(self): y = [self.index] * 1024 self.index += 1 if self.index 1024: self.index = 0 Gdk.threads_enter() self.line.set_ydata(y) self.axes.set_title(%d % self.index) self.canvas.draw() Gdk.threads_leave() return True def __init__(self): self.index = 0 self.x = range(1024) # Initialise the threads system and allow threads to work with GTK GLib.threads_init() # Draw scope self.figure = Figure(dpi=100) self.canvas = FigureCanvas(self.figure) # a Gtk.DrawingArea #self.widget.alignment_ScopeDisplay.add(self.canvas) # Draw initial scope self.axes = self.figure.add_subplot(111) self.line, = self.axes.plot(self.x, [0]* 1024) self.axes.set_title(None) self.axes.set_xbound(0.0, 1024) self.axes.set_ybound(-16, 1040) self.window_main = Gtk.Window(title=pyMatPlotLibTest) self.window_main.connect(destroy, lambda x: Gtk.main_quit()) self.window_main.add(self.canvas) self.window_main.show_all() # Ticker for the update of the input state monitoring Gdk.threads_add_timeout(priority = GLib.PRIORITY_DEFAULT_IDLE, interval = 10, # msec function = self.update_gui) Gtk.main() if __name__ == __main__: gui = pyMatPlotLibTest() View
Re: [Matplotlib-users] matplotlib.backends.backend_gtk3cairo memory leak
I take it that it doesn't happen using the GTK3Agg backend? GTK3Agg is unimplemented at the GTK3-end: File c:\Python34\lib\site-packages\matplotlib\backends\backend_gtk3agg.py, line 69, in on_draw_event buf, cairo.FORMAT_ARGB32, width, height) NotImplementedError: Surface.create_for_data: Not Implemented yet. What about the threading portion? Does it happen if you take the threading out? I removed all calls to threads and swapped Gdk.threads_add_timeout to Glib.timeout_add. This made little difference. However if I comment the call to self.canvas.draw(), the python memory utilisation sits at 30.8Mb (but the graph does not update of course). Thanks David -- View this message in context: http://matplotlib.1069221.n5.nabble.com/matplotlib-backends-backend-gtk3cairo-memory-leak-tp45614p45616.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matplotlib.backends.backend_gtk3cairo memory leak
Thanks, however GTK3Agg is unimplemented in at the GTK3-end: File c:\Python34\lib\site-packages\matplotlib\backends\backend_gtk3agg.py, line 69, in on_draw_event buf, cairo.FORMAT_ARGB32, width, height) NotImplementedError: Surface.create_for_data: Not Implemented yet. Regards David From: ben.v.r...@gmail.com [mailto:ben.v.r...@gmail.com] On Behalf Of Benjamin Root Sent: 26 May 2015 14:53 To: David Hughes Cc: Matplotlib Users Subject: Re: [Matplotlib-users] matplotlib.backends.backend_gtk3cairo memory leak I take it that it doesn't happen using the GTK3Agg backend? What about the threading portion? Does it happen if you take the threading out? Ben Root On Tue, May 26, 2015 at 8:23 AM, David dhug...@rapiscansystems.commailto:dhug...@rapiscansystems.com wrote: Hi, I seem to have a memory leak while generating a 'live' plot display. This wasn't the case for GTK2, but the example below is consuming ~800k/second (Matplotlib 1.4.3, PyGI aio-3.14.0_rev18, Windows 7 x64, python 3.4.3). I have checked the garbage collector but it doesn't show anything interesting (no massive incrementing count of uncollected items). Anyway, I would be very grateful if somebody could confirm and/or fix this (or tell me what I'm doing wrong). Many thanks David Code below: from gi.repository import Gtk, Gdk, GLib from matplotlib.figure import Figure # Tell matplotlib to use a GTK canvas for drawing #from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as FigureCanvas from matplotlib.backends.backend_gtk3cairo import FigureCanvasGTK3Cairo as FigureCanvas # Application Class class pyMatPlotLibTest(object): def update_gui(self): y = [self.index] * 1024 self.index += 1 if self.index 1024: self.index = 0 Gdk.threads_enter() self.line.set_ydata(y) self.axes.set_title(%d % self.index) self.canvas.draw() Gdk.threads_leave() return True def __init__(self): self.index = 0 self.x = range(1024) # Initialise the threads system and allow threads to work with GTK GLib.threads_init() # Draw scope self.figure = Figure(dpi=100) self.canvas = FigureCanvas(self.figure) # a Gtk.DrawingArea #self.widget.alignment_ScopeDisplay.add(self.canvas) # Draw initial scope self.axes = self.figure.add_subplot(111) self.line, = self.axes.plot(self.x, [0]* 1024) self.axes.set_title(None) self.axes.set_xbound(0.0, 1024) self.axes.set_ybound(-16, 1040) self.window_main = Gtk.Window(title=pyMatPlotLibTest) self.window_main.connect(destroy, lambda x: Gtk.main_quit()) self.window_main.add(self.canvas) self.window_main.show_all() # Ticker for the update of the input state monitoring Gdk.threads_add_timeout(priority = GLib.PRIORITY_DEFAULT_IDLE, interval = 10, # msec function = self.update_gui) Gtk.main() if __name__ == __main__: gui = pyMatPlotLibTest() View this message in context: matplotlib.backends.backend_gtk3cairo memory leakhttp://matplotlib.1069221.n5.nabble.com/matplotlib-backends-backend-gtk3cairo-memory-leak-tp45614.html Sent from the matplotlib - users mailing list archivehttp://matplotlib.1069221.n5.nabble.com/matplotlib-users-f3.html at Nabble.com. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.netmailto:Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Lorenz: A Composition
Hi, For a little right brain diversion, here's what I created using matplotlib: https://www.youtube.com/watch?v=gWkFnPHbHokfeature=youtu.be Enjoy! --Prahas -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Set a 3-D point?
Hi, For those of you following the trials and tribulations of moi, I hacked the solution. The assignment is: x0 = [ [-1.0,0.0,0.5] ] I printed the orig x0. Printed mine. Noticed mine was missing a set of brackets. Tried it. Success! --Prahas On Sun, Mar 29, 2015 at 10:07 AM, Prahas David Nafissian prahas.mu...@gmail.com wrote: Hi Mat-Plotters, I'm trying to modify the below code so that I can set the initial conditions to (-1,0,0.5). The code below randomly sets the initial conditions: ** # I changed the equation -- it's not Lorenz. N_trajectories = 1 def lorentz_deriv((x, y, z), t0, aa=1.1, yy=0.87): Compute the time-derivative of a Lorentz system. return [y*(z-1+x*x)+yy*x, x*(3*z+1-x*x)+yy*y, -2*z*(aa+x*y)] # Choose random starting points, uniformly distributed from -15 to 15 np.random.seed(1) *# Here's the statement which assigns the initial conditions:* x0 = -15 + 30 * np.random.random((N_trajectories, 3)) ** I tried simply doing this: x0 = (-1,0,0.5) but I get this error: ValueError: need more than 1 value to unpack What am I missing? What is the correct way to make the assignment? Thanks! --Prahas -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Set a 3-D point?
Hi Mat-Plotters, I'm trying to modify the below code so that I can set the initial conditions to (-1,0,0.5). The code below randomly sets the initial conditions: ** # I changed the equation -- it's not Lorenz. N_trajectories = 1 def lorentz_deriv((x, y, z), t0, aa=1.1, yy=0.87): Compute the time-derivative of a Lorentz system. return [y*(z-1+x*x)+yy*x, x*(3*z+1-x*x)+yy*y, -2*z*(aa+x*y)] # Choose random starting points, uniformly distributed from -15 to 15 np.random.seed(1) *# Here's the statement which assigns the initial conditions:* x0 = -15 + 30 * np.random.random((N_trajectories, 3)) ** I tried simply doing this: x0 = (-1,0,0.5) but I get this error: ValueError: need more than 1 value to unpack What am I missing? What is the correct way to make the assignment? Thanks! --Prahas -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Lorenz -- another Q
Hi,
Given the Lorenz code shared yesterday, is there a way
to generate a log file of the x,y,z points generated?
Thanks in advance.
--Prahas
In case you deleted the code:
import numpy as np
from scipy import integrate
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.colors import cnames
from matplotlib import animation
# orig value of N_traj was 20 -- very cool this way.
N_trajectories = 1
def lorentz_deriv((x, y, z), t0, sigma=10., beta=8./3, rho=28.0):
Compute the time-derivative of a Lorentz system.
return [sigma * (y - x), x * (rho - z) - y, x * y - beta * z]
# Choose random starting points, uniformly distributed from -15 to 15
np.random.seed(1)
# changing from -15,30 to 10,5 below starts the drawing in the middle,
# rather than getting the long line from below
# if using N_Traj 1, return to orig values.
# x0 = -15 + 30 * np.random.random((N_trajectories, 3))
x0 = 10 + 5 * np.random.random((N_trajectories, 3))
# Solve for the trajectories
# orig values: 0,4,1000
# 3rd value -- lower it, it gets choppier.
# 2nd value -- increase it -- more points, but speedier.
# change middle num from 4 to 15 -- this adds points
t = np.linspace(0, 40, 3000)
x_t = np.asarray([integrate.odeint(lorentz_deriv, x0i, t)
for x0i in x0])
# Set up figure 3D axis for animation
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1], projection='3d')
# changing off to on below adds axises. slows it down but you
# can fix that with interval value in the animation call
ax.axis('on')
# choose a different color for each trajectory
colors = plt.cm.jet(np.linspace(0, 1, N_trajectories))
# set up lines and points -- this is a correction from
# the orig jake code. the next four lines...
lines = [ax.plot([], [], [], '-', c=c)[0]
for c in colors]
pts = [ax.plot([], [], [], 'o', c=c)[0]
for c in colors]
# prepare the axes limits
ax.set_xlim((-25, 25))
ax.set_ylim((-35, 35))
ax.set_zlim((5, 55))
# set point-of-view: specified by (altitude degrees, azimuth degrees)
ax.view_init(30, 0)
# initialization function: plot the background of each frame
def init():
for line, pt in zip(lines, pts):
line.set_data([], [])
line.set_3d_properties([])
pt.set_data([], [])
pt.set_3d_properties([])
return lines + pts
# animation function. This will be called sequentially with the frame number
def animate(i):
# we'll step two time-steps per frame. This leads to nice results.
i = (2 * i) % x_t.shape[1]
for line, pt, xi in zip(lines, pts, x_t):
x, y, z = xi[:i].T
line.set_data(x, y)
line.set_3d_properties(z)
pt.set_data(x[-1:], y[-1:])
pt.set_3d_properties(z[-1:])
# changed 0.3 to 0.05 below -- this slows the rotation of the view.
# changed 30 to 20 below
# changing 20 to (20 + (.1 * i)) rotates on the Z axis. trippy.
ax.view_init(10, 0.1 * i)
# ax.view_init(10, 100)
fig.canvas.draw()
return lines + pts
# instantiate the animator. I've deleted the blit switch (for Mac)
# enlarging frames=500 works now -- it failed before because I didn't give it
# enough data -- by changing the t=np.linspace line above I generate
more points.
# interval larger slows it down
# changed inteval from 30 to 200, frames from 500 to 3000
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=3000, interval=200)
# Save as mp4. This requires mplayer or ffmpeg to be installed. COMPLEX!
# Instead, use a screen record program: Quicktime on the Mac; MS
Expression Encoder on PC.
# anim.save('PDNlorentz_attractor.mp4', fps=15, extra_args=['-vcodec',
'libx264'])
plt.show()
--
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
___
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Re: [Matplotlib-users] Lorenz -- another Q
Hello,
Solved the write issue.
I tried numpy savetxt but it chokes on 3D arrays.
So I'm doing this:
x_t.tofile('test3.txt',sep= ,format=%f)
Only issue -- no end-of-lines. But I can write a quick
Pascal program to fix this...
Once again, thanks!
--
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
___
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Re: [Matplotlib-users] Lorenz - solution
I think you need to ask Jake Vanderplas -- the code
is all his! See the link in the email to get to his blog...
Thanks again!
On Tue, Mar 10, 2015 at 8:49 AM, Benjamin Root ben.r...@ou.edu wrote:
+1000!!
Great job! Would you mind if I clean it up a bit and add it to the
mplot3d/animation gallery? Full credit, of course.
On Tue, Mar 10, 2015 at 11:30 AM, Prahas David Nafissian
prahas.mu...@gmail.com wrote:
Friends,
I thought you'd like to see the solution.
Many thanks to Jake Vanderplas for his code and teachings:
https://jakevdp.github.io/blog/2013/02/16/animating-the-lorentz-system-in-3d/
If you start a new IP Notebook session, run as your first entry:
%pylab
and then copy and paste the text below and run it, you should be good to
go
(on a Mac, at least).
There are several parameters I've changed from his original, and I've
commented as I've changed. The original code is at the link above.
There is one error in his code -- I've documented it below.
Again, thanks to the community, Jake, and Ben Root.
--Prahas
**
import numpy as np
from scipy import integrate
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.colors import cnames
from matplotlib import animation
# orig value of N_traj was 20 -- very cool this way.
N_trajectories = 1
def lorentz_deriv((x, y, z), t0, sigma=10., beta=8./3, rho=28.0):
Compute the time-derivative of a Lorentz system.
return [sigma * (y - x), x * (rho - z) - y, x * y - beta * z]
# Choose random starting points, uniformly distributed from -15 to 15
np.random.seed(1)
# changing from -15,30 to 10,5 below starts the drawing in the middle,
# rather than getting the long line from below
# if using N_Traj 1, return to orig values.
# x0 = -15 + 30 * np.random.random((N_trajectories, 3))
x0 = 10 + 5 * np.random.random((N_trajectories, 3))
# Solve for the trajectories
# orig values: 0,4,1000
# 3rd value -- lower it, it gets choppier.
# 2nd value -- increase it -- more points, but speedier.
# change middle num from 4 to 15 -- this adds points
t = np.linspace(0, 40, 3000)
x_t = np.asarray([integrate.odeint(lorentz_deriv, x0i, t)
for x0i in x0])
# Set up figure 3D axis for animation
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1], projection='3d')
# changing off to on below adds axises. slows it down but you
# can fix that with interval value in the animation call
ax.axis('on')
# choose a different color for each trajectory
colors = plt.cm.jet(np.linspace(0, 1, N_trajectories))
# set up lines and points -- this is a correction from
# the orig jake code. the next four lines...
lines = [ax.plot([], [], [], '-', c=c)[0]
for c in colors]
pts = [ax.plot([], [], [], 'o', c=c)[0]
for c in colors]
# prepare the axes limits
ax.set_xlim((-25, 25))
ax.set_ylim((-35, 35))
ax.set_zlim((5, 55))
# set point-of-view: specified by (altitude degrees, azimuth degrees)
ax.view_init(30, 0)
# initialization function: plot the background of each frame
def init():
for line, pt in zip(lines, pts):
line.set_data([], [])
line.set_3d_properties([])
pt.set_data([], [])
pt.set_3d_properties([])
return lines + pts
# animation function. This will be called sequentially with the frame
number
def animate(i):
# we'll step two time-steps per frame. This leads to nice results.
i = (2 * i) % x_t.shape[1]
for line, pt, xi in zip(lines, pts, x_t):
x, y, z = xi[:i].T
line.set_data(x, y)
line.set_3d_properties(z)
pt.set_data(x[-1:], y[-1:])
pt.set_3d_properties(z[-1:])
# changed 0.3 to 0.05 below -- this slows the rotation of the
view.
# changed 30 to 20 below
# changing 20 to (20 + (.1 * i)) rotates on the Z axis. trippy.
ax.view_init(10, 0.1 * i)
# ax.view_init(10, 100)
fig.canvas.draw()
return lines + pts
# instantiate the animator. I've deleted the blit switch (for Mac)
# enlarging frames=500 works now -- it failed before because I didn't give
it
# enough data -- by changing the t=np.linspace line above I generate
more points.
# interval larger slows it down
# changed inteval from 30 to 200, frames from 500 to 3000
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=3000, interval=200)
# Save as mp4. This requires mplayer or ffmpeg to be installed.
COMPLEX!
# Instead, use a screen record program: Quicktime on the Mac; MS
Expression Encoder on PC.
# anim.save('PDNlorentz_attractor.mp4', fps=15, extra_args=['-vcodec',
'libx264'])
plt.show()
--
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Re: [Matplotlib-users] Lorenz - solution
@ Adam -- thanks!
@ Everyone: given the Lorenz code shared, is there a way
to generate a log file of the x,y,z points generated?
Thanks in advance.
--Prahas
On Tue, Mar 10, 2015 at 8:59 AM, Adam Hughes hughesada...@gmail.com wrote:
That's pretty swag!
On Tue, Mar 10, 2015 at 11:49 AM, Benjamin Root ben.r...@ou.edu wrote:
+1000!!
Great job! Would you mind if I clean it up a bit and add it to the
mplot3d/animation gallery? Full credit, of course.
On Tue, Mar 10, 2015 at 11:30 AM, Prahas David Nafissian
prahas.mu...@gmail.com wrote:
Friends,
I thought you'd like to see the solution.
Many thanks to Jake Vanderplas for his code and teachings:
https://jakevdp.github.io/blog/2013/02/16/animating-the-lorentz-system-in-3d/
If you start a new IP Notebook session, run as your first entry:
%pylab
and then copy and paste the text below and run it, you should be good to
go
(on a Mac, at least).
There are several parameters I've changed from his original, and I've
commented as I've changed. The original code is at the link above.
There is one error in his code -- I've documented it below.
Again, thanks to the community, Jake, and Ben Root.
--Prahas
**
import numpy as np
from scipy import integrate
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.colors import cnames
from matplotlib import animation
# orig value of N_traj was 20 -- very cool this way.
N_trajectories = 1
def lorentz_deriv((x, y, z), t0, sigma=10., beta=8./3, rho=28.0):
Compute the time-derivative of a Lorentz system.
return [sigma * (y - x), x * (rho - z) - y, x * y - beta * z]
# Choose random starting points, uniformly distributed from -15 to 15
np.random.seed(1)
# changing from -15,30 to 10,5 below starts the drawing in the middle,
# rather than getting the long line from below
# if using N_Traj 1, return to orig values.
# x0 = -15 + 30 * np.random.random((N_trajectories, 3))
x0 = 10 + 5 * np.random.random((N_trajectories, 3))
# Solve for the trajectories
# orig values: 0,4,1000
# 3rd value -- lower it, it gets choppier.
# 2nd value -- increase it -- more points, but speedier.
# change middle num from 4 to 15 -- this adds points
t = np.linspace(0, 40, 3000)
x_t = np.asarray([integrate.odeint(lorentz_deriv, x0i, t)
for x0i in x0])
# Set up figure 3D axis for animation
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1], projection='3d')
# changing off to on below adds axises. slows it down but you
# can fix that with interval value in the animation call
ax.axis('on')
# choose a different color for each trajectory
colors = plt.cm.jet(np.linspace(0, 1, N_trajectories))
# set up lines and points -- this is a correction from
# the orig jake code. the next four lines...
lines = [ax.plot([], [], [], '-', c=c)[0]
for c in colors]
pts = [ax.plot([], [], [], 'o', c=c)[0]
for c in colors]
# prepare the axes limits
ax.set_xlim((-25, 25))
ax.set_ylim((-35, 35))
ax.set_zlim((5, 55))
# set point-of-view: specified by (altitude degrees, azimuth degrees)
ax.view_init(30, 0)
# initialization function: plot the background of each frame
def init():
for line, pt in zip(lines, pts):
line.set_data([], [])
line.set_3d_properties([])
pt.set_data([], [])
pt.set_3d_properties([])
return lines + pts
# animation function. This will be called sequentially with the frame
number
def animate(i):
# we'll step two time-steps per frame. This leads to nice results.
i = (2 * i) % x_t.shape[1]
for line, pt, xi in zip(lines, pts, x_t):
x, y, z = xi[:i].T
line.set_data(x, y)
line.set_3d_properties(z)
pt.set_data(x[-1:], y[-1:])
pt.set_3d_properties(z[-1:])
# changed 0.3 to 0.05 below -- this slows the rotation of the
view.
# changed 30 to 20 below
# changing 20 to (20 + (.1 * i)) rotates on the Z axis. trippy.
ax.view_init(10, 0.1 * i)
# ax.view_init(10, 100)
fig.canvas.draw()
return lines + pts
# instantiate the animator. I've deleted the blit switch (for Mac)
# enlarging frames=500 works now -- it failed before because I didn't
give it
# enough data -- by changing the t=np.linspace line above I generate
more points.
# interval larger slows it down
# changed inteval from 30 to 200, frames from 500 to 3000
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=3000, interval=200)
# Save as mp4. This requires mplayer or ffmpeg to be installed.
COMPLEX!
# Instead, use a screen record program: Quicktime on the Mac; MS
Expression Encoder on PC.
# anim.save('PDNlorentz_attractor.mp4', fps=15, extra_args=['-vcodec',
'libx264'])
plt.show
[Matplotlib-users] Lorenz - solution
Friends,
I thought you'd like to see the solution.
Many thanks to Jake Vanderplas for his code and teachings:
https://jakevdp.github.io/blog/2013/02/16/animating-the-lorentz-system-in-3d/
If you start a new IP Notebook session, run as your first entry:
%pylab
and then copy and paste the text below and run it, you should be good to go
(on a Mac, at least).
There are several parameters I've changed from his original, and I've
commented as I've changed. The original code is at the link above.
There is one error in his code -- I've documented it below.
Again, thanks to the community, Jake, and Ben Root.
--Prahas
**
import numpy as np
from scipy import integrate
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.colors import cnames
from matplotlib import animation
# orig value of N_traj was 20 -- very cool this way.
N_trajectories = 1
def lorentz_deriv((x, y, z), t0, sigma=10., beta=8./3, rho=28.0):
Compute the time-derivative of a Lorentz system.
return [sigma * (y - x), x * (rho - z) - y, x * y - beta * z]
# Choose random starting points, uniformly distributed from -15 to 15
np.random.seed(1)
# changing from -15,30 to 10,5 below starts the drawing in the middle,
# rather than getting the long line from below
# if using N_Traj 1, return to orig values.
# x0 = -15 + 30 * np.random.random((N_trajectories, 3))
x0 = 10 + 5 * np.random.random((N_trajectories, 3))
# Solve for the trajectories
# orig values: 0,4,1000
# 3rd value -- lower it, it gets choppier.
# 2nd value -- increase it -- more points, but speedier.
# change middle num from 4 to 15 -- this adds points
t = np.linspace(0, 40, 3000)
x_t = np.asarray([integrate.odeint(lorentz_deriv, x0i, t)
for x0i in x0])
# Set up figure 3D axis for animation
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1], projection='3d')
# changing off to on below adds axises. slows it down but you
# can fix that with interval value in the animation call
ax.axis('on')
# choose a different color for each trajectory
colors = plt.cm.jet(np.linspace(0, 1, N_trajectories))
# set up lines and points -- this is a correction from
# the orig jake code. the next four lines...
lines = [ax.plot([], [], [], '-', c=c)[0]
for c in colors]
pts = [ax.plot([], [], [], 'o', c=c)[0]
for c in colors]
# prepare the axes limits
ax.set_xlim((-25, 25))
ax.set_ylim((-35, 35))
ax.set_zlim((5, 55))
# set point-of-view: specified by (altitude degrees, azimuth degrees)
ax.view_init(30, 0)
# initialization function: plot the background of each frame
def init():
for line, pt in zip(lines, pts):
line.set_data([], [])
line.set_3d_properties([])
pt.set_data([], [])
pt.set_3d_properties([])
return lines + pts
# animation function. This will be called sequentially with the frame number
def animate(i):
# we'll step two time-steps per frame. This leads to nice results.
i = (2 * i) % x_t.shape[1]
for line, pt, xi in zip(lines, pts, x_t):
x, y, z = xi[:i].T
line.set_data(x, y)
line.set_3d_properties(z)
pt.set_data(x[-1:], y[-1:])
pt.set_3d_properties(z[-1:])
# changed 0.3 to 0.05 below -- this slows the rotation of the view.
# changed 30 to 20 below
# changing 20 to (20 + (.1 * i)) rotates on the Z axis. trippy.
ax.view_init(10, 0.1 * i)
# ax.view_init(10, 100)
fig.canvas.draw()
return lines + pts
# instantiate the animator. I've deleted the blit switch (for Mac)
# enlarging frames=500 works now -- it failed before because I didn't give it
# enough data -- by changing the t=np.linspace line above I generate
more points.
# interval larger slows it down
# changed inteval from 30 to 200, frames from 500 to 3000
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=3000, interval=200)
# Save as mp4. This requires mplayer or ffmpeg to be installed. COMPLEX!
# Instead, use a screen record program: Quicktime on the Mac; MS
Expression Encoder on PC.
# anim.save('PDNlorentz_attractor.mp4', fps=15, extra_args=['-vcodec',
'libx264'])
plt.show()
--
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things parallel software development, from weekly thought leadership blogs to
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Re: [Matplotlib-users] Newbie Q re: Lorenz attractor
Dear Ben, Amit, and Ryan, Thanks so much for your input! Looking forward to finding the time to give it a go! Best, --Prahas On Sun, Mar 8, 2015 at 7:14 PM, Benjamin Root ben.r...@ou.edu wrote: Yes, absolutely it will work... so long as you do not use blitting. Blitting for mplot3d is pretty much useless anyway (I think draws of the axes occur anyway regardless of the blit mode), but it is also broken for the macosx backend, anyway. Cheers! Ben Root On Sun, Mar 8, 2015 at 8:59 PM, Amit Saha amitsaha...@gmail.com wrote: On Mon, Mar 9, 2015 at 7:31 AM, Prahas David Nafissian prahas.mu...@gmail.com wrote: Hi, I want to create an animation of the Lorenz attractor, plotting each new point as it is generated by the equations. So we see the graph being drawn over time. You will very likely need to use the animation API for this. I recently tried to demonstrate the Henon function in a fashion that it appears I am drawing it over time: https://www.youtube.com/watch?v=76ll818RlpQ You can see the code linked from there: https://github.com/amitsaha/playground/blob/master/recipes/henon_animation.py That might give you a starting point of what you are trying to do. Also, as it is being drawn, I want to be able to rotate the screen in 3 dimensions. Sorry, nothing much I can add here. Best, Amit. -- http://echorand.me -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Newbie Q re: Lorenz attractor
Hi, I want to create an animation of the Lorenz attractor, plotting each new point as it is generated by the equations. So we see the graph being drawn over time. Also, as it is being drawn, I want to be able to rotate the screen in 3 dimensions. Will MatPlot do this on a Mac (10.8.5)? Thanks! PS -- here is code using MatPlot to create the full Lorenz: http://matplotlib.org/examples/mplot3d/lorenz_attractor.html -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Get contourf image as array
Thanks Ben. I'll take a look through the archive. On 10/16/14, 9:43 AM, Benjamin Root wrote: What you are looking for is called rasterization. Matplotlib does this deep within the codebase and is not accessible (believe me, I tried). However, there have been other discussions in this mailing list about how to use GDAL to rasterize a set of polygons (represented as paths), including some links to stack-overflow questions. It isn't a complete end-to-end solution, but the pieces are there. Cheers! Ben Root On Wed, Oct 15, 2014 at 2:09 PM, David Hoese dho...@gmail.com mailto:dho...@gmail.com wrote: For the first question, if I save the figure (as a PNG I'm guessing, unless you can save into a more array-like format), I'd have to make sure that there were no labels or ticks and that the axes fit the whole figure. I'd also have to get the dpi and size information correct, but I suppose it would be possible that way. I was hoping for something a little easier and in-memory. This might be the simplest answer the more I think about it. If I'm starting from the paths, I'd still have to write them to the grid array. I thought maybe the backend could do that and I magically get the image. I'll look in to using savefig and getting the data out. -Dave On 10/15/14, 12:42 PM, Joy merwin monteiro wrote: pardon the query if it seems dumb, but why don't you do a savefig() after plotting the data and then convert it to any format you like? alternatively, contour() and contourf() both create paths that can be accessed: cf = contourf(.) output = cf.collections.pop() paths = output.get_paths()[i] # for the various contours the x,y coordinates can then be accessed as xcoords = paths.vertices.transpose()[0] ycoords = paths.vertices.transpose()[1] you can then do whatever you wish with them. Joy On Wed, Oct 15, 2014 at 9:11 PM, David Hoese dho...@gmail.com mailto:dho...@gmail.com mailto:dho...@gmail.com mailto:dho...@gmail.com wrote: I've been searching and reading through source code and google searches to see if this is possible, but no luck so far. I'm basically trying to map some data using Basemap, use contourf to map it to an image, and then put that image in a geotiff (or other format) for use in other GIS programs. I have other tools for remapping data and creating geotiffs, but the contour image looks better. All I would need to get this to work would be an array representing the image inside the axes of a contourf plot. I found a lot of geotiff - Basemap png results, but I would like the reverse. Since the plots are made using paths/patches I'm guessing I would have to have a backend render the image and then extract the image somehow. Does anyone have some tips or tricks to do something like this? Or am I thinking about this completely wrong? Thanks for any help and if you could CC me in any replies it would be much appreciated. -Dave -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net mailto:Matplotlib-users@lists.sourceforge.net mailto:Matplotlib-users@lists.sourceforge.net mailto:Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- The best ruler, when he finishes his tasks and completes his affairs, the people say “It all happened naturally” - Te Tao Ch'ing -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net mailto:Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Get contourf image as array
I've been searching and reading through source code and google searches to see if this is possible, but no luck so far. I'm basically trying to map some data using Basemap, use contourf to map it to an image, and then put that image in a geotiff (or other format) for use in other GIS programs. I have other tools for remapping data and creating geotiffs, but the contour image looks better. All I would need to get this to work would be an array representing the image inside the axes of a contourf plot. I found a lot of geotiff - Basemap png results, but I would like the reverse. Since the plots are made using paths/patches I'm guessing I would have to have a backend render the image and then extract the image somehow. Does anyone have some tips or tricks to do something like this? Or am I thinking about this completely wrong? Thanks for any help and if you could CC me in any replies it would be much appreciated. -Dave -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Get contourf image as array
For the first question, if I save the figure (as a PNG I'm guessing, unless you can save into a more array-like format), I'd have to make sure that there were no labels or ticks and that the axes fit the whole figure. I'd also have to get the dpi and size information correct, but I suppose it would be possible that way. I was hoping for something a little easier and in-memory. This might be the simplest answer the more I think about it. If I'm starting from the paths, I'd still have to write them to the grid array. I thought maybe the backend could do that and I magically get the image. I'll look in to using savefig and getting the data out. -Dave On 10/15/14, 12:42 PM, Joy merwin monteiro wrote: pardon the query if it seems dumb, but why don't you do a savefig() after plotting the data and then convert it to any format you like? alternatively, contour() and contourf() both create paths that can be accessed: cf = contourf(.) output = cf.collections.pop() paths = output.get_paths()[i] # for the various contours the x,y coordinates can then be accessed as xcoords = paths.vertices.transpose()[0] ycoords = paths.vertices.transpose()[1] you can then do whatever you wish with them. Joy On Wed, Oct 15, 2014 at 9:11 PM, David Hoese dho...@gmail.com mailto:dho...@gmail.com wrote: I've been searching and reading through source code and google searches to see if this is possible, but no luck so far. I'm basically trying to map some data using Basemap, use contourf to map it to an image, and then put that image in a geotiff (or other format) for use in other GIS programs. I have other tools for remapping data and creating geotiffs, but the contour image looks better. All I would need to get this to work would be an array representing the image inside the axes of a contourf plot. I found a lot of geotiff - Basemap png results, but I would like the reverse. Since the plots are made using paths/patches I'm guessing I would have to have a backend render the image and then extract the image somehow. Does anyone have some tips or tricks to do something like this? Or am I thinking about this completely wrong? Thanks for any help and if you could CC me in any replies it would be much appreciated. -Dave -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net mailto:Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- The best ruler, when he finishes his tasks and completes his affairs, the people say “It all happened naturally” - Te Tao Ch'ing -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Scientific Python introduction
NumPy, SciPy, MatPlotLib Users Science teachers: I have written an introduction to scientific python that you may find useful. You can download it from GitHub and use it freely: https://github.com/djpine/pyman I wrote this manual/book for undergraduates taking science and engineering courses that use programming to solve science and engineering problems. It is not for experts. I am sharing it with the hope that others may find it useful. It includes an introduction to very basic programming, numpy, matplotlib, scipy, as well as instructions on how to download and install Python and these three libraries. It also includes an introduction to IPython notebooks. Corrections and suggestions for improvements are welcome. David Pine-- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] PGF backend
Hello !
I would like to have some hints about the matplotlib usage, especially
the PGF/tikz backend.
I use a latex document, and almost only tikz figures.
I have a couple of problems with the matplotlib package.
The first is the preemptive behaviour of the matplotlib package over the
used fonts. I would like the text to be let as it, without adding
stuff like \sffamily\ttffont, and so on.
For example, if I write $L^2$ as a legend axis, I want this text to be
let as it, without any modification by the pgf backend.
A second point, is that I would like to not use the
\begin{pgffigure}\end{pgffigure}, the \makeatletter and fancy stuff like
that. I want to take care myself of the latex code. Is it possible ?
Finally, Would it be possible to specify the size of the graphic
somewhere ? The documentation is rather vague about it.
Thank you for help.
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[Matplotlib-users] Problem with matplotlib under aix 6.1
hello, Sorry for my poor english. I have a big problem with matplotlib under AIX6.1. My configuration : OS : AIX 6.1 XLC : 12.1.0.0 Python 2.7.5-1 I installed Python and all dependencies from www.oss4aix.org/download/RPMS with the rpm files. This is the all packages that I installed: rpm -ivh gcc/libgcc-4.4.7-1.aix6.1.ppc.rpm rpm -ivh libffi/libffi-3.0.13-1.aix5.1.ppc.rpm rpm -ivh libffi/libffi-devel-3.0.13-1.aix5.1.ppc.rpm rpm -ivh expat/expat-2.1.0-1.aix5.1.ppc.rpm rpm -ivh expat/expat-devel-2.1.0-1.aix5.1.ppc.rpm rpm -ivh libiconv/libiconv-1.14-2.aix5.1.ppc.rpm glib2/glib2-2.36.3-1.aix5.1.ppc.rpm gettext/gettext-0.17-1.aix5.1.ppc.rpm --nodeps (missing libxlsmp.a(smprt.o)) rpm -ivh pkg-config/pkg-config-0.28-1.aix5.1.ppc.rpm rpm -ivh zlib/zlib-1.2.8-1.aix5.1.ppc.rpm rpm -ivh zlib/zlib-devel-1.2.8-1.aix5.1.ppc.rpm rpm -ivh libpng/libpng-1.6.3-1.aix5.1.ppc.rpm rpm -ivh libpng/libpng-devel-1.6.3-1.aix5.1.ppc.rpm rpm -ivh freetype2/freetype2-2.5.0-1.aix5.1.ppc.rpm rpm -ivh freetype2/freetype2-devel-2.5.0-1.aix5.1.ppc.rpm rpm -ivh fontconfig/fontconfig-2.8.0-2.aix5.1.ppc.rpm rpm -ivh fontconfig/fontconfig-devel-2.8.0-2.aix5.1.ppc.rpm rpm -ivh libXrender/libXrender-0.9.7-2.aix6.1.ppc.rpm rpm -ivh libXrender/libXrender-devel-0.9.7-2.aix6.1.ppc.rpm rpm -ivh libXft/libXft-2.3.1-1.aix5.1.ppc.rpm rpm -ivh libXft/libXft-devel-2.3.1-1.aix5.1.ppc.rpm rpm -Uvh tcl/tcl-8.5.14-1.aix5.1.ppc.rpm rpm -ivh tcl/tcl-devel-8.5.14-1.aix5.1.ppc.rpm rpm -Uvh tk/tk-8.5.14-1.aix5.1.ppc.rpm rpm -ivh tk/tk-devel-8.5.14-1.aix5.1.ppc.rpm rpm -ivh info/info-5.1-1.aix5.1.ppc.rpm rpm -ivh readline/readline-6.2-4.aix5.1.ppc.rpm rpm -ivh readline/readline-devel-6.2-4.aix5.1.ppc.rpm rpm -ivh openssl/openssl-1.0.1e-2.aix5.1.ppc.rpm rpm -ivh openssl/openssl-devel-1.0.1e-2.aix5.1.ppc.rpm rpm -ivh gdbm/gdbm-1.10-1.aix5.1.ppc.rpm rpm -ivh gdbm/gdbm-devel-1.10-1.aix5.1.ppc.rpm rpm -ivh gmp/gmp-5.0.5-1.aix5.1.ppc.rpm rpm -ivh gmp/gmp-devel-5.0.5-1.aix5.1.ppc.rpm rpm -ivh gettext/gettext-devel-0.17-1.aix5.1.ppc.rpm rpm -ivh db4/db4-4.7.25-2.aix5.1.ppc.rpm rpm -ivh db4/db4-devel-4.7.25-2.aix5.1.ppc.rpm rpm -ivh bzip2/bzip2-1.0.6-1.aix5.1.ppc.rpm rpm -ivh bzip2/bzip2-devel-1.0.6-1.aix5.1.ppc.rpm rpm -ivh sqlite/sqlite-3.7.17-1.aix5.1.ppc.rpm rpm -ivh sqlite/sqlite-devel-3.7.17-1.aix5.1.ppc.rpm rpm -ivh python/python-libs-2.7.5-1.aix6.1.ppc.rpm rpm -ivh python/python-2.7.5-1.aix6.1.ppc.rpm rpm -ivh python/python-devel-2.7.5-1.aix6.1.ppc.rpm rpm -ivh python/tkinter-2.7.5-1.aix6.1.ppc.rpm rpm -ivh python/python-tools-2.7.5-1.aix6.1.ppc.rpm rpm -ivh python/python-test-2.7.5-1.aix6.1.ppc.rpm In the first step I spent a lot of time to compile matplotlib. This is what I did to install matplotlib : From sources I installed NUMPY, SETUPTOOLS, PYTHON-DATEUTIL With easy_install I installed TORNADO, PYPARSING I need to do some changes in sources of matplotlib: Patch 0 --- CXX/WrapPython.h2013-09-18 14:47:26.0 -0500 +++ CXX/WrapPython.h.orig 2013-09-18 14:47:07.0 -0500 @@ -38,9 +38,6 @@ #ifndef __PyCXX_wrap_python_hxx__ #define __PyCXX_wrap_python_hxx__ - #includestdio.h - #includeunistd.h - // On some platforms we have to include time.h to get select defined #if !defined(__WIN32__) !defined(WIN32) !defined(_WIN32) !defined(_WIN64) #include sys/time.h Patch 1 --- src/ft2font.h 2013-09-18 14:43:11.0 -0500 +++ src/ft2font.h.orig 2013-09-18 14:42:19.0 -0500 @@ -1,9 +1,5 @@ /* -*- mode: c++; c-basic-offset: 4 -*- */ - #includestdio.h - #includeunistd.h - - /* A python interface to freetype2 */ #ifndef _FT2FONT_H #define _FT2FONT_H Patch 2 --- src/mplutils.h 2013-09-18 14:46:06.0 -0500 +++ src/mplutils.h.orig 2013-09-18 14:45:32.0 -0500 @@ -12,9 +12,6 @@ * */ - #includestdio.h - #includeunistd.h - #ifndef _MPLUTILS_H #define _MPLUTILS_H Patch 3 --- ttconv/pprdrv.h 2013-09-18 14:49:07.0 -0500 +++ ttconv/pprdrv.h.orig2013-09-18 14:48:47.0 -0500 @@ -21,9 +21,6 @@ ** This file last revised 5 December 1995. */ - #includestdio.h - #includeunistd.h - #include vector #include cassert I create a link in the sources directory : ln -s /opt/freeware/lib/python2.7/config Modules I create a xlC script cat xlC EOF /bin/bash Modules/ld_so_aix EOF chmod a+x xlC python setup.py install With all this, the compilation ends. When I check the use of matplotlib import matplotlib import numpy as np from matplotlib import pyplot a=np.arange(100) pyplot.plot(a) At this point I'm so happy !! BUT, when I want plot the array pyplot.show() I had a segmentation fault .. HELP ! My first question : Do somebody is able to plot something with matplotlib uner AIX 6.1 And HOW ??? Do you know a howtodo page to do a correct installation ? Thank you ! David -- October Webinars: Code for Performance Free Intel webinars can
[Matplotlib-users] v.0.99.1.1 DeprecationWarning: Use the new widget gtk.Tooltip() self.tooltips = gtk.Tooltips()
I am new to python and when using Matplotlib 0.99.1.1 [Scientific Linux 6.3, Python 2.6] to plot I get the following error: /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621: DeprecationWarning: Use the new widget gtk.Tooltip self.tooltips = gtk.Tooltips() This is when the program reaches: plt.show() Where plt is the matplotlib.pyplot. Prior to this point of the code I am able to produce pdf files of the figure by using plt.savefig(fname). Reading other online comments I have tried to update Matplotlib. First I installed the dependences via sudo yum-builddep python-matplotlib Then: sudo yum install matplotlib This then tells me that I have the latest version of matplotlib and therefore does nothing. There are more recent versions available from the Matplotlib website. I tried to install the latest version after unpacking the tar.gz file. After using the command: sudo python setup.py install I get the message below ending with error: command 'gcc' failed with exit status 1 Can anyone suggest a way to install the latest matplotlib or stop the message I get with using plt.show()? Jonathan basedirlist is: ['/usr/local', '/usr', 'usr/lib64'] BUILDING MATPLOTLIB matplotlib: 1.2.1 python: 2.6.6 (r266:84292, Jun 18 2012, 09:57:52) [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] platform: linux2 REQUIRED DEPENDENCIES numpy: 1.4.1 freetype2: 9.22.3 OPTIONAL BACKEND DEPENDENCIES libpng: 1.2.49 Tkinter: Tkinter: 73770, Tk: 8.5, Tcl: 8.5 * Guessing the library and include directories for * Tcl and Tk because the tclConfig.sh and * tkConfig.sh could not be found and/or parsed. Gtk+: gtk+: 2.18.9, glib: 2.22.5, pygtk: 2.16.0, pygobject: 2.20.0 Mac OS X native: no Qt: no Qt4: Qt: 4.6.2, PyQt4: 4.7.4 PySide: no Cairo: 1.8.6 OPTIONAL DATE/TIMEZONE DEPENDENCIES dateutil: 1.4.1 pytz: 2010h OPTIONAL USETEX DEPENDENCIES dvipng: no ghostscript: 8.70 latex: 3.141592 pdftops: 0.12.4 [Edit setup.cfg to suppress the above messages] pymods ['pylab'] packages ['matplotlib', 'matplotlib.backends', 'matplotlib.backends.qt4_editor', 'matplotlib.projections', 'matplotlib.testing', 'matplotlib.testing.jpl_units', 'matplotlib.tests', 'mpl_toolkits', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axisartist', 'matplotlib.sphinxext', 'matplotlib.tri', 'matplotlib.delaunay'] running install running build running build_py copying lib/matplotlib/mpl-data/matplotlibrc - build/lib.linux-x86_64-2.6/matplotlib/mpl-data running build_ext building 'matplotlib.backends._backend_agg' extension gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/include -I/usr/include -Iusr/lib64/include -Iusr/lib64/python2.6/include -Iusr/lib64/python2.6/site-packages/include -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/lib64/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/usr/include/python2.6 -c agg24/src/agg_trans_affine.cpp -o build/temp.linux-x86_64-2.6/agg24/src/agg_trans_affine.o gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/include -I/usr/include -Iusr/lib64/include -Iusr/lib64/python2.6/include -Iusr/lib64/python2.6/site-packages/include -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/lib64/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/usr/include/python2.6
Re: [Matplotlib-users] Matplotlib-users Digest, Vol 82, Issue 16
You likely need to show() the canvas. I usually do this by calling fig.canvas.show() before the for loop. Since you are using a Qt4 backend the canvas used by the figure is a QWidget, the basic component of a Qt4 GUI. I don't know if there is a more matplotlib specific way of doing this, but when dealing with a larger system this is how I do it. I would also add a sleep (from time import sleep) of a couple seconds for testing to make sure you are getting through the entire for loop before you can see it. Please CC in any replies, thanks. -Dave On 3/11/13 8:58 AM, ndbeck...@gmail.com wrote: I want to update a plot in real time. I did some goog search, and saw various answers. Trouble is, they aren't working. Here's a typical example: import matplotlib.pyplot as plt import numpy as np fig=plt.figure() plt.axis([0,1000,0,1]) i=0 x=list() y=list() while i 1000: temp_y=np.random.random() x.append(i) y.append(temp_y) plt.scatter(i,temp_y) i+=1 plt.draw() If I run this, it draws nothing. This is my matplotlibrc: backend : Qt4Agg mathtext.fontset: stix -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] real time plotting
Oops forgot to change the subject line. On 3/11/13 9:34 AM, David Hoese wrote: You likely need to show() the canvas. I usually do this by calling fig.canvas.show() before the for loop. Since you are using a Qt4 backend the canvas used by the figure is a QWidget, the basic component of a Qt4 GUI. I don't know if there is a more matplotlib specific way of doing this, but when dealing with a larger system this is how I do it. I would also add a sleep (from time import sleep) of a couple seconds for testing to make sure you are getting through the entire for loop before you can see it. Please CC in any replies, thanks. -Dave On 3/11/13 8:58 AM, ndbeck...@gmail.com wrote: I want to update a plot in real time. I did some goog search, and saw various answers. Trouble is, they aren't working. Here's a typical example: import matplotlib.pyplot as plt import numpy as np fig=plt.figure() plt.axis([0,1000,0,1]) i=0 x=list() y=list() while i 1000: temp_y=np.random.random() x.append(i) y.append(temp_y) plt.scatter(i,temp_y) i+=1 plt.draw() If I run this, it draws nothing. This is my matplotlibrc: backend : Qt4Agg mathtext.fontset: stix -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] real time plotting
Someone may have to correct me, but I think this has to do with the Qt4
event loop and it not being run properly. When you get into real time
plotting it can get kind of tricky. In your case (I got the same
results). I have made real-time PyQt4 GUIs before and have always used
separate QThreads and Qt signals/slots to update the plot. I've never
used GTK so I'm not sure why that worked vs Qt, I would think they would
use similar principles but matplotlib does some magic behind the scenes
sometimes. You can see different results if you comment out the while
loop and import the module into your python/ipython interpreter. After
doing this you'll see the figure pop up (you don't even need the
fig.canvas.show() for this part if interactive mode is on. I went one
step further and turned the while loop into a function:
def one_iter(i):
# Contents of while loop
Calling this in the interpreter shows the figure updating after each
call, but running in a loop (even with sleep) won't show any updates
until the loop is done. In my opinion you have a few choices that really
depend on your programming comfort level:
1. Don't make a real-time plot.
Do you really need a real-time plot that updates from some
external source?
2. Maybe you should look at the matplotlib animation functionality
(http://matplotlib.org/api/animation_api.html). I like this tutorial:
http://jakevdp.github.com/blog/2012/08/18/matplotlib-animation-tutorial/. This
won't get you a real-time GUI exactly, but it can help if what you're
doing isn't too complicated. It can also be nice for making videos of
plot animations.
3. If you need a GUI with multiple plots and you need for future feature
creep, I would research making PyQt4 GUIs, QThreads, Qt signals and
slots, and putting matplotlib figures into a PyQt4 GUI. This is complex
if you are not familiar with GUI programming and will take a while.
Sorry I couldn't be of more help, but it really depends on what exactly
you are doing. Mainly, what do you mean by real-time? Do you really
mean animation? Let me know what you come up with, I'm interested.
-Dave
P.S. Why use a while loop? You can do the same thing with:
for i in range(1000):
# Do stuff
On 3/11/13 10:34 AM, Neal Becker wrote:
I added fig.canvas.show(). It still does nothing.
If I add
mpl.use ('GTK'), now it seems to be doing realtime plotting.
import matplotlib as mpl
import matplotlib.pyplot as plt
plt.ion()
import numpy as np
fig=plt.figure()
plt.axis([0,1000,0,1])
i=0
x=list()
y=list()
fig.canvas.show()
while i 1000:
temp_y=np.random.random()
x.append(i)
y.append(temp_y)
plt.scatter(i,temp_y)
i+=1
plt.draw()
On Mon, Mar 11, 2013 at 10:35 AM, David Hoese dho...@gmail.com
mailto:dho...@gmail.com wrote:
Oops forgot to change the subject line.
On 3/11/13 9:34 AM, David Hoese wrote:
You likely need to show() the canvas. I usually do this by
calling fig.canvas.show() before the for loop.
Since you are using a Qt4 backend the canvas used by the
figure is a QWidget, the basic component of a Qt4 GUI. I don't
know if there is a more matplotlib specific way of doing this,
but when dealing with a larger system this is how I do it.
I would also add a sleep (from time import sleep) of a
couple seconds for testing to make sure you are getting
through the entire for loop before you can see it.
Please CC in any replies, thanks.
-Dave
On 3/11/13 8:58 AM, ndbeck...@gmail.com
mailto:ndbeck...@gmail.com wrote:
I want to update a plot in real time. I did some goog
search, and saw various
answers. Trouble is, they aren't working.
Here's a typical example:
import matplotlib.pyplot as plt
import numpy as np
fig=plt.figure()
plt.axis([0,1000,0,1])
i=0
x=list()
y=list()
while i 1000:
temp_y=np.random.random()
x.append(i)
y.append(temp_y)
plt.scatter(i,temp_y)
i+=1
plt.draw()
If I run this, it draws nothing.
This is my matplotlibrc:
backend : Qt4Agg
mathtext.fontset: stix
--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] real time plotting
I agree, I don't think that will work with mpl's animation stuff or at
least I wouldn't want to do it that way. I've created GUIs that received
data from a weather instrument in real-time. I did method 3 that I
mentioned before because I knew the scientists using it were going to
want more and more features.
...I FOUND A WAY FOR YOU TO CHEAT:
You can use the Qt processEvents() method to have it process
drawing/painting operation between the event loop iterations. This
method is frowned upon when doing real Qt GUIs, but eh go for it. If you
aren't doing anything more serious than watching the output of your
processing as it goes then try this:
import matplotlib
matplotlib.use('qt4agg')
import matplotlib as mpl
import matplotlib.pyplot as plt
plt.ion()
import numpy as np
from time import sleep
from PyQt4 import QtGui,QtCore
fig=plt.figure()
plt.axis([0,1000,0,1])
i=0
x=list()
y=list()
while i 1000:
temp_y=np.random.random()
x.append(i)
y.append(temp_y)
plt.scatter(i,temp_y)
i+=1
plt.draw()
sleep(1)
QtGui.qApp.processEvents()
Good luck,
Dave
On 3/11/13 12:59 PM, Neal Becker wrote:
I go through a compute loop that takes maybe a few seconds per pass,
then plot a new point on the graph. Do I have to? No - I thought mpl
was supposed to do this and wanted to learn how. If it really doesn't
work I'll do something else.
I don't think animation is correct here - I had the impression
animation is where my update would be run as a callback, with a main
loop that calls me periodically. Could that fit the model I
described, where a lengthy computation produces a new value every
few/10s of seconds?
On Mon, Mar 11, 2013 at 1:55 PM, David Hoese dho...@gmail.com
mailto:dho...@gmail.com wrote:
Someone may have to correct me, but I think this has to do with
the Qt4 event loop and it not being run properly. When you get
into real time plotting it can get kind of tricky. In your case (I
got the same results). I have made real-time PyQt4 GUIs before and
have always used separate QThreads and Qt signals/slots to update
the plot. I've never used GTK so I'm not sure why that worked vs
Qt, I would think they would use similar principles but matplotlib
does some magic behind the scenes sometimes. You can see different
results if you comment out the while loop and import the module
into your python/ipython interpreter. After doing this you'll see
the figure pop up (you don't even need the fig.canvas.show() for
this part if interactive mode is on. I went one step further and
turned the while loop into a function:
def one_iter(i):
# Contents of while loop
Calling this in the interpreter shows the figure updating after
each call, but running in a loop (even with sleep) won't show any
updates until the loop is done. In my opinion you have a few
choices that really depend on your programming comfort level:
1. Don't make a real-time plot.
Do you really need a real-time plot that updates from some
external source?
2. Maybe you should look at the matplotlib animation functionality
(http://matplotlib.org/api/animation_api.html). I like this
tutorial:
http://jakevdp.github.com/blog/2012/08/18/matplotlib-animation-tutorial/.
This won't get you a real-time GUI exactly, but it can help if
what you're doing isn't too complicated. It can also be nice for
making videos of plot animations.
3. If you need a GUI with multiple plots and you need for future
feature creep, I would research making PyQt4 GUIs, QThreads, Qt
signals and slots, and putting matplotlib figures into a PyQt4
GUI. This is complex if you are not familiar with GUI programming
and will take a while.
Sorry I couldn't be of more help, but it really depends on what
exactly you are doing. Mainly, what do you mean by real-time? Do
you really mean animation? Let me know what you come up with, I'm
interested.
-Dave
P.S. Why use a while loop? You can do the same thing with:
for i in range(1000):
# Do stuff
On 3/11/13 10:34 AM, Neal Becker wrote:
I added fig.canvas.show(). It still does nothing.
If I add
mpl.use ('GTK'), now it seems to be doing realtime plotting.
import matplotlib as mpl
import matplotlib.pyplot as plt
plt.ion()
import numpy as np
fig=plt.figure()
plt.axis([0,1000,0,1])
i=0
x=list()
y=list()
fig.canvas.show()
while i 1000:
temp_y=np.random.random()
x.append(i)
y.append(temp_y)
plt.scatter(i,temp_y)
i+=1
plt.draw()
On Mon, Mar 11, 2013 at 10:35 AM, David Hoese dho...@gmail.com
mailto:dho...@gmail.com wrote:
Oops forgot to change the subject line.
On 3/11/13 9:34 AM, David Hoese wrote:
You likely need to show() the canvas. I usually do
[Matplotlib-users] importing basemap then shapely causes error
I've asked this question on GIS stack exchange site, but thought it would be good to post here too. The SE question is here: http://gis.stackexchange.com/questions/50394/importing-matplotlib-basemap-and-shapely I have a python script that uses matplotlib's basemap and another part that uses shapely to do an intersection of 2 polygons. If basemap is imported before shapely and I run the intersection I get this exception: | intersect_poly= grid_poly.intersection(data_poly) File /sw/lib/python2.7/site-packages/shapely/geometry/base.py, line334, in intersection return geom_factory(self.impl['intersection'](self, other)) File /sw/lib/python2.7/site-packages/shapely/topology.py, line53, in __call__ This operation produced a null geometry. Reason: unknown) shapely.geos.TopologicalError: This operation produced a null geometry. Reason: unknown| If I import shapely first, everything works fine. I would assume this is because of some funkiness in the way they are accessing the GEOS library. I've checked that in both situations the same library file is loaded in shapely (print shapely.geos._lgeos). Does anyone have an idea as to why this is happening and if there is a right way of doing this? Does this happen for anyone else? In the mean time I can just make sure to import shapely first (not sure if that affects basemap yet). Otherwise maybe I'll skim through the basemap source. I'm using OSX(10.7) with a fink install that has libgeos3.3.3-shlibs, libgeos3.3.1-shlibs, libgeos3.3.1, libgeos3.3.0-shlibs, libgeos3.3.0, and shapely-py27 (1.2.16-1) installed. The current basemap version in fink is 1.0.2. And here's a simple test script that reproduces the problem (flip the imports and it works): |from mpl_toolkitsimport basemap from shapelyimport geometry g_ring= [(-88.462425, 26.992203), (-57.847187, 26.992203), (-57.847187, 17.599869), (-88.462425, 17.599869), (-88.462425, 26.992203)] grid_g_ring= [(-123.044, 59.8440001), (-49.3849998, 57.2890001), (-65.0909994, 14.3350001), (-113.133, 16.369), (-123.044, 59.8440001)] data_poly= geometry.Polygon(g_ring) grid_poly= geometry.Polygon(grid_g_ring) print grid_poly.intersection(data_poly).area| Thanks again. Please CC me in any replies. -Dave -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Hiding labels in a legend?
Hello- Prior to version 1.2 of MPL I was able to hide labels for certain lines in the legend by setting the label=None when plotting a line, however in 1.2 it is now showing the legend entry and visibly printing None. Is there a workaround to hide the label? Thanks, David -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Hiding labels in a legend?
On Tue, Jan 22, 2013 at 1:20 PM, Benjamin Root ben.r...@ou.edu wrote: On Tue, Jan 22, 2013 at 1:57 PM, David Erickson halcyon1...@gmail.com wrote: Hello- Prior to version 1.2 of MPL I was able to hide labels for certain lines in the legend by setting the label=None when plotting a line, however in 1.2 it is now showing the legend entry and visibly printing None. Is there a workaround to hide the label? Thanks, David I think you want _nolegend_ for those labels. The hiding of the labels for None was an undocumented feature, I think, and has been fixed. http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.legend Perfect, thanks Ben! -David -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Fwd:
http://smallshop.lt/gbwpmas.php -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122912 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Colormap norm (vmin, vmax) based on visible part of figure
Hi all, I'm wondering if anyone knows how to compute colorbar limits (vmin, vmax) based only on the visible portion of the figure. My use-case is a pcolormesh(x, y, z) drawn over a Basemap instance. The coordinates x and y cover the entire globe, but I'm only mapping the Arctic. What happens is that the normalization is done over the entire z array, while only a subset of z actually appears on the map. The colors appearing on the map thus cover only a small fraction of the entire color range. From what I managed to understand, pcolormesh creates a collections of patches colorcoded based on the array attribute. So my question is if there is a builtin way to know which items of this collections are clipped so I can mask this part of the array ? Thanks a lot, David -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] create an new axis with y-offset in the same subplot
Greetings, With the help of sankey-toolbox, we can plot sankey-diagrams automaticly: The position of a sankey-object is automaticly calculated based on the position of its prior-object and cannot be given manually; and when a sankey-diagram is initialized, the position of the first sankey-object will be assigned with the input of an axis. (the (0,0)-point will be the center-point of this object) And Here is the situation: i want to draw two sankey-diagrams in the same subplot with a given y-offset, therefore are two coordinate systems with y-offset required. I have tried the 'add_axes' method, but with this method a new subplot is created and there will be a graphic scaling problem. Now this is the question: Is it possible to create a new coordinate system with a given y-offset, without creating new subplot? -- View this message in context: http://matplotlib.1069221.n5.nabble.com/create-an-new-axis-with-y-offset-in-the-same-subplot-tp40006.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] histogran2d and polar axis
Hi, This one has been driving me crazy all day. I have three vectors, azimuth, frequency and power, which I would like to histogram and plot on a polar axis. I can plot a scatter plot this way no problem but the histogram gets messed up somehow. An example is below, anybody know how to do this properly?? import random import numpy as np import matplotlib.pyplot as plt baz = np.zeros((20)) freq = np.zeros((20)) pwr = np.zeros((20)) for x in range(20): baz[x] = random.randint(20,25)*10 freq[x] = random.randint(1,10)*10 pwr[x] = random.randint(-10,-1)*10 baz = baz*np.pi/180. abins = np.linspace(0,2*np.pi,360) sbins = np.linspace(1, 100) H, xedges, yedges = np.histogram2d(baz, freq, bins=(abins,sbins), weights=pwr) plt.figure(figsize=(14,14)) plt.subplot(111, polar=True) #plt.scatter(baz, freq, c=pwr) plt.pcolormesh(H) plt.show() -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Figure zoom crosshair color
Hello, I have what I hope is a simple question. When producing a figure/plot, I have a window which pops up with the figure inside and a few tool buttons along the bottom, including Zoom to rectangle. Clicking the Zoom tool button, I'm presented with a black crosshair to select my zoom rectangle. Many of the images I work with are predominantly black; is there any way to change the color of the crosshair so as to make it more visible? Thanks. -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Qt4/PySide memory leak
I've run into a large memory leak using Matplotlib with PySide and the
Qt4 back end. I'm using :
Python 3.2
Numpy 1.6.2
Pyside 1.1.1 (qt474)
Matplotlib 1.2 (first the Capetown Group port to Python 3, then 1.2 RC2)
on Windows XP 32 bit
I've tried using the Python 2.7 branch of all of the above and don't see
the problem. I don't see the problem with the Tk back end. I don't see
the problem with the Qt4 back end and PyQt4. Only with the above
mentioned versions and using the Qt4 back end with PySide.
The following script will reproduce the problem :
import matplotlib
matplotlib.use('Qt4Agg')
matplotlib.rcParams['backend.qt4']='PySide'
import pylab
arrayX = []
arrayY = []
for nIndex in range(0, 100):
arrayX.append(nIndex)
arrayY.append(nIndex)
Figure = matplotlib.pyplot.figure(1)
Axes = Figure.add_axes([ 0.05, 0.05, 0.95, 0.95])
Axes.plot(arrayX,
arrayY,
color = blue,
marker = o,
markersize = 5.0)
Axes.set_xlim(arrayX[0], arrayX[len(arrayX) - 1])
Axes.set_ylim(arrayY[0], arrayY[len(arrayY) - 1])
matplotlib.pyplot.show()
I run the above, grab the lower right sizing handle on the plot window
and start resizing the window. Watching the python process in task
manager, each resize leaks a noticeable amount of memory. A few minutes
of this will get process memory up to ~2.5 GB. At that point it
crashes.
I'm new here, am I in the right place?
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[Matplotlib-users] Fwd: NavigationToolbar2WxAgg Buttons Disappear
(Corrects the top posting of the earlier replies, Sorry) On Aug 15, 2012, at 5:17 AM, Benjamin Root wrote: On Wednesday, August 15, 2012, David Grudoski wrote: Hi All, I've encountered this problem with the both NavigationToolbar2Wx and the NavigationToolbar2WxAgg. When I click the Zoom or Pan button the button disappears. The functionality is maintained so if a click the location that the button used to be displayed at the toggle action still works its just that the button is no longer displayed. Can any one help me fix this? Thanks David Which version of matplotlib are you using? Ben Root From: David Grudoski da...@wemeasureit.com Date: August 15, 2012 6:30:20 AM PDT To: Benjamin Root ben.r...@ou.edu Cc: matplotlib-users@lists.sourceforge.net matplotlib-users@lists.sourceforge.net Subject: Re: [Matplotlib-users] NavigationToolbar2WxAgg Buttons Disappear I'm running: Matplotlib 1.1.0 wxPython 2.9.2.4 osx-carbon (classic) Python 2.6 on Mac OSX 10.6.8 I tried running the wxcursor_demo.py from the Matplotlib examples it also behave the same way. When the zoom or pan icon is selected it disappears from the toolbar but the space it occupies behaves as if it is still there just not visible. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] NavigationToolbar2WxAgg Buttons Disappear
Hi All,
I've encountered this problem with the both NavigationToolbar2Wx and the
NavigationToolbar2WxAgg.
When I click the Zoom or Pan button the button disappears. The functionality is
maintained so if a click the location that the button used to be displayed at
the toggle action still works its just that the button is no longer displayed.
Can any one help me fix this?
Thanks
David
Here's the code that demonstrated the problem
##
#Start of Code#
##
#!/usr/bin/env python
# encoding: UTF-8
Basic wxPython App w DrawPanel.py
import sys
reload(sys)
sys.setdefaultencoding(utf-8)
import os
import time
import numpy as np
import matplotlib
matplotlib.use('WXAgg')
from matplotlib.backends.backend_wxagg import Toolbar, FigureCanvasWxAgg
from matplotlib.figure import Figure
import pylab as plt
import wx
from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg
class DrawPanel(wx.Panel):
This class constructs a Matplotlib figure and canvas to allow for
plots.
def __init__(self, parent):
wx.Panel.__init__(self, parent, -1)
#Create the widgets
self.figure = Figure(figsize=(1,1))
self.canvas = FigureCanvasWxAgg(self, -1, self.figure)
self.toolbar = NavigationToolbar2WxAgg(self.canvas)
sizer = wx.BoxSizer(wx.VERTICAL)
# add to sizer allows resizing
sizer.Add(self.toolbar, 0, wx.LEFT|wx.TOP)
sizer.Add(self.canvas, 1, wx.LEFT|wx.TOP|wx.GROW)
self.SetSizer(sizer)
self.Fit()
# plot some data
self.x=np.arange(0,10,.1)
self.y=plt.sin(self.x)
self.init_plot()
def init_plot(self):
self.figure.clf()
self.ax = self.figure.gca()
self.ax.plot(self.x, self.y)
self.canvas.draw()
class MainFrame(wx.Frame):
This is the Main Frame
#--
def __init__(self):
Constructor
wx.Frame.__init__(self, None, title=Basic wxPython App w
DrawPanel,size=(800,600))
# Create StatusBar
self.sb=self.CreateStatusBar()
self.SetStatusText('Basic wxPython App w DrawPanel')
#--
self.Freeze() # need this to prevent flicker during plot
resize/redraw
self.mainpanel = DrawPanel(self)
self.Layout()
self.Thaw()
self.Show()
#--
if __name__ == __main__:
app = wx.App(False)
frame = MainFrame()
app.MainLoop()
##
#End of Code #
##
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Re: [Matplotlib-users] NavigationToolbar2WxAgg Buttons Disappear
I'm running: Matplotlib 1.1.0 wxPython 2.9.2.4 osx-carbon (classic) Python 2.6 on Mac OSX 10.6.8 On Aug 15, 2012, at 5:17 AM, Benjamin Root wrote: On Wednesday, August 15, 2012, David Grudoski wrote: Hi All, I've encountered this problem with the both NavigationToolbar2Wx and the NavigationToolbar2WxAgg. When I click the Zoom or Pan button the button disappears. The functionality is maintained so if a click the location that the button used to be displayed at the toggle action still works its just that the button is no longer displayed. Can any one help me fix this? Thanks David Which version of matplotlib are you using? Ben Root -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Font in figures
Hello, I want to ask some questions about fonts in figures. I think that the best figures are achieved when the font used is the same as in the surrounding text in all the figure. This is the case when I use the latex notation (between $$), but unfortunately the police used for the axis is not the same (this is sans-serif font). On the other hand, you could have a sans-serif font in your document, and thus you would like your equations to be also sans-serif as far it is possible. The reason I write to this mailing is because I want to know if it exists general recipes to have the same font in all the figure with matplotlib. The first thing I thought about as a general recipie is to use an 'epslatex' output, which is then compiled with latex to give an eps or a pdf file, but I am not sure if it is possible to achieve such a result. If you have some idea about that, let me know. Thanks, David -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Increasing font size in axis ticks
Hello, I know how one can increase the font size in the xlabel and ylabel fields. I use the methode presented in: http://matplotlib.sourceforge.net/examples/pylab_examples/dannys_example.html But I don't know how to increase the font size for the numbers labelling the xticks or the yticks, and found nothing in the doc. May you help ? David -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] ginput with undefined number of points
Hi, I trying to define an area in a pcolor plot (several plots) using the ginput(). However since it is an irregular shape and will be different in each plot so I cant define how many points there will be before hand, I've tried the following but it requires a double click at each point, which I would like to avoid as it duplicates points |x = randn(10,10) imshow(x) button = False points = [] while button == False: points.append(ginput(1)) button = waitforbuttonpress() | Anyone know a better way to go about this?? thanks Dave -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Dark or inverted color scheme
I got pretty good results with the code below. Note that I am reading the
FLIP_COLORS from a gui checkbox.
FLIP_COLORS = self.dark_background_flag.get()
if FLIP_COLORS:
matplotlib.rcParams['figure.facecolor'] = '0.0'
matplotlib.rcParams['axes.edgecolor'] = 'grey'
matplotlib.rcParams['text.color'] = 'white'
matplotlib.rcParams['ytick.color'] = '#00ff00'
matplotlib.rcParams['xtick.color'] = '#0ED5D5'
matplotlib.rcParams['axes.labelcolor'] = '#0ED5D5'
matplotlib.rcParams['axes.facecolor'] = 'black'
matplotlib.rcParams['grid.color'] = '0.3'
matplotlib.rcParams['grid.linestyle'] = '-'
matplotlib.rcParams['lines.markeredgewidth'] = 0.0
else:
matplotlib.rcdefaults()
## I seems like setting matplotlib.rcParams['figure.facecolor']
isn't
## enough. I think this is a bug and set_facecolor() is a
work-around.
fig.set_facecolor(matplotlib.rcParams['figure.facecolor'])
This will flip and also flip back. I found a few colors didn't follow
the crowd. For example, axes.ylabel.color doesn't seem to have
an entry in rcParams. For this, I have to modify the plot generation
statments something like:
ax.set_ylabel('Voltage (volts)',
color=matplotlib.rcParams['ytick.color'])
That sets the ylabel text to be the same as the tick marks. I also have to
do things like that to change line colors and such when
going flipping colors.
DavidS
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[Matplotlib-users] TypeError: coercing to Unicode: need string or buffer, dict found
Hi, Anyone know how to solve this error? Exception Type: TypeError Exception Value: coercing to Unicode: need string or buffer, dict found Can you help me?? See mycode: http://dpaste.com/751460/ And see my Traceback: http://dpaste.com/750773/ Thanks, -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Matplotlib-users Digest, Vol 72, Issue 25
Hi Mike, About this question: TypeError: coercing to Unicode: need string or buffer, dict found The version of matplotlib that i'm using is matplotlib-0.99.1-py2.6 And how do I remove the font cache in ~ / .matplotlib / fontList.cache My Operating System is Windows. Thanks, On Wed, May 23, 2012 at 11:15 AM, matplotlib-users-requ...@lists.sourceforge.net wrote: Send Matplotlib-users mailing list submissions to matplotlib-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/matplotlib-users or, via email, send a message with subject or body 'help' to matplotlib-users-requ...@lists.sourceforge.net You can reach the person managing the list at matplotlib-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of Matplotlib-users digest... Today's Topics: 1. Re: Difference in show and output file (rajtendulkar) 2. TypeError: coercing to Unicode: need string orbuffer, dict found (Wal?ria Antunes David) 3. Re: TypeError: coercing to Unicode: need string or buffer, dict found (Michael Droettboom) 4. Re: barchart errorbars always in both directions (Benjamin Root) 5. Re: Slow imshow when zooming or panning with several synced subplots (Sergi Pons Freixes) 6. Re: barchart errorbars always in both directions (Meesters, Aesku.Kipp Institute) -- Message: 1 Date: Wed, 23 May 2012 02:49:05 -0700 (PDT) From: rajtendulkar pranav.tendul...@gmail.com Subject: Re: [Matplotlib-users] Difference in show and output file To: matplotlib-users@lists.sourceforge.net Message-ID: 33894599.p...@talk.nabble.com Content-Type: text/plain; charset=us-ascii Just in case, if anyone needs the answer, I figured it out. I used the transData transform in order to draw the lines correctly. Here is the code - # The code below is to add the lines near the tick labels fig = barGraph.fig xAxisLim=barGraph.ax.xaxis.get_view_interval() tickLocArray = barGraph.ax.xaxis.get_majorticklocs() yStart=-70 yEnd=-0.5 line = Line2D([xAxisLim[0], xAxisLim[0]], [yStart,yEnd],linewidth=2, color='black', transform=barGraph.ax.transData) fig.lines.append(line) for i in xrange(11): lnWidth=2 yStartOffset=0 if((i+1)%4 != 0): lnWidth=1 yStartOffset=20 xOffset = tickLocArray[i] + (tickLocArray[i+1] - tickLocArray[i])/2 line = Line2D([xOffset, xOffset], [yStart+yStartOffset,yEnd],linewidth=lnWidth, color='black', transform=barGraph.ax.transData) fig.lines.append(line) line = Line2D([xAxisLim[1], xAxisLim[1]], [yStart,yEnd],linewidth=2, color='black', transform=barGraph.ax.transData) fig.lines.append(line) plt.figtext(0.247, 0.05, '1') plt.figtext(0.523, 0.05, '2') plt.figtext(0.797, 0.05, '4') Thank You! Raj rajtendulkar wrote: Dear All, I am trying to write a program in matplotlib to generate stacked bar graphs. My problem is that the commands - plt.show() and self.fig.savefig(fileName) generate different outputs. I tried different output formats like PDF, PNG, EPS. But the problem remains the same. This happens for the lines that I am trying to draw outside the plot. I am trying to draw vertical lines between xticklabels. I have uploaded the data file and the code file. http://old.nabble.com/file/p33893817/data.dat data.dat http://old.nabble.com/file/p33893817/matplot1.py matplot1.py Could anyone explain how to resolve this problem? Thank You, Raj -- View this message in context: http://old.nabble.com/Difference-in-show-and-output-file-tp33893817p33894599.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- Message: 2 Date: Wed, 23 May 2012 09:16:09 -0300 From: Wal?ria Antunes David waleriantu...@gmail.com Subject: [Matplotlib-users] TypeError: coercing to Unicode: need string or buffer, dict found To: Matplotlib Users matplotlib-users@lists.sourceforge.net Message-ID: CAEwvc_uK2icxVBzF5Aykka-_Mig4EoCNovgt2jPJHT=xqdv...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, Anyone know how to solve this error? Exception Type: TypeError Exception Value: coercing to Unicode: need string or buffer, dict found Can you help me?? See mycode: http://dpaste.com/751460/ And see my Traceback: http://dpaste.com/750773/ Thanks, -- next part -- An HTML attachment was scrubbed... -- Message: 3 Date: Wed, 23 May 2012 08:29:48 -0400 From: Michael Droettboom md...@stsci.edu Subject: Re: [Matplotlib-users] TypeError: coercing to Unicode: need string or buffer, dict found To: matplotlib
[Matplotlib-users] basemap and fill_between()
Hi, I'm having a problem usinf fill_between() with basemap. I plot two great circles and want to shade the region between them. My code is below, it doesnt give any error just creates the plot without filling the area. Does anyone know if it's possible to do this or should I try a different method? Thanks, David from mpl_toolkits.basemap import Basemap from pylab import * ### PARAMETERS FOR MATPLOTLIB : import matplotlib as mpl rcParams['font.size'] = 10. rcParams['font.family'] = 'Comic Sans MS' rcParams['axes.labelsize'] = 8. rcParams['xtick.labelsize'] = 6. rcParams['ytick.labelsize'] = 6. def shoot(lon, lat, azimuth, maxdist=None): Shooter Function Original javascript on http://williams.best.vwh.net/gccalc.htm Translated to python by Thomas Lecocq glat1 = lat * pi / 180. glon1 = lon * pi / 180. s = maxdist / 1.852 faz = azimuth * pi / 180. EPS= 0.005 if ((abs(cos(glat1))EPS) and not (abs(sin(faz))EPS)): alert(Only N-S courses are meaningful, starting at a pole!) a=6378.13/1.852 f=1/298.257223563 r = 1 - f tu = r * tan(glat1) sf = sin(faz) cf = cos(faz) if (cf==0): b=0. else: b=2. * arctan2 (tu, cf) cu = 1. / sqrt(1 + tu * tu) su = tu * cu sa = cu * sf c2a = 1 - sa * sa x = 1. + sqrt(1. + c2a * (1. / (r * r) - 1.)) x = (x - 2.) / x c = 1. - x c = (x * x / 4. + 1.) / c d = (0.375 * x * x - 1.) * x tu = s / (r * a * c) y = tu c = y + 1 while (abs (y - c) EPS): sy = sin(y) cy = cos(y) cz = cos(b + y) e = 2. * cz * cz - 1. c = y x = e * cy y = e + e - 1. y = (((sy * sy * 4. - 3.) * y * cz * d / 6. + x) * d / 4. - cz) * sy * d + tu b = cu * cy * cf - su * sy c = r * sqrt(sa * sa + b * b) d = su * cy + cu * sy * cf glat2 = (arctan2(d, c) + pi) % (2*pi) - pi c = cu * cy - su * sy * cf x = arctan2(sy * sf, c) c = ((-3. * c2a + 4.) * f + 4.) * c2a * f / 16. d = ((e * cy * c + cz) * sy * c + y) * sa glon2 = ((glon1 + x - (1. - c) * d * f + pi) % (2*pi)) - pi baz = (arctan2(sa, b) + pi) % (2 * pi) glon2 *= 180./pi glat2 *= 180./pi baz *= 180./pi return (glon2, glat2, baz) #Create a basemap around N. Atlantic m = Basemap(llcrnrlon=-45.0,llcrnrlat=30.0,urcrnrlon=15.0,urcrnrlat=75.0, resolution='i',projection='merc',lon_0=-17.5,lat_0=60.0) m.drawcountries(linewidth=0.5) m.drawcoastlines(linewidth=0.5) m.bluemarble() m.drawparallels(arange(40.,75.,10.),labels=[1,0,0,0],color='black',dashes=[1,0],labelstyle='+/-',linewidth=0.2) # draw parallels m.drawmeridians(arange(-45.,15.,10.),labels=[0,0,0,1],color='black',dashes=[1,0],labelstyle='+/-',linewidth=0.2) # draw meridians # Shade region defined by great circles. x1, y1 = -9.1676613, 51.602 az1 = 270. az2 = 290. maxdist = 2000 x2, y2, baz = shoot(x1, y1, az1, maxdist) x3, y3, baz = shoot(x1, y1, az2, maxdist) m.drawgreatcircle(x1, y1, x2, y2, del_s=10, color='gray', lw=1.) m.drawgreatcircle(x1, y1, x3, y3, del_s=10, color='gray', lw=1.) a=linspace(x3,x1) b=linspace(y2,y1) c=linspace(y3,y1) fill_between(a, b, c, where=None, alpha=0.2) show() -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] symlog linear to log transition plot position?
On 5/3/2012 7:01 AM, Michael Droettboom wrote: On 05/03/2012 09:48 AM, Benjamin Root wrote: On Wed, May 2, 2012 at 3:59 PM, David Erickson deric...@stanford.edu mailto:deric...@stanford.edu wrote: On 5/1/2012 5:41 AM, Benjamin Root wrote: On Tue, May 1, 2012 at 6:42 AM, David Erickson deric...@stanford.edu mailto:deric...@stanford.edu wrote: Hi I need to use the symlog yscale in my graph, I have a lot of data that needs to be displayed linearly, with a small fraction at the upper end of the range that needs to be displayed in log scale due to its distance from the main data. The symlog scale works great, however I'd like to adjust the actual vertical graph position where it crosses from linear to log (not the threshold), because right now only ~25% of the y space is being given to linear, and I'd like it to be more like 80%. Is this possible? Thanks! David Isn't linthreshy what you are looking for? It denotes the range where the scale is linear. So, if it is 25, then from -25 to 25 the scale will be linear. After 25, it will be log. Maybe I am missing something in your description? Cheers! Ben Root Hi Ben, No unfortunately linthreshy only controls the crossover point from linear to log scale, it does not give you control over where this occurs on the figure's y coordinates. I've attached a picture to explain, currently the linear part of the graph is only being given around 25% of the vertical space, I'd like to reverse that and give linear ~75% and log at the top only the remaining 25%. Is this possible? I've been digging around in the SymmetricalLogScale and SymmetricalLogLocator classes and can't even tell how this range is allocated. Thanks in advance!! -David David, Thanks, that is much clearer what you are looking for. You are right, I can't seem to find any sort of obvious way to get what you want. Reading the docs for the SymLog scale indicates to me that the author intended for the logrithmic portion to be most interesting and the linear portion was only supposed to be a work-around the whole log(0) issue. Could you file an issue on the github page so that we can mark it as a feature request? Just getting to this after some unexpected absences. Yes -- that is how symlog was originally intended, so there isn't currently any way to configure it. Please file the issue and assign it to me. I'll have a look at what needs to be added to support this. Mike Perfect, thanks Mike! -David -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] symlog linear to log transition plot position?
On 5/1/2012 5:41 AM, Benjamin Root wrote: On Tue, May 1, 2012 at 6:42 AM, David Erickson deric...@stanford.edu mailto:deric...@stanford.edu wrote: Hi I need to use the symlog yscale in my graph, I have a lot of data that needs to be displayed linearly, with a small fraction at the upper end of the range that needs to be displayed in log scale due to its distance from the main data. The symlog scale works great, however I'd like to adjust the actual vertical graph position where it crosses from linear to log (not the threshold), because right now only ~25% of the y space is being given to linear, and I'd like it to be more like 80%. Is this possible? Thanks! David Isn't linthreshy what you are looking for? It denotes the range where the scale is linear. So, if it is 25, then from -25 to 25 the scale will be linear. After 25, it will be log. Maybe I am missing something in your description? Cheers! Ben Root Hi Ben, No unfortunately linthreshy only controls the crossover point from linear to log scale, it does not give you control over where this occurs on the figure's y coordinates. I've attached a picture to explain, currently the linear part of the graph is only being given around 25% of the vertical space, I'd like to reverse that and give linear ~75% and log at the top only the remaining 25%. Is this possible? I've been digging around in the SymmetricalLogScale and SymmetricalLogLocator classes and can't even tell how this range is allocated. Thanks in advance!! -David attachment: symlog.png-- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] symlog linear to log transition plot position?
Hi I need to use the symlog yscale in my graph, I have a lot of data that needs to be displayed linearly, with a small fraction at the upper end of the range that needs to be displayed in log scale due to its distance from the main data. The symlog scale works great, however I'd like to adjust the actual vertical graph position where it crosses from linear to log (not the threshold), because right now only ~25% of the y space is being given to linear, and I'd like it to be more like 80%. Is this possible? Thanks! David -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] installing basemap
Hi again,
So I removed everything and started again ( with version 1-0-2 :) )
but am still having trouble, GEOS_DIR seems to be set correctly but I
get the following error when trying to make the GEOS library with,
sudo make; make install
make[3]: Entering directory `/home/davcra/basemap-1.0.2/geos-3.3.1/src'
test -z /home/davcra/lib || /bin/mkdir -p /home/davcra/lib
/bin/sh ../libtool --mode=install /usr/bin/install -c libgeos.la
'/home/davcra/lib'
libtool: install: /usr/bin/install -c .libs/libgeos-3.3.1.so
/home/davcra/lib/libgeos-3.3.1.so
libtool: install: (cd /home/davcra/lib { ln -s -f libgeos-3.3.1.so
libgeos.so || { rm -f libgeos.so ln -s libgeos-3.3.1.so libgeos.so;
}; })
libtool: install: /usr/bin/install -c .libs/libgeos.lai
/home/davcra/lib/libgeos.la
libtool: install: /usr/bin/install -c .libs/libgeos.a /home/davcra/lib/libgeos.a
libtool: install: chmod 644 /home/davcra/lib/libgeos.a
libtool: install: ranlib /home/davcra/lib/libgeos.a
libtool: finish:
PATH=/usr/ncl_files/bin:/usr/ncl_files/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/davcra/.local/bin:/home/davcra/bin:/sbin
ldconfig -n /home/davcra/lib
--
Libraries have been installed in:
/home/davcra/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
--
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/davcra/basemap-1.0.2/geos-3.3.1/src'
make[2]: Leaving directory `/home/davcra/basemap-1.0.2/geos-3.3.1/src'
make[1]: Leaving directory `/home/davcra/basemap-1.0.2/geos-3.3.1/src'
Making install in capi
make[1]: Entering directory `/home/davcra/basemap-1.0.2/geos-3.3.1/capi'
make[2]: Entering directory `/home/davcra/basemap-1.0.2/geos-3.3.1/capi'
test -z /home/davcra/lib || /bin/mkdir -p /home/davcra/lib
/bin/sh ../libtool --mode=install /usr/bin/install -c
libgeos_c.la '/home/davcra/lib'
libtool: install: warning: relinking `libgeos_c.la'
libtool: install: (cd /home/davcra/basemap-1.0.2/geos-3.3.1/capi;
/bin/sh /home/davcra/basemap-1.0.2/geos-3.3.1/libtool --tag CXX
--mode=relink g++ -DGEOS_INLINE -pedantic -Wall -ansi -Wno-long-long
-ffloat-store -g -O2 -version-info 8:1:7 -no-undefined -o libgeos_c.la
-rpath /home/davcra/lib libgeos_c_la-geos_c.lo
libgeos_c_la-geos_ts_c.lo ../src/libgeos.la )
mv: cannot move `libgeos_c.so.1.7.1' to `libgeos_c.so.1.7.1U': Permission denied
libtool: install: error: relink `libgeos_c.la' with the above command
before installing it
make[2]: *** [install-libLTLIBRARIES] Error 1
make[2]: Leaving directory `/home/davcra/basemap-1.0.2/geos-3.3.1/capi'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/davcra/basemap-1.0.2/geos-3.3.1/capi'
make: *** [install-recursive] Error 1
any ideas??
thanks
D
On 3/31/12 5:48 AM, David Craig wrote:
Hi, I previously installed basemap by using the yum command. This
installed version 0.99.4. I want to install the latest version so I
can use shaded relief etc. This may be more of a linux problem but as
I am more familiar with python than linux I thought someone here may
be able to help.
Following the website instructions
(http://matplotlib.github.com/basemap/users/installing.html) I
downloaded the latest version and untarred it. Then in the basemap
directory (which contains geos-3.2.0) I try to set the environment
variable GEOS_DIR to point to the location of libgeos_c and geos_c.h.
I use the find command to locate the files,
/find / -name geos_c.h/ returns the location of that file as
//usr/lib/basemap-1.0.1/geos-3.2.0/capi/geos_c.h/
and
/find / -name libgeos*/
returns
//libgeos_c_la-geos_c.Plo
/usr/lib/libgeos-3.3.1.so http://libgeos-3.3.1.so
/usr/lib/libgeos_c.so.1.7.1
/usr/lib/libgeos_c.so.1/
so I set GEOS_DIR to /usr/lib(not sure if this is correct).
I then cd to the basemap directory and run,
python setup.py install
[davcra@... basemap-1.0.1]$ sudo python setup.py install
[sudo] password for davcra:
checking for GEOS lib in /root
checking for GEOS lib in /usr
checking for GEOS lib in /usr/local
checking for GEOS lib in /sw
checking for GEOS lib in /opt
checking for GEOS lib in /opt/local
Can't find geos library . Please set the
environment variable GEOS_DIR to point to the location
[Matplotlib-users] trouble with pcolor
Hi, I am trying to use pcolor to visualise three variables. For example if I have a value for z at x and a value for z at y something like [x1, x2, x3] = [z1, z2, z3] and [y1, y2, y3] = [z2, z1, z3]. Then I use meshgrid to create the grid for x and y, X, Y = meshgrid(x, y) the result is two array's of shape (3,3). I then need to reshape Z to use pcolor, which is what I am having trouble with. I know I want a result like, y3 0 0 z3 y2 z1 0 0 y1 0 z2 0 x1 x2 x3 but have no idea how to create it. Anyone able to help?? thanks D -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] installing basemap
Hi, I previously installed basemap by using the yum command. This installed version 0.99.4. I want to install the latest version so I can use shaded relief etc. This may be more of a linux problem but as I am more familiar with python than linux I thought someone here may be able to help. Following the website instructions ( http://matplotlib.github.com/basemap/users/installing.html) I downloaded the latest version and untarred it. Then in the basemap directory (which contains geos-3.2.0) I try to set the environment variable GEOS_DIR to point to the location of libgeos_c and geos_c.h. I use the find command to locate the files, *find / -name geos_c.h* returns the location of that file as * /usr/lib/basemap-1.0.1/geos-3.2.0/capi/geos_c.h* and *find / -name libgeos** returns */libgeos_c_la-geos_c.Plo /usr/lib/libgeos-3.3.1.so /usr/lib/libgeos_c.so.1.7.1 /usr/lib/libgeos_c.so.1* so I set GEOS_DIR to /usr/lib(not sure if this is correct). I then cd to the basemap directory and run, python setup.py install [davcra@David basemap-1.0.1]$ sudo python setup.py install [sudo] password for davcra: checking for GEOS lib in /root checking for GEOS lib in /usr checking for GEOS lib in /usr/local checking for GEOS lib in /sw checking for GEOS lib in /opt checking for GEOS lib in /opt/local Can't find geos library . Please set the environment variable GEOS_DIR to point to the location where geos is installed (for example, if geos_c.h is in /usr/local/include, and libgeos_c is in /usr/local/lib, set GEOS_DIR to /usr/local), or edit the setup.py script manually and set the variable GEOS_dir (right after the line that says set GEOS_dir manually here. The problem seems to be with GEOS_DIR but I am not sure what I should set it to. Thanks D -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Clearing figures from memory
A while ago I had exactly the same problem. I was running a script that
create a lot of figures and saved them (as .png and .eps files) for
viewing later (so not using the interactive viewing feature from
pyplot). If I remember well, there was also a problem with the close()
statement leaving some stuff in memory. Unfortunately I don't remember
how the details went and how it got fixed. I guess I should have used
the mailing list or created a bug report.
Anyway, when I need to generate a massive amount of figures these days I
bypass the pyplot interface completely and go straight for the
matplotlib API (at least as far as I understand this approach myself).
When using pyplot, some figure tweaks did not persist upon saving, but
that might as well have been due to my limited matplotlib knowledge. The
procedure was inspired by this blog post:
http://sjohannes.wordpress.com/2010/06/11/using-matplotlib-in-a-web-application/
and goes as follows:
from matplotlib.figure import Figure
# dependent on the backend you use
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as
FigCanvas
# set figure size, dpi and initiate a workable fig object
fig = Figure(figsize=(figsize_x, figsize_y), dpi=dpi)
canvas = FigCanvas(fig)
fig.set_canvas(canvas)
# tweak white spacings
fig.subplots_adjust(left=wsleft, bottom=wsbottom, right=wsright,
top=wstop, wspace=wspace, hspace=hspace)
# big main title
fig.suptitle(grandtitle, size='x-large')
# create a subplot
ax = fig.add_subplot(nr_rows, nr_cols, plot_nr)
# do all your plotting stuff here on ax
# save the figure and close
fig.savefig('/path/to/figure/figname.png')
canvas.close()
fig.clear()
If interested, I can give you a more elaborate and working example of
which parameters I tune how exactly.
Regards,
David
On 23/03/12 19:45, Eric Firing wrote:
On 03/23/2012 08:05 AM, Albert Kottke wrote:
I am having problems clearing figures from memory. After saving the
figure, I use pyplot.close() on the figure handle and then del all of
the data and figure, as shown here:
fig.savefig('plots/%(record_id)05i' % recording)
plt.close(fig)
del accel, fourier_amp, fig, time, disp
gc.collect()
Despite this, the figures don't appear to be closing. I am trying to
make 30k plots and I have to kill script every couple thousand and
restart because I run out of memory.
Any suggestions?
You are running a standalone script, correct? Make sure you are using
only the agg backend. Before the first import of pyplot, do
import matplotlib
matplotlib.use(agg)
I don't know if that will help, but it can't hurt.
You might find matplotlib.cbook.report_memory() to be useful in tracking
down the problem.
Eric
Albert
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[Matplotlib-users] Problem using plot_surface.
Hi, I have three variables I would like to plot using plot_surface but I keep getting the error given at the bottom. Anyone know what I am doing wrong?? My code is as follows, fig3 = plt.figure() ax = Axes3D(fig3) X = np.zeros((78,1)) Y = np.zeros((78,1)) Z = np.zeros((78,1)) for p in range(len(data)): X[p,0] = data[p][1] #distance Y[p,0] = data[p][3] #azimuth Z[p,0] = data[p][4] #snr X, Y = np.meshgrid(X, Y) surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.jet) ValueErrorTraceback (most recent call last) /home/davcra/python_scripts/plot_snr_az.py in module() 48 Z[p,0] = data[p][4] #snr 49 X, Y = np.meshgrid(X, Y) --- 50 surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.jet) 51 #fig.colorbar(surf, shrink=0.5, aspect=5) 52 #plt.show() /usr/lib64/python2.6/site-packages/mpl_toolkits/mplot3d/axes3d.pyc in plot_surface(self, X, Y, Z, *args, **kwargs) 616 normals.append(np.cross(v1, v2)) 617 -- 618 polyc = art3d.Poly3DCollection(polys, *args, **kwargs) 619 if cmap is not None: 620 polyc.set_array(np.array(avgz)) /usr/lib64/python2.6/site-packages/mpl_toolkits/mplot3d/art3d.pyc in __init__(self, verts, *args, **kwargs) 282 ''' 283 -- 284 PolyCollection.__init__(self, verts, *args, **kwargs) 285 self._zsort = 1 286 self._sort_zpos = None /usr/lib64/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, verts, sizes, closed, **kwargs) 666 Collection.__init__(self,**kwargs) 667 self._sizes = sizes -- 668 self.set_verts(verts, closed) 669 __init__.__doc__ = cbook.dedent(__init__.__doc__) % artist.kwdocd 670 /usr/lib64/python2.6/site-packages/mpl_toolkits/mplot3d/art3d.pyc in set_verts(self, verts, closed) 304 def set_verts(self, verts, closed=True): 305 '''Set 3D vertices.''' -- 306 self.get_vector(verts) 307 # 2D verts will be updated at draw time 308 PolyCollection.set_verts(self, [], closed) /usr/lib64/python2.6/site-packages/mpl_toolkits/mplot3d/art3d.pyc in get_vector(self, segments3d) 297 segis.append((si, ei)) 298 si = ei -- 299 xs, ys, zs = zip(*points) 300 ones = np.ones(len(xs)) 301 self._vec = np.array([xs, ys, zs, ones]) ValueError: need more than 0 values to unpack WARNING: Failure executing file: plot_snr_az.py thanks, David -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] move legend to the foreground: how to use set_zorder() correctly?
Hi All, I am plotting on two different y-axes: one on the left (ax1) and one on the right (ax2). Both share the same x-axes. The problem I am facing relates back to the zorder of the legend (at least, that is what I think): I want it to be on the foreground at all times. In order to do so, I change the zorder of the ax1.legend (left y axes) such that the ax2.plots (right y-axes) are under ax1.legend. However, that doesn't work: all the plots on the right axes (so using ax2) end up above the legend 1 on the left, despite having a lower zorder. Note that I am also giving the grids on both ax1 and ax2 a lower zorder value compared to the legends, but the grid still ends up on top of legend 1 on the left. # version info: # Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3] on linux2 # NumPy 1.6.1, Matplotlib 1.1.0 import pylab as plt import numpy as np # plotting on the left y-axes, ax1 = plt.axes(zorder=10) ax1.plot(range(0,5,1), 'r', label='ax1 ax1 ax1 ax1', zorder=11) ax1.plot(np.arange(3,4.1,1), 'r--', label='ax1 ax1 ax1 ax1', zorder=12) gr1 = ax1.grid(zorder=13) # legend of the left y-axes, force high zorder leg1 = ax1.legend(loc='upper left') leg1.set_zorder(30) # plotting on the right y-axes, ax2 = plt.twinx() ax2.set_zorder(20) ax2.plot(range(4,-1,-1), 'b', label='ax2 ax2 ax2 ax2', zorder=21) ax2.plot(np.arange(4,2.9,-1), np.arange(3,4.1,1), 'b--', label='ax2 ax2 ax2 ax2', zorder=22) gr2 = ax2.grid(zorder=23) # legend of the right y-axes, force high zorder leg2 = ax2.legend(loc='upper right') leg2.set_zorder(40) print '=== zorder:' print ' ax1: %i' % ax1.get_zorder() print ' ax2: %i' % ax2.get_zorder() print 'leg1: %i' % leg1.get_zorder() print 'leg2: %i' % leg2.get_zorder() What am I missing here? Thanks, David -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] move legend to the foreground
Hi All, I am plotting on two different y-axes: one on the left (ax1) and one on the right (ax2). Both share the same x-axes. The problem I am facing relates back to the zorder of the legend (at least, that is what I think): I want it to be on the foreground at all times. In order to do so, I change the zorder of the ax1.legend (left y axes) such that the ax2.plots (right y-axes) are under ax1.legend. However, that doesn't work: all the plots on the right axes (so using ax2) end up above the legend 1 on the left, despite having a lower zorder. Note that I am also giving the grids on both ax1 and ax2 a lower zorder value compared to the legends, but the grid still ends up on top of legend 1 on the left. # version info: # Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3] on linux2 # NumPy 1.6.1, Matplotlib 1.1.0 import pylab as plt import numpy as np # plotting on the left y-axes, ax1 = plt.axes(zorder=10) ax1.plot(range(0,5,1), 'r', label='ax1 ax1 ax1 ax1', zorder=11) ax1.plot(np.arange(3,4.1,1), 'r--', label='ax1 ax1 ax1 ax1', zorder=12) gr1 = ax1.grid(zorder=13) # legend of the left y-axes, force high zorder leg1 = ax1.legend(loc='upper left') leg1.set_zorder(30) # plotting on the right y-axes, ax2 = plt.twinx() ax2.set_zorder(20) ax2.plot(range(4,-1,-1), 'b', label='ax2 ax2 ax2 ax2', zorder=21) ax2.plot(np.arange(4,2.9,-1), np.arange(3,4.1,1), 'b--', label='ax2 ax2 ax2 ax2', zorder=22) gr2 = ax2.grid(zorder=23) # legend of the right y-axes, force high zorder leg2 = ax2.legend(loc='upper right') leg2.set_zorder(40) print '=== zorder:' print ' ax1: %i' % ax1.get_zorder() print ' ax2: %i' % ax2.get_zorder() print 'leg1: %i' % leg1.get_zorder() print 'leg2: %i' % leg2.get_zorder() What am I missing here? Thanks, David -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] 3d plotting
Hi,
I'm using surface_plot to view the results of solving the 2d wave equation.
It works fine (code is below) except I would like to add a color bar and
fix the limits on the vertical axis. When I add the color bar a new one is
added in every iteration instead of overwriting the previous one, anyone
know how I can prevent this?
Also is it possible to specify a view point when plotting?
Thanks
D
import matplotlib.pyplot as plt
import numpy as np
import pylab as py
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
pi = np.pi
#Set up grid.
fig = py.figure()
ax = Axes3D(fig)
nx = 50
nz = 50
X = np.arange(0, nx, 1)
Y = np.arange(0, nz, 1)
X, Y = np.meshgrid(X, Y)
nsteps = 100
# Constants for equation.
c = 4000
dt = 1e-4
h = 1
# Set up source.
xs = 0
zs = 0
#fig2 = py.figure()
ts = np.arange(dt,nsteps*dt,dt)
s = 0.5*np.sin(2*pi*100*ts)
#py.plot(ts,s)
#py.show()
# Homogeneous pressure field.
p = np.zeros([nx, nz, nsteps])
# Solve equation.
for t in range(0,nsteps-1):
for z in range(0,nz-1):
for x in range(0,nx-1):
p[xs,zs,t] = s[t]
k = (c*dt/h)**2
p[x,z,t] = 2*p[x,z,t-1] - p[x,z,t-2] +
k*(p[x+1,z,t-1]-4*p[x,z,t-1]+p[x-1,z,t-1]+p[x,z+1,t-1]+p[x,z-1,t-1])
snap = p[:,:,t]
surf = ax.plot_surface(X,Y,snap, rstride=1, cstride=1, cmap=cm.jet,
linewidth=0)
#fig.colorbar(surf, shrink=0.5, aspect=5)
#py.draw()
py.savefig('/home/davcra/Desktop/plots/2Dwave/'+str(t))
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Re: [Matplotlib-users] Figure save hack
Hi, This sounds actually very interesting. I have been thinking about how to save matplotlib figures in a way comparable to the Matlab .fig format: a file that holds the data (for instance using HDF5/pytables, some figures might hold a lot of data) and the plotting commands to exactly reconstruct the figure. However, I never got around of thinking about an actual implementation for Matplotlib. Hopefully your work can inspire me to actually get it started , and I will try to find some time to dig in your code the coming weeks. At the Spyder mailing list the idea of saving figures a la Matlab briefly popped before as well: http://groups.google.com/group/spyderlib/browse_thread/thread/bf582bac96ff875/d5e94fe9296afbe5 I think saving figures in this manner would be a nice feature for matplotlib. Thanks for sharing this! Regards, David PS: sorry to Sebastian for sending the message twice On 15/03/12 11:22, Sebastian Berg wrote: Hey, last weekend I wrote a hook which can track figure creation. Basically it takes care of creating the new figure and wraps it to track all changes to it. Its a hack, and the code is not cleaned up or tested much, but I like to do scripts that I run with many parameters to create plots and it works well to allow me to open the figures in a way that I can zoom, etc. and would allow editing (a bit) later on too. So while I doubt the approach can be made something serious, and there are probably things that don't work (right now 3D Axis can be done with a bit extra but mouse zooming does not work inside a 3D Axis, though I think its likely not difficult to change), I thought I would put it online because I am not aware of any way to save matplotlib figures: https://github.com/seberg/haunter-for-matplotlib-figures Maybe someone finds it useful or interesting :) Regards, Sebastian Berg -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] draw lines in basemap
Hi,
I'm trying to produce a map with 12 locations marked on it and straight
lines plotted between each point and all other points on the map. I have
the map with the locations ok but am having trouble getting the lines.
My code is below anyone know how to do this??
Thanks
D
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import matplotlib.lines as lines
import numpy as np
m = Basemap(llcrnrlon=-11.5,llcrnrlat=51.0,urcrnrlon=-4.5,urcrnrlat=56.0,
resolution='i',projection='cass',lon_0=-4.36,lat_0=54.7)
lats = [53.5519317,53.8758499, 54.2894659, 55.2333142,
54.9846137,54.7064869, 51.5296651, 51.5536226, 51.7653115, 52.1625237,
52.5809163, 52.9393892]
lons = [-9.9413447, -9.9621948, -8.9583439, -7.6770179, -8.3771698,
-8.7406732, -8.9529546, -9.7907148, -10.1531573, -10.4099873,
-9.8456417, -9.4344939]
x, y = m(lons, lats)
for i in range(len(lons)):
for j in range(len(lons)):
if i == j: continue
m.plot([x[i],y[i]],[x[j],y[j]],'k')
m.plot(x, y, 'bD', markersize=10)
m.drawcoastlines()
#m.drawmapboundary()
#plt.savefig('/media/A677-86E0/dot_size'+str(i)+'.png')
plt.show()
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[Matplotlib-users] basemap problem
Hi, I recently installed basemap and python imaging library on my laptop. I have an i686 machine with fedora 16 on it. I just tried some test plots and basemap seems to work fine but according to the documentation to use the bluemarble(), etopo(), shadedrelief() and warpimage() instance methods I need PIL. SO I installed it via yum, $ sudo yum install python-imaging.i686 however only the bluemarble method works. If I try any of the others I get the following error. AttributeErrorTraceback (most recent call last) /usr/lib/python2.7/site-packages/IPython/utils/py3compat.pyc in execfile(fname, *where) 173 else: 174 filename = fname -- 175 __builtin__.execfile(filename, *where) /home/davcra/Desktop/python_scripts/blue_marble.py in module() 10 11 --- 12 m.shadedrelief() 13 plt.show() AttributeError: 'Basemap' object has no attribute 'shadedrelief' Anyone know what I did wrong Thanks David -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] surface plot
Hi, I have an array defined by 3 variables p(x,z,t). I would like to produce a surface plot with colors defined by p and animate it. That is plot the value of p at all x and z, over time (t). My code to get p is below but I really have no idea how to plot this. Anyone know the best way to go about this? thanks, D # 2D Finite Distance Wave Equation. from pylab import * from numpy import math ion() # Set up variables. nx = 100 nz = 100 nsteps = 300 c = 3500 dt = 10**-4 h = 1 t = arange(0,nsteps,dt) # Define source as a spike. s = zeros(nsteps) s[1] = 1 s[2] = 2 s[3] = 1 # Position source. xs = 50 zs = 50 ##plot(t,s) ##show() # Set up pressure field. p=empty([nx,nz,nsteps]) for t in range(0,nsteps-1): for z in range(0,nz-1): for x in range(0,nx-1): p[x,z,t] = 0 # Solve wave equation. for t in range(2,nsteps-1): for z in range(1,nz-1): for x in range(2,nx-1): p[xs,zs,t] = s[t] k = (c*dt/h)**2 p[x,z,t] = 2*p[x,z,t-1] - p[x,z,t-2] + k*(p[x+1,z,t-1]-4*p[x,z,t-1]+p[x-1,z,t-1]+p[x,z+1,t-1]+p[x,z-1,t-1]) #Plot somehow draw() #close() -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] x-axis ticks and labels
Hi, I am trying to relabel the x-axis on a plot. I want it to have 10 evenly spaced labels ranging from 274 at zero to 283 at one increment short of the axis. My code is as follows: im.axes.xaxis.set_major_locator(py.MaxNLocator(10)) im.axes.xaxis.set_ticklabels(range(274,284)) My understanding is that MaxNLocator defines the number of spaces between labels. I've tried a few variations on the above but can only seem to get the last label to be 282 or 284. Anyone know what I am doing wrong. Thanks D -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] add a single x tick label
Hi, I have a plot of a time series and I would like to add a single extra tick mark and label to the plot in a different color to the already existing tick marks. Is this possible?? Thanks, D -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Change xaxis labels
Hi, I have a plot and the xaxis shows number of seconds after a start point. I would like to convert them to days anyone know how to do this. I have looked at the documentation but cant find what I need. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] specgram memory problem
I'm using a lenovo laptop with fedora 16. It has 2.9 GiB memory and 4 intel core CPUs @ 2.3GHz each. Available disk space is 147.9GiB. numpy 1.6.0 matplotlib 1.0.1 On 6 Feb 2012, at 10:29, Fabrice Silva wrote: On Sat, Feb 4, 2012 at 9:44 AM, Fabrice Silva si...@lma.cnrs- mrs.fr wrote: Le vendredi 03 février 2012 à 17:39 +, David Craig a écrit : sure how to get it to plot the outputs from specgram. I use specgram as follows, Pxx, freqs, bins, im = plt.specgram(..) what am I trying imshow?? plt.specgram computes the spectrogram and when calls imshow to display the resulting array into an image Please tell the shape of Pxx, and try the following import numpy as np import matplotlib.pyplot as plt a = np.empty((12000, 14400), dtype=float) plt.imshow(a) plt.show() Le samedi 04 février 2012 à 10:30 +, David Craig a écrit : Pxx has shape (6001, 1430) and when I tried the lines of code it returned the following memory error, Traceback (most recent call last): File /usr/lib/python2.7/site-packages/matplotlib/backends/ backend_gtk.py, line 394, in expose_event self._render_figure(self._pixmap, w, h) File /usr/lib/python2.7/site-packages/matplotlib/backends/ backend_gtkagg.py, line 75, in _render_figure FigureCanvasAgg.draw(self) File /usr/lib/python2.7/site-packages/matplotlib/backends/ backend_agg.py, line 394, in draw self.figure.draw(self.renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/figure.py, line 798, in draw func(*args) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/axes.py, line 1946, in draw a.draw(renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 354, in draw im = self.make_image(renderer.get_image_magnification()) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 569, in make_image transformed_viewLim) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 201, in _get_unsampled_image x = self.to_rgba(self._A, self._alpha) File /usr/lib/python2.7/site-packages/matplotlib/cm.py, line 193, in to_rgba x = self.norm(x) File /usr/lib/python2.7/site-packages/matplotlib/colors.py, line 802, in __call__ val = ma.asarray(value).astype(np.float) File /usr/lib/python2.7/site-packages/numpy/ma/core.py, line 2908, in astype output = self._data.astype(newtype).view(type(self)) MemoryError Please, answer on the mailing list, It confirms that the troubles lie in the rendering of images. Could you tell the versions of numpy and matplotlib you are using, and the characteristics of the computer you are working on ? -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] specgram memory problem
uname -a gives, Linux David 3.2.2-1.fc16.i686 #1 SMP Thu Jan 26 03:38:31 UTC 2012 i686 i686 i386 GNU/Linux On Mon, Feb 6, 2012 at 6:07 PM, Benjamin Root ben.r...@ou.edu wrote: On Mon, Feb 6, 2012 at 11:59 AM, David Craig dcdavem...@gmail.com wrote: I'm using a lenovo laptop with fedora 16. It has 2.9 GiB memory and 4 intel core CPUs @ 2.3GHz each. Available disk space is 147.9GiB. numpy 1.6.0 matplotlib 1.0.1 32-bit or 64-bit OS? Please use 'uname -a' to tell us, because you can install a 32-bit OS on a 64-bit machine. Ben Root -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] specgram memory problem
Hi, I am using matplotlib to produce some spectrograms for seismic data. I am looking at a 10 day period with a sample rate of 20sps. I would like to have my spectrogram to be composed of 10 minute windows with an overlap of 90%. However when I try and run my script I run out of memory. I can produce the spectrogram for a maximum of 3 days before an error occurs. I have also tried to produce a spectrogram for each day and stick them together using subplot, but I then get the error given below. Anyone know a way around this?? Thanks, David Traceback (most recent call last): File /usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py, line 394, in expose_event self._render_figure(self._pixmap, w, h) File /usr/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py, line 75, in _render_figure FigureCanvasAgg.draw(self) File /usr/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py, line 394, in draw self.figure.draw(self.renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/figure.py, line 798, in draw func(*args) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/axes.py, line 1946, in draw a.draw(renderer) File /usr/lib/python2.7/site-packages/matplotlib/artist.py, line 55, in draw_wrapper draw(artist, renderer, *args, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 354, in draw im = self.make_image(renderer.get_image_magnification()) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 569, in make_image transformed_viewLim) File /usr/lib/python2.7/site-packages/matplotlib/image.py, line 201, in _get_unsampled_image x = self.to_rgba(self._A, self._alpha) File /usr/lib/python2.7/site-packages/matplotlib/cm.py, line 194, in to_rgba x = self.cmap(x, alpha=alpha, bytes=bytes) File /usr/lib/python2.7/site-packages/matplotlib/colors.py, line 551, in __call__ rgba = np.empty(shape=xa.shape+(4,), dtype=lut.dtype) MemoryError -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] specgram
Hi, I am trying to produce a spectrogram for my data set and am having an issue with the color map. My data is filtered between 0.02 and 1.0Hz, but specgram() produces an image in the range 0 to 10Hz. Also the color map is not set properly. I would like to have it so the colormap ranges from the min and max powers obtained by specgram. Anyone know how to do this? My code is below. Pxx, freqs, bins, im = plt.specgram(data, NFFT=nfft, Fs=sps, detrend=py.detrend_none, window=py.window_hanning, noverlap=nfft/2, cmap=None, xextent=None, pad_to=None, sides='default', scale_by_freq=None) plt.ylim(0,1) plt.colorbar() plt.show() thanks, D -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] seconds to julian time
Hi, I have a plot that covers a 10 day period on its x-axis in seconds. I would like to change it to julian days, is this possible with matplotlib and if so how do I do it?? D -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] psd
Hi I have some data for a 24hr period with a sample rate of 100 samples/second. I want to create a power spectrum using matplotlibs function psd. I want it to have 10 minute windows with a 50% overlap, but cant seem to get the syntax right. My code is as follows: NFFT = len(data) Fs = 100 window=np.hanning(Fs*60*10) noverlap = window*0.5 plt.psd(data, NFFT, Fs, window, noverlap ) anyone kow how to do this properly??? Thanks, D -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] psd
Hi, thanks for that. I've made the following changes: NFFT = 100*60*10# Linked to window size Fs = stream[0].stats.sampling_rate win = np.hanning(NFFT) overlap = NFFT/2 power, freq = plt.psd(data, NFFT, Fs, win, overlap) but it returns the following error: Traceback (most recent call last): File /home/davcra/Desktop/python_scripts/welchPSD.py, line 20, in module power, freq = plt.psd(data, NFFT, Fs, win, overlap) File /usr/lib/python2.7/site-packages/matplotlib/pyplot.py, line 2322, in psd ret = ax.psd(x, NFFT, Fs, Fc, detrend, window, noverlap, pad_to, sides, scale_by_freq, **kwargs) File /usr/lib/python2.7/site-packages/matplotlib/axes.py, line 7876, in psd sides, scale_by_freq) File /usr/lib/python2.7/site-packages/matplotlib/mlab.py, line 389, in psd scale_by_freq) File /usr/lib/python2.7/site-packages/matplotlib/mlab.py, line 419, in csd noverlap, pad_to, sides, scale_by_freq) File /usr/lib/python2.7/site-packages/matplotlib/mlab.py, line 268, in _spectral_helper thisX = windowVals * detrend(thisX) TypeError: 'int' object is not callable On Mon, Jan 30, 2012 at 12:13 PM, Fabrice Silva si...@lma.cnrs-mrs.frwrote: Le lundi 30 janvier 2012 à 11:45 +, David Craig a écrit : Hi I have some data for a 24hr period with a sample rate of 100 samples/second. I want to create a power spectrum using matplotlibs function psd. I want it to have 10 minute windows with a 50% overlap, but cant seem to get the syntax right. My code is as follows: NFFT = len(data) Fs = 100 window=np.hanning(Fs*60*10) noverlap = window*0.5 plt.psd(data, NFFT, Fs, window, noverlap ) anyone kow how to do this properly??? Be careful to use a suitable value for NFFT. It must be linked to your windows size, not the total data length, and you would rather use a power of 2 for efficience. Do not use it to increase the frequency resolution (use pad_to instead). Fs = 100 NFFT = Fs*60*10 Pxx, f = plt.psd(data, NFFT, Fs, window=np.hanning(NFFT), NFFT/2) -- Fabrice Silva -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Grid problem?
When I try to turn on the grid for just one axis, seemingly in perfect
accordance with the documentation at
http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.grid
it seems like there is a problem.
My commands are pasted below.
Am I doing this wrong? I am doing the best I can to follow the documentation
exactly.
Thanks for any help!
import matplotlib
matplotlib.use('MacOSX')
import matplotlib.pyplot as plt
fig=plt.figure()
ax=fig.add_subplot(111)
ax.plot([1,2,3])
ax.set_xlabel('Hi there')
ax.grid(True, axis='x')
bombayduck:~$ python
Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type help, copyright, credits or license for more information.
import matplotlib
matplotlib.use('MacOSX')
import matplotlib.pyplot as plt
fig=plt.figure()
ax=fig.add_subplot(111)
ax.plot([1,2,3])
[matplotlib.lines.Line2D object at 0x1a27e30]
ax.set_xlabel('Hi there')
matplotlib.text.Text object at 0x1a58030
ax.grid(True, axis='x')
Traceback (most recent call last):
File stdin, line 1, in module
File
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axes.py,
line 1823, in grid
self.xaxis.grid(b, **kwargs)
File
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axis.py,
line 965, in grid
if len(kwargs): artist.setp(tick.gridline,**kwargs)
File
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/artist.py,
line 1169, in setp
func = getattr(o,funcName)
AttributeError: 'Line2D' object has no attribute 'set_axis'
-dave--
A neuroscientist is at the video arcade, when someone makes him a $1000 bet
on Pac-Man. He smiles, gets out his screwdriver and takes apart the Pac-Man
game. Everyone says What are you doing? The neuroscientist says Well,
since we all know that Pac-Man is based on electric signals traveling
through these circuits, obviously I can understand it better than the other
guy by going straight to the source!
--
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[Matplotlib-users] Grid problem?
When I try to turn on the grid for just one axis, seemingly in perfect
accordance with the documentation at
http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.grid
it seems like there is a problem. I am able to make a graph, but trying to
turn on the grid for just one axis causes an error.
My commands are pasted below.
Am I doing this wrong? I am doing the best I can to follow the documentation
exactly.
Thanks for any help!
import matplotlib
matplotlib.use('MacOSX')
import matplotlib.pyplot as plt
fig=plt.figure()
ax=fig.add_subplot(111)
ax.plot([1,2,3])
ax.set_xlabel('Hi there')
ax.grid(True, axis='x')
bombayduck:~$ python
Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type help, copyright, credits or license for more information.
import matplotlib
matplotlib.use('MacOSX')
import matplotlib.pyplot as plt
fig=plt.figure()
ax=fig.add_subplot(111)
ax.plot([1,2,3])
[matplotlib.lines.Line2D object at 0x1a27e30]
ax.set_xlabel('Hi there')
matplotlib.text.Text object at 0x1a58030
ax.grid(True, axis='x')
Traceback (most recent call last):
File stdin, line 1, in module
File
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axes.py,
line 1823, in grid
self.xaxis.grid(b, **kwargs)
File
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axis.py,
line 965, in grid
if len(kwargs): artist.setp(tick.gridline,**kwargs)
File
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/artist.py,
line 1169, in setp
func = getattr(o,funcName)
AttributeError: 'Line2D' object has no attribute 'set_axis'
-dave--
A neuroscientist is at the video arcade, when someone makes him a $1000 bet
on Pac-Man. He smiles, gets out his screwdriver and takes apart the Pac-Man
game. Everyone says What are you doing? The neuroscientist says Well,
since we all know that Pac-Man is based on electric signals traveling
through these circuits, obviously I can understand it better than the other
guy by going straight to the source!
--
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Re: [Matplotlib-users] matplotlib 1.1 TypeError: a float is required problem
I experienced the same problem on the macosx backend, switched to Qt4Agg and no problems. import matplotlib matplotlib.use(Qt4Agg) -Dave On 1/6/12 10:08 AM, md...@stsci.edu wrote: I suspect this bug is specific to the macosx backend. Can you switch to another backend and confirm it doesn't happen there? (I can't reproduce it on Linux). Mike -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matplotlib 1.1 TypeError: a float is required problem
Hi Ken, You're getting that error because you probably don't have Qt4 installed on your Mac (I do). I'm not sure what backends come with matplotlib and will work for you (maybe someone here knows). You can use any of the following: GTK GTKAgg GTKCairo CocoaAgg FltkAgg MacOSX QtAgg Qt4Agg TkAgg WX WXAgg Agg Cairo GDK PS PDF SVG Template Like Qt4, some of those may need to be installed. I also have Gtk installed (never used it before) and GTKAgg works for me, but not GTK. It's also important to know that not all of those backends are interactive (they don't all show a window) and the figure must be saved to a file. Also make sure that the 2 lines I provided need to be BEFORE any other matplotlib/pyplot imports. Hope you find something that works for you, at least until the macosx bug is fixed. I'm not an expert, sorry. -Dave On 1/6/12 10:35 AM, Mingkui Li wrote: Hi, Dave, I tried the two lines of code you posted, but when I ran the example I mentioned above I got such error: ImportError: No module named sip Seems I can't import any other libs from matplotlib after matplotlib.use(Qt4Agg) I'm kind of a newbie, sorry. Ken On Sat, Jan 7, 2012 at 12:22 AM, David Hoese dho...@gmail.com mailto:dho...@gmail.com wrote: I experienced the same problem on the macosx backend, switched to Qt4Agg and no problems. import matplotlib matplotlib.use(Qt4Agg) -Dave On 1/6/12 10:08 AM, md...@stsci.edu mailto:md...@stsci.edu wrote: I suspect this bug is specific to the macosx backend. Can you switch to another backend and confirm it doesn't happen there? (I can't reproduce it on Linux). Mike -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net mailto:Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Mingkui Li -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matplotlib on OS X Lion or FreeBSD
Paul, Have you tried using virtualenv with Python 2.7? I'm in the same situation and I find using a virtual environment for different configuration schemes allows me to have the up-to-date Python modules without the Mac's semi-legacy Python version. It's fairly simple to set up - if you're interested I can discuss the details with you. Cheers, Dave David Welch david.m.we...@gmail.com Something you entered transcended parameters. So much is unknown. -Salon Magazine, Error Haiku Challenge On 29Dec, 2011, at 9:15 AM, Paul Beard wrote: This is turning out to be complicated. Is there any easier way? It may be something as simple as a damaged archive, as this doesn't look right: [/home/paul/src/basemap-1.0.2]:: find . -name setup.py (p...@shuttle.paulbeard.org)-(07:02 AM / Thu Dec 29) It makes this step difficult: 3) cd back to the top level basemap directory (basemap-X.Y.Z) and run the usual 'python setup.py install'. Check your installation by running from mpl_toolkits.basemap import Basemap at the python prompt. I have tried easy-install (it wasn't). I have tried pulling from git: python setup.py build Traceback (most recent call last): File setup.py, line 42, in module from setupext import build_agg, build_gtkagg, build_tkagg,\ File /usr/home/paul/src/matplotlib/setupext.py, line 184, in module basedirlist = basedir[sys.platform] KeyError: 'freebsd8' I tried the packaged version on OS X Lion: Screen Shot 2011-12-29 at 6.59.57 AM.png Built for OS X 10.3? Really? I'm not installing fink or macports or homebrew: if it doesn't install from source without a duplicated file hierarchy I'm not interested. Any hope here? -- Paul Beard Are you trying to win an argument or solve a problem? -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] How to do million data-point plots with Matplotlib?
I have experimented with path.simplify and can't see any appreciable improvements. Incidently, I also experimented with other back ends. I found that all the back ends involving Agg behave similarly. However, using the 'GTK' backend it renders the whole 1 million points and does it very fast (about 5x faster than Agg backends). I also found that gnuplot can render the whole million points very fast using the 'x11' terminal. I am guessing that both matplotlib's GTK backend and gnuplot's 'x11' terminal use the hardware accelerated display driver. David -- Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Matplotlib-users Digest, Vol 67, Issue 23
Eric, I installed mpl from git (git clone git://github.com/matplotlib/matplotlib.git, unless I was suppose to use one of the branches) and same problem. I looked at my code again and thought there should be a canvas.draw() before calling c.copy_from_bbox(a.bbox), but still the same problem. However, I did have it work the first time I added c.draw() and used the git mpl, and by work I mean that everything stayed visible on the figure. When people start coming in to my work I'll ask them to run my sample code and see what happens. It almost seems like mpl is handling the window activation event funny, is there an easy way to print out the callbacks being used by a mpl figure? For now, I will subclass QApplication, and implement notify() to print out events as they come in, but still...this is just weird. Thanks. -Dave On 12/14/11 10:30 PM, Eric Firing wrote: David, It works for me on linux with mpl from git. I haven't tried to figure it out, but it is conceivable that the problem you are seeing was fixed with this: commit b624546ae60dc5878e75a32f41a160d383548b8f Author: Eric Firingefir...@hawaii.edu Date: Tue Oct 18 08:06:21 2011 -1000 backend_qt4agg: draw() immediately calls FigureCanvasAgg.draw() This is the latest in a series of modifications to the Qt4Agg drawing strategy going back several years. It simplifies the code and should solve the problem introduced in 6938b0025; that is, delaying the Agg draw operation until the paintEvent breaks code expecting that draw operation to have occurred immediately. The problem was reported here: http://sourceforge.net/mailarchive/message.php?msg_id=28245744 Eric -- 10 Tips for Better Server Consolidation Server virtualization is being driven by many needs. But none more important than the need to reduce IT complexity while improving strategic productivity. Learn More! http://www.accelacomm.com/jaw/sdnl/114/51507609/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Blitting with qt4
Oops forgot to change subject. On 12/15/11 10:02 AM, David Hoese wrote: Eric, I installed mpl from git (git clone git://github.com/matplotlib/matplotlib.git, unless I was suppose to use one of the branches) and same problem. I looked at my code again and thought there should be a canvas.draw() before calling c.copy_from_bbox(a.bbox), but still the same problem. However, I did have it work the first time I added c.draw() and used the git mpl, and by work I mean that everything stayed visible on the figure. When people start coming in to my work I'll ask them to run my sample code and see what happens. It almost seems like mpl is handling the window activation event funny, is there an easy way to print out the callbacks being used by a mpl figure? For now, I will subclass QApplication, and implement notify() to print out events as they come in, but still...this is just weird. Thanks. -Dave On 12/14/11 10:30 PM, Eric Firing wrote: David, It works for me on linux with mpl from git. I haven't tried to figure it out, but it is conceivable that the problem you are seeing was fixed with this: commit b624546ae60dc5878e75a32f41a160d383548b8f Author: Eric Firingefir...@hawaii.edu Date: Tue Oct 18 08:06:21 2011 -1000 backend_qt4agg: draw() immediately calls FigureCanvasAgg.draw() This is the latest in a series of modifications to the Qt4Agg drawing strategy going back several years. It simplifies the code and should solve the problem introduced in 6938b0025; that is, delaying the Agg draw operation until the paintEvent breaks code expecting that draw operation to have occurred immediately. The problem was reported here: http://sourceforge.net/mailarchive/message.php?msg_id=28245744 Eric -- 10 Tips for Better Server Consolidation Server virtualization is being driven by many needs. But none more important than the need to reduce IT complexity while improving strategic productivity. Learn More! http://www.accelacomm.com/jaw/sdnl/114/51507609/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Blitting with qt4
Eric, Good news I think I got it to work. So using the same code I sent you originally, I applied the following changes: 1. Install matplotlib from git (this did fix things that I wasn't noticing) 2. Add c.draw() before c.copy_from_bbox 3. Copy f.bbox instead of a.bbox (I think this makes sense since I want it to hold on to the title,ticks, and labels, a.bbox is only the content inside the axis rectangle) 4. Restore f_bbox, blit f.bbox. ...and it seems to work. The git version of mpl did fix this, although restoring just the a.bbox was only keeping the axis rectangle so it made it look like even worse of a bug. Using the new version I noticed this and then started using f.bbox which seems to work the way I want it. Now, my final question is: Is this actually doing what I want performance-wise. When I blit just f.bbox, is it really only repainting the updated line or is it redrawing most of the figure? If you need a copy of the new version of my test code let me know. Thanks for any more clarity/help you can give. -Dave P.S. Is there a book or tutorial or website where I can learn more about how the rendering/painting of stuff like this works. For example, if I could better understand why your bug fix was needed. On 12/15/11 10:04 AM, David Hoese wrote: Oops forgot to change subject. On 12/15/11 10:02 AM, David Hoese wrote: Eric, I installed mpl from git (git clone git://github.com/matplotlib/matplotlib.git, unless I was suppose to use one of the branches) and same problem. I looked at my code again and thought there should be a canvas.draw() before calling c.copy_from_bbox(a.bbox), but still the same problem. However, I did have it work the first time I added c.draw() and used the git mpl, and by work I mean that everything stayed visible on the figure. When people start coming in to my work I'll ask them to run my sample code and see what happens. It almost seems like mpl is handling the window activation event funny, is there an easy way to print out the callbacks being used by a mpl figure? For now, I will subclass QApplication, and implement notify() to print out events as they come in, but still...this is just weird. Thanks. -Dave On 12/14/11 10:30 PM, Eric Firing wrote: David, It works for me on linux with mpl from git. I haven't tried to figure it out, but it is conceivable that the problem you are seeing was fixed with this: commit b624546ae60dc5878e75a32f41a160d383548b8f Author: Eric Firingefir...@hawaii.edu Date: Tue Oct 18 08:06:21 2011 -1000 backend_qt4agg: draw() immediately calls FigureCanvasAgg.draw() This is the latest in a series of modifications to the Qt4Agg drawing strategy going back several years. It simplifies the code and should solve the problem introduced in 6938b0025; that is, delaying the Agg draw operation until the paintEvent breaks code expecting that draw operation to have occurred immediately. The problem was reported here: http://sourceforge.net/mailarchive/message.php?msg_id=28245744 Eric -- 10 Tips for Better Server Consolidation Server virtualization is being driven by many needs. But none more important than the need to reduce IT complexity while improving strategic productivity. Learn More! http://www.accelacomm.com/jaw/sdnl/114/51507609/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] How can I place a table on a plot in Matplotlib?
I'm not having any success in getting the matplotlib table commands to work. Here's an example of what I'd like to do: Can anyone help with the table construction code? Thanks import pylab as plt plt.figure() ax=plt.gca() y=[1,2,3,4,5,4,3,2,1,1,1,1,1,1,1,1] plt.plot([10,10,14,14,10],[2,4,4,2,2],'r') col_labels=['col1','col2','col3'] row_labels=['row1','row2','row3'] table_vals=[11,12,13,21,22,23,31,32,33] # the rectangle is where I want to place the table plt.text(11,4.1,'Table Title',size=8) plt.plot(y) plt.show() -- 10 Tips for Better Server Consolidation Server virtualization is being driven by many needs. But none more important than the need to reduce IT complexity while improving strategic productivity. Learn More! http://www.accelacomm.com/jaw/sdnl/114/51507609/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] [ploting data] Live data
I'm not sure how experienced you are with multithreaded programs, but here is some sample code (I mentioned it can get complicated). I suggest you research Qt4 QThreads and also Qt4 Signals and slots to better understand the code below. It is a working sample so you should be able to run it in a terminal and notice that the GUI is responsive and that you have messages being printed out on the terminal. The code I provided below is more complicated than you may need for a proof-of-concept kind of program, but if you will be communicating with physical devices I suggest something like this. I am by no means and expert, but I have been doing something similar to what you are doing. I also suggest maybe separating the device communication into another module/class, especially if others are going to (re)use your code. Good Luck, Dave P.S. There are a lot of Qt4/PyQt4 threading examples online, but not all of them correct. What I posted below is what I have found to be considered correct by most people. # ### Sample Code ### # import time from PyQt4 import QtGui,QtCore class MyWindow(QtGui.QWidget): def __init__(self): QtGui.QWidget.__init__(self) # Sample GUI elements to test responsiveness the_choices = [item]*20 self.choices = QtGui.QComboBox() self.choices.addItems(the_choices) self.layout = QtGui.QVBoxLayout(self) self.layout.addWidget(self.choices) self.setLayout(self.layout) def handle_new_data(self): # This is where you could redraw any matplotlib plots # Maybe send data through the signal/slot connection print Updating data class MyInstrument(QtCore.QObject): signal_new_data = QtCore.pyqtSignal(name=signal_new_data) signal_closing = QtCore.pyqtSignal(name=signal_closing) def run(self): self._timer = QtCore.QTimer() self._timer.timeout.connect(self._run) self._timer.start(0) def _run(self): time.sleep(1) print Running the instrument function time.sleep(1) self.signal_new_data.emit() def close(self): print Closing instrument thread self._timer.stop() # Redundant timer stop self._timer.timeout.disconnect() self.signal_closing.emit() if __name__ == __main__: app = QtGui.QApplication([ ]) w = MyWindow() w.show() instrument = MyInstrument() instrument_thread = QtCore.QThread() instrument.moveToThread(instrument_thread) instrument_thread.started.connect(instrument.run) instrument.signal_new_data.connect(w.handle_new_data) # Make the close function run in the main thread so you can interrupt the sleeps app.lastWindowClosed.connect(instrument.close, QtCore.Qt.DirectConnection) # You could also call quit manually after exec_() returns instrument.signal_closing.connect(instrument_thread.quit) instrument_thread.start() app.exec_() #instrument_thread.quit() print Waiting for instrument thread... instrument_thread.wait() print SUCCESS ## ### End of Sample Code ### ## On 12/14/11 3:51 AM, Fabien Lafont wrote: I prefer to use the multi-thread method beacause it's easier for me and my colaborators to have the entire acquisition process at the same place. Until then I use a simple one but I hope to use a more complex one in few weeks ( put different voltages on different devices then measure many voltages or current). If I use the domino technique (call the next operation by the end of the previous) it can be complex to read and to edit. Thank you very much anyway! How can I write a multi-thread process? I've just tried to add qApp.processEvents() at the end of my while loop but it doesn't change anything... Thanks again, Fabien 2011/12/13 David Hoesedho...@gmail.com: Yeah I didn't think about suggesting that, but I think it might get complicated. I think he would have to start a one shot timer to call a function to set the voltage. Then that function would also start another one shot timer to call another function that would read from the sample. That function then would start a one shot timer to call the first function again. This way he can be sure that things are called in order and that timing is consistent, just in case the GUI gets complicated or something makes the event loop slow down. He could also use multiple threads. Whatever works for Fabien I guess. -Dave On 12/13/11 1:00 PM, matplotlib-users-requ...@lists.sourceforge.net wrote: From: Drain, Theodore R (343P)theodore.r.dr...@jpl.nasa.gov Subject: Re: [Matplotlib-users] [ploting data] Live data Perhaps I'm missing something, but why not use QTimer? You can't really every call sleep in a single threaded gui (for reasons you've encountered). If you need to poll something, create
Re: [Matplotlib-users] [ploting data] Live data
I don't know what you mean by ApplicationWindow, is that a class or just a name for the main GUI window. I also don't really know what calling the graphical application means, but I'm sure the book can help you more than I can. Again, good luck. -Dave On 12/14/11 10:17 AM, Fabien Lafont wrote: Thanks David, I start to read the Mark summerfield' book about PyQt programming. In fact I realized I don't need multi-threading because I can remove the Timer and just need to call the graphical application from the while loop. How can I call the ApplicationWindow class from my while loop? I'll try to read a bit more about PyQt to understand how it works :) thanks again! Fabien 2011/12/14 David Hoesedho...@gmail.com: I'm not sure how experienced you are with multithreaded programs, but here is some sample code (I mentioned it can get complicated). I suggest you research Qt4 QThreads and also Qt4 Signals and slots to better understand the code below. It is a working sample so you should be able to run it in a terminal and notice that the GUI is responsive and that you have messages being printed out on the terminal. The code I provided below is more complicated than you may need for a proof-of-concept kind of program, but if you will be communicating with physical devices I suggest something like this. I am by no means and expert, but I have been doing something similar to what you are doing. I also suggest maybe separating the device communication into another module/class, especially if others are going to (re)use your code. Good Luck, Dave P.S. There are a lot of Qt4/PyQt4 threading examples online, but not all of them correct. What I posted below is what I have found to be considered correct by most people. # ### Sample Code ### # import time from PyQt4 import QtGui,QtCore class MyWindow(QtGui.QWidget): def __init__(self): QtGui.QWidget.__init__(self) # Sample GUI elements to test responsiveness the_choices = [item]*20 self.choices = QtGui.QComboBox() self.choices.addItems(the_choices) self.layout = QtGui.QVBoxLayout(self) self.layout.addWidget(self.choices) self.setLayout(self.layout) def handle_new_data(self): # This is where you could redraw any matplotlib plots # Maybe send data through the signal/slot connection print Updating data class MyInstrument(QtCore.QObject): signal_new_data = QtCore.pyqtSignal(name=signal_new_data) signal_closing = QtCore.pyqtSignal(name=signal_closing) def run(self): self._timer = QtCore.QTimer() self._timer.timeout.connect(self._run) self._timer.start(0) def _run(self): time.sleep(1) print Running the instrument function time.sleep(1) self.signal_new_data.emit() def close(self): print Closing instrument thread self._timer.stop() # Redundant timer stop self._timer.timeout.disconnect() self.signal_closing.emit() if __name__ == __main__: app = QtGui.QApplication([ ]) w = MyWindow() w.show() instrument = MyInstrument() instrument_thread = QtCore.QThread() instrument.moveToThread(instrument_thread) instrument_thread.started.connect(instrument.run) instrument.signal_new_data.connect(w.handle_new_data) # Make the close function run in the main thread so you can interrupt the sleeps app.lastWindowClosed.connect(instrument.close, QtCore.Qt.DirectConnection) # You could also call quit manually after exec_() returns instrument.signal_closing.connect(instrument_thread.quit) instrument_thread.start() app.exec_() #instrument_thread.quit() print Waiting for instrument thread... instrument_thread.wait() print SUCCESS ## ### End of Sample Code ### ## On 12/14/11 3:51 AM, Fabien Lafont wrote: I prefer to use the multi-thread method beacause it's easier for me and my colaborators to have the entire acquisition process at the same place. Until then I use a simple one but I hope to use a more complex one in few weeks ( put different voltages on different devices then measure many voltages or current). If I use the domino technique (call the next operation by the end of the previous) it can be complex to read and to edit. Thank you very much anyway! How can I write a multi-thread process? I've just tried to add qApp.processEvents() at the end of my while loop but it doesn't change anything... Thanks again, Fabien 2011/12/13 David Hoesedho...@gmail.com: Yeah I didn't think about suggesting that, but I think it might get complicated. I think he would have to start a one shot timer to call a function to set the voltage. Then that function would also start another one shot timer to call another function
[Matplotlib-users] Blitting with qt4
Does anyone know if using the blit method from FigureCanvasQTAgg is not fully supported? I'm having a problem where I'm animating a plot using the blit method and I click on/activate the window the background of the figure disappears (axes and line stay visible). I'm not sure if this is just me (Mac OS X Lion, Qt4 4.8.6, Matplotlib 1.1.0), but the following code reproduces the error: ### from PyQt4 import QtGui,QtCore from matplotlib.figure import Figure from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg from time import sleep app = QtGui.QApplication([ ]) f = Figure() c = FigureCanvasQTAgg(f) a = f.add_subplot(111) a.set_title(A Title) bbox = c.copy_from_bbox(a.bbox) lines = a.plot([1,2,3],[1,2,3]) c.draw() c.show() wait = raw_input(Press a key to continue...) def update(i): a.lines[0].set_ydata([i,1,i]) print a.bbox.bounds c.restore_region(bbox, bbox=a.bbox) a.draw_artist(a.lines[0]) c.blit(a.bbox) sleep(1) app.processEvents() for i in range(20): update(i) wait = raw_input(Press a key to continue...) ### To see the problem, run the code, watch the plot to make sure its updating properly, then click on the window to put it in focus/activate it. I'm hoping that I'm just doing something stupid and its an easy fix. It seems to work until I click on the window (in Mac OS X Lion Terminal the window is opened in the background and the Terminal window stays in focus). Thanks for any help. -Dave -- Cloud Computing - Latest Buzzword or a Glimpse of the Future? This paper surveys cloud computing today: What are the benefits? Why are businesses embracing it? What are its payoffs and pitfalls? http://www.accelacomm.com/jaw/sdnl/114/51425149/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] [ploting data] Live data
Fabien,
The GUI not being responsive might be my fault, I've never used a timer
of 0 and processEvents(). I think what might be happening is that when
you call processEvents, the timer of 0 calls your principal function
again, which calls processEvents again, and so on. Try a timer of 2
again, that should stop the timer from being constantly triggered.
Later today, once I get to work, I'll run some tests of my own and
figure out if that's really the problem. Email me if you make any progress.
-Dave
On 12/13/2011 2:30 AM, Fabien Lafont wrote:
Hey David,
I'm doing this program to control an experiment, so I want to put the
voltage on the sample, then wait two seconds to be sure there is no
current fluctuations then measure the curent with multimeters and
finally plot the datas. That's why I need the sleep... In fact I
wanted to use in parallel the timer to refresh the graph and a while
loop to extract the datas.
If I use startTimer(0) it works but the GUI is almost unresponsive.
I'm trying to use qApp.processEvents() but up to now I don't manage to
see the window appears...
Thanks again for your help
Fabien
2011/12/12 David Hoesedho...@gmail.com:
Hey Fabien,
So you made your principal function run on a timer every 2 seconds? And by
lag do you mean that the GUI is unresponsive? I'm still not seeing when
the loop stops, but what you can do is set the timer at a 0 interval so it
will call the principal function as fast as it can (but with no loop). The
problem with this is that you have those 2 sleep calls in the function. I'm
not sure why you have the sleeps, but if you need them you have two choices:
1. Make you GUI multi-threaded and you could emit a Qt signal from the data
thread when the GUI thread needs to update the GUI. Yes this could get
complicated, but if the sleeps are required then its probably the best way.
2. (From what I've been told, the Qt experts don't approve this) You can use
app.processEvents() in your loop (after each sleep maybe) and this will
pause your function and tell the main event loop to process any queued
events (like GUI actions/events) which will make your GUI more responsive.
If that doesn't make sense let me know.
-Dave
On 12/12/11 9:16 AM, Fabien Lafont wrote:
Hi David! Sorry about the delay I was abroad and without any way to
connect to the internet.
Thank you very much. I've tried to put the principal inside the
timerEvent. It work but it lags. In fact I've set the interval of the
Timer to 2 seconds because the principal loop takes roughly 2seconds
but it's not very accurate...
Is there a way to do the principal loop, show it on the screen, then
redo the loop?
Thanks again!
Fabien
2011/12/5 David Hoesedho...@gmail.com:
If I'm understanding your question correctly and reading your code
correctly, you're asking why the timer method of doing things works, but
the
principal() while loop method does not.
I had a couple solutions that involved the main event loop, but I just
noticed 2 main things that are probably wrong with your code:
1. You are calling 'principal' from inside __init__ so you never actually
return from __init__ which means that you never call window.show() and
therefore never call qApp.exec_(). If you really want to use the
'principal' method you would have to connect it to a one shot timer anyway
to have it run after you have started the application ('qApp.exec_()'). I
think the recommended way would be to use the timer the way you did in your
latest email.
2. At least in the way my email client reads your original code, your
calls to the matplotlib drawing functions aren't inside the while loop and
the while loop never ends...although this doesn't matter if you don't fix
#1
above.
Hope that made sense.
-Dave
On 12/5/11 1:44 PM, matplotlib-users-requ...@lists.sourceforge.net wrote:
Message: 3
Date: Mon, 5 Dec 2011 15:46:02 +0100
From: Fabien Lafontlafont.fab...@gmail.com
Subject: Re: [Matplotlib-users] [ploting data] Live data
Cc:matplotlib-users@lists.sourceforge.net
Message-ID:
CAC9H_cjrgQBE6e6+jzZHyfYHonTeAg0XwU7c_2G-hu=s+z7...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Thx all for your remarks,
I can't understand why this code works (when I use the timer method):
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Re: [Matplotlib-users] [ploting data] Live data
Yeah I didn't think about suggesting that, but I think it might get complicated. I think he would have to start a one shot timer to call a function to set the voltage. Then that function would also start another one shot timer to call another function that would read from the sample. That function then would start a one shot timer to call the first function again. This way he can be sure that things are called in order and that timing is consistent, just in case the GUI gets complicated or something makes the event loop slow down. He could also use multiple threads. Whatever works for Fabien I guess. -Dave On 12/13/11 1:00 PM, matplotlib-users-requ...@lists.sourceforge.net wrote: From: Drain, Theodore R (343P)theodore.r.dr...@jpl.nasa.gov Subject: Re: [Matplotlib-users] [ploting data] Live data Perhaps I'm missing something, but why not use QTimer? You can't really every call sleep in a single threaded gui (for reasons you've encountered). If you need to poll something, create a QTimer for 2 seconds and have it call a measurement function to update the data. You shouldn't need any processEvents calls or sleep. -- Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] [ploting data] Live data
Hey Fabien,
So you made your principal function run on a timer every 2 seconds? And
by lag do you mean that the GUI is unresponsive? I'm still not seeing
when the loop stops, but what you can do is set the timer at a 0
interval so it will call the principal function as fast as it can (but
with no loop). The problem with this is that you have those 2 sleep
calls in the function. I'm not sure why you have the sleeps, but if you
need them you have two choices:
1. Make you GUI multi-threaded and you could emit a Qt signal from the
data thread when the GUI thread needs to update the GUI. Yes this could
get complicated, but if the sleeps are required then its probably the
best way.
2. (From what I've been told, the Qt experts don't approve this) You can
use app.processEvents() in your loop (after each sleep maybe) and this
will pause your function and tell the main event loop to process any
queued events (like GUI actions/events) which will make your GUI more
responsive.
If that doesn't make sense let me know.
-Dave
On 12/12/11 9:16 AM, Fabien Lafont wrote:
Hi David! Sorry about the delay I was abroad and without any way to
connect to the internet.
Thank you very much. I've tried to put the principal inside the
timerEvent. It work but it lags. In fact I've set the interval of the
Timer to 2 seconds because the principal loop takes roughly 2seconds
but it's not very accurate...
Is there a way to do the principal loop, show it on the screen, then
redo the loop?
Thanks again!
Fabien
2011/12/5 David Hoesedho...@gmail.com:
If I'm understanding your question correctly and reading your code
correctly, you're asking why the timer method of doing things works, but the
principal() while loop method does not.
I had a couple solutions that involved the main event loop, but I just
noticed 2 main things that are probably wrong with your code:
1. You are calling 'principal' from inside __init__ so you never actually
return from __init__ which means that you never call window.show() and
therefore never call qApp.exec_(). If you really want to use the
'principal' method you would have to connect it to a one shot timer anyway
to have it run after you have started the application ('qApp.exec_()'). I
think the recommended way would be to use the timer the way you did in your
latest email.
2. At least in the way my email client reads your original code, your calls
to the matplotlib drawing functions aren't inside the while loop and the
while loop never ends...although this doesn't matter if you don't fix #1
above.
Hope that made sense.
-Dave
On 12/5/11 1:44 PM, matplotlib-users-requ...@lists.sourceforge.net wrote:
Message: 3
Date: Mon, 5 Dec 2011 15:46:02 +0100
From: Fabien Lafontlafont.fab...@gmail.com
Subject: Re: [Matplotlib-users] [ploting data] Live data
Cc:matplotlib-users@lists.sourceforge.net
Message-ID:
CAC9H_cjrgQBE6e6+jzZHyfYHonTeAg0XwU7c_2G-hu=s+z7...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Thx all for your remarks,
I can't understand why this code works (when I use the timer method):
--
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
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Microsoft is holding a special Learn Windows Azure training event for
developers. It will provide a great way to learn Windows Azure and what it
provides. You can attend the event by watching it streamed LIVE online.
Learn more at http://p.sf.net/sfu/ms-windowsazure
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[Matplotlib-users] How to do million data-point plots with Matplotlib?
I have been working on a program that uses Matplotlib to plot data consisting of around one million points. Sometimes the plots succeed but often I get an exception: OverFlowError: Agg rendering complexity exceeded. I can make this message go away by plotting the data in chunks as illustrated in the demo code below. However, the extra code is a chore which I don't think should be necessary - I hope the developers will be able to fix this issue sometime soon. I know that the development version has some modifications to addressing this issue. I wonder if it is expected to make the problem go away? By the way, this plot takes about 30 seconds to render on my I7 2600k. The main program reaches the show() statement quickly and prints Done plotting?. Then I see that the program reaches 100% usage on one CPU core (4 real, 8 virtual on the 2600k) until the plot is displayed. I wonder if there is any way to persuade Matplotlib to run some of the chunks in parallel so as to use more CPU cores? Plotting something other than random data, the plots run faster and the maximum chunk size is smaller. The maximum chunk size also depends on the plot size - it is smaller for larger plots. I am wondering if I could use this to plot course and fine versions of the plots. The course plot is zoomed in version of the small-sized raster. That would be better than decimation as all the points would at least be there. Thanks in advance, David --- start code - ## Demo program shows how to chunk plots to avoid the exception: ## ## OverflowError: Agg rendering complexity exceeded. ## Consider downsampling or decimating your data. ## ## David Smith December 2011. from pylab import * import numpy as np nPts=600100 x = np.random.rand(nPts) y = np.random.rand(nPts) ## This seems to always succeed if Npts = 2, but fails ## for Npts 3. For points between, it sometimes succeeds ## and sometimes fails. figure(1) plot (x, y) ## Chunking the plot alway succeeds. figure(2) chunk_size=2 iStarts=range(x.size/chunk_size) for iStart in iStarts: print Plotting chunk starting at %d\n % iStart plot(x[iStart:iStart+chunk_size], y[iStart:iStart+chunk_size], '-b') left_overs = nPts % chunk_size if left_overs 0: print Leftovers %d points\n % left_overs plot(x[-left_overs-1:], y[-left_overs-1:], '-r') print done plotting? show() -- end code Please don't reply to this post It is rediculous to plot 1 million points on screen. I am routinely capturing million-point traces from oscilloscopes and other test equipment and to I need to be able to spot features in the data (glitches if you will) that may not show up plotting decimated data. I can then zoom the plot to inspect these features. -- Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] missing data in plot
Dear All, I'm using matplotlib to generate graph from measured data in one of our accelerators. The issue I have, that the data vector is huge. We talk, say about 5 points to be displayed in a single graph, and I have to assure, that those points are really there. Otherwise the image will be broken. Now, I did a plot like this one: http://svnweb.cern.ch/world/wsvn/fimdab/trunk/doc/broken_acquisitions/broken_picture.pdf The top-picture is somehow still correct, however bottom picture, which should display data on the sample x-axis places as top one, is evidently broken. The problem was traced somewhere into matplotlib, because the original data used to construct the graph are fine. Moreover, if I plot the same data, but just require different x-axis setting to 'zoom' on a part, e.g. 350-600 of the original image linked above, I get correct data output: http://svnweb.cern.ch/world/wsvn/fimdab/trunk/doc/broken_acquisitions/correct_picture.pdf This leads me to a conclusion, that matplotlib somehow 'chooses' the data to be displayed. How can I force it to display all the data? I do not mind if not all the data are displayed in the graph, but it seems that it does not bother to skip as well the peaks, which are of utmost importance... any help appreciated. The source code to display the graphs is shown in function writePdfBSlots in following code: http://svnweb.cern.ch/world/wsvn/fimdab/trunk/SW/Python/captTest.py thanks for any help david -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] [ploting data] Live data
If I'm understanding your question correctly and reading your code correctly,
you're asking why the timer method of doing things works, but the principal()
while loop method does not.
I had a couple solutions that involved the main event loop, but I just noticed
2 main things that are probably wrong with your code:
1. You are calling 'principal' from inside __init__ so you never actually
return from __init__ which means that you never call window.show() and
therefore never call qApp.exec_(). If you really want to use the 'principal'
method you would have to connect it to a one shot timer anyway to have it run
after you have started the application ('qApp.exec_()'). I think the
recommended way would be to use the timer the way you did in your latest email.
2. At least in the way my email client reads your original code, your calls to
the matplotlib drawing functions aren't inside the while loop and the while
loop never ends...although this doesn't matter if you don't fix #1 above.
Hope that made sense.
-Dave
On 12/5/11 1:44 PM, matplotlib-users-requ...@lists.sourceforge.net wrote:
Message: 3
Date: Mon, 5 Dec 2011 15:46:02 +0100
From: Fabien Lafontlafont.fab...@gmail.com
Subject: Re: [Matplotlib-users] [ploting data] Live data
Cc:matplotlib-users@lists.sourceforge.net
Message-ID:
CAC9H_cjrgQBE6e6+jzZHyfYHonTeAg0XwU7c_2G-hu=s+z7...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Thx all for your remarks,
I can't understand why this code works (when I use the timer method):
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Re: [Matplotlib-users] [ploting data] Live data
I think you forget to set the layout on your central widget. self.main_widget.setLayout(vbl) # in your case -Dave On 12/4/2011 9:57 AM, matplotlib-users-requ...@lists.sourceforge.net wrote: 2011/12/2 Daniel Hyamsdhy...@gmail.com: I don't have PyQt installed, so I couldn't test the code, but don't you want to be using extend and not append, if you are returning a list from your two get_info() functions? On Fri, Dec 2, 2011 at 8:13 AM, Fabien Lafontlafont.fab...@gmail.com wrote: Hello everyone, I'm trying to plot live data extracting from remote devices (here it's simulated by get_info1 and 2 the result is always 0.8 or 0.9 I can't understand why it doesnt plot the graph at the end of the while loop. Does somebody has an idea? -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Matplotlib.tests sub-modules missing
/include/freetype2 -isysroot
/Developer/SDKs/MacOSX10.6.sdk -pipe -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API
-DPYCXX_ISO_CPP_LIB=1 -I.
-I/tmp/virtualenv/matplotlibtest/lib/python2.6/site-packages/numpy/core/include
-I.
-I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
src/_png.cpp -o build/temp.macosx-10.6-universal-2.6/src/_png.o
cc1plus: warning: command line option -Wstrict-prototypes is valid for
C/ObjC but not for C++
cc1plus: warning: command line option -Wstrict-prototypes is valid for
C/ObjC but not for C++
g++-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -Wall -undefined
dynamic_lookup -bundle -arch i386 -arch x86_64 -L/usr/X11/lib
-syslibroot,/Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64
-I/usr/X11/include -I/usr/X11/include/freetype2 -isysroot
/Developer/SDKs/MacOSX10.6.sdk build/temp.macosx-10.6-universal-2.6/src/_png.o
build/temp.macosx-10.6-universal-2.6/src/mplutils.o
build/temp.macosx-10.6-universal-2.6/CXX/cxx_extensions.o
build/temp.macosx-10.6-universal-2.6/CXX/cxxsupport.o
build/temp.macosx-10.6-universal-2.6/CXX/IndirectPythonInterface.o
build/temp.macosx-10.6-universal-2.6/CXX/cxxextensions.o -lpng -lz -lstdc++ -lm
-o build/lib.macosx-10.6-universal-2.6/matplotlib/_png.so
building 'matplotlib.backends._macosx' extension
gcc-4.2 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -arch i386 -arch
x86_64 -I/usr/X11/include -I/usr/X11/include/freetype2 -isysroot
/Developer/SDKs/MacOSX10.6.sdk -pipe -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API
-DPYCXX_ISO_CPP_LIB=1
-I/tmp/virtualenv/matplotlibtest/lib/python2.6/site-packages/numpy/core/include
-I.
-I/tmp/virtualenv/matplotlibtest/lib/python2.6/site-packages/numpy/core/include
-Isrc -Iagg24/include -I.
-I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
src/_macosx.m -o build/temp.macosx-10.6-universal-2.6/src/_macosx.o
src/_macosx.m: In function âFigureManager_initâ:
src/_macosx.m:3363: warning: class 'View' does not implement the
'NSWindowDelegate' protocol
src/_macosx.m: In function âFigureManager_initâ:
src/_macosx.m:3363: warning: class 'View' does not implement the
'NSWindowDelegate' protocol
g++-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -Wall -undefined
dynamic_lookup -bundle -arch i386 -arch x86_64 -L/usr/X11/lib
-syslibroot,/Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64
-I/usr/X11/include -I/usr/X11/include/freetype2 -isysroot
/Developer/SDKs/MacOSX10.6.sdk
build/temp.macosx-10.6-universal-2.6/src/_macosx.o
build/temp.macosx-10.6-universal-2.6/CXX/cxx_extensions.o
build/temp.macosx-10.6-universal-2.6/CXX/cxxextensions.o
build/temp.macosx-10.6-universal-2.6/CXX/cxxsupport.o
build/temp.macosx-10.6-universal-2.6/CXX/IndirectPythonInterface.o
build/temp.macosx-10.6-universal-2.6/src/agg_py_transforms.o
build/temp.macosx-10.6-universal-2.6/src/path_cleanup.o -lstdc++ -lm -o
build/lib.macosx-10.6-universal-2.6/matplotlib/backends/_macosx.so -framework
Cocoa
warning: no files found matching 'MANIFEST'
warning: no files found matching 'examples/data/*'
warning: no files found matching 'lib/mpl_toolkits'
Successfully installed matplotlib
Cleaning up...
Cheers,
Dave
--
David Welch
david.m.we...@gmail.com
On 11Nov, 2011, at 3:01 PM, Michael Droettboom wrote:
Have you tried removing the build directory and install directories to
force a full rebuild? It sounds like the build or install got stuck at
some point. I've never seen it not copy *.py files in a package before.
Mike
On 11/11/2011 03:12 PM, David Welch wrote:
Update: test folders are in the build directory, they are just not
being copied during build.
*bump*
On 11/10/11, David Welchdavid.m.we...@gmail.com wrote:
Hello,
I am installing matplotlib on Snow Leopard 10.6. I downloaded v1.1.0 from
the sourceforge site and installed in this manner:
$ export CFLAGS=-arch i386 -arch x86_64 -I/usr/X11/include
-I/usr/X11/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk
$ export LDFLAGS=-Wall -undefined dynamic_lookup -bundle -arch i386 -arch
x86_64 -L/usr/X11/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk
$ export FFLAGS=-arch i386 -arch x86_64
$ tar -xf matplotlib-1.1.0.tar.gz
$ cd matplotlib-1.1.0
$ python setup.py build
$ python setup.py install
$
$ python
import matplotlib as mpl
mpl.test(1)
...EEE
==
ERROR: Failure: AttributeError ('module' object has no attribute
'test_backend_svg')
--
Traceback (most recent call last):
File /private/tmp/test/lib/python2.6/site-packages/nose/loader.py, line
379, in loadTestsFromName
module = resolve_name(addr.module)
File /private/tmp/test/lib/python2.6/site-packages/nose/util.py, line
331, in resolve_name
obj = getattr(obj, part
Re: [Matplotlib-users] Matplotlib.tests sub-modules missing
Has ANYONE installed matplotlib on OSX 10.6 and had the module tests pass?
Specifically in a virtualenv setup?
-Dave
--
David Welch
david.m.we...@gmail.com
On 11Nov, 2011, at 2:12 PM, David Welch wrote:
Update: test folders are in the build directory, they are just not
being copied during build.
*bump*
On 11/10/11, David Welch david.m.we...@gmail.com wrote:
Hello,
I am installing matplotlib on Snow Leopard 10.6. I downloaded v1.1.0 from
the sourceforge site and installed in this manner:
$ export CFLAGS=-arch i386 -arch x86_64 -I/usr/X11/include
-I/usr/X11/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk
$ export LDFLAGS=-Wall -undefined dynamic_lookup -bundle -arch i386 -arch
x86_64 -L/usr/X11/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk
$ export FFLAGS=-arch i386 -arch x86_64
$ tar -xf matplotlib-1.1.0.tar.gz
$ cd matplotlib-1.1.0
$ python setup.py build
$ python setup.py install
$
$ python
import matplotlib as mpl
mpl.test(1)
...EEE
==
ERROR: Failure: AttributeError ('module' object has no attribute
'test_backend_svg')
--
Traceback (most recent call last):
File /private/tmp/test/lib/python2.6/site-packages/nose/loader.py, line
379, in loadTestsFromName
module = resolve_name(addr.module)
File /private/tmp/test/lib/python2.6/site-packages/nose/util.py, line
331, in resolve_name
obj = getattr(obj, part)
AttributeError: 'module' object has no attribute 'test_backend_svg'
(etc.)
#
The failure is for all modules in matplotlib.tests except for test_agg,
test_cbook, test_mlab, and test_transform.
Is the sourceforge achive incomplete?
-Dave
--
David Welch
david.m.we...@gmail.com
--
Dept. of Psychiatry
Dept. of Biomedical Engineering
University of Iowa
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Re: [Matplotlib-users] Matplotlib.tests sub-modules missing
Update: test folders are in the build directory, they are just not
being copied during build.
*bump*
On 11/10/11, David Welch david.m.we...@gmail.com wrote:
Hello,
I am installing matplotlib on Snow Leopard 10.6. I downloaded v1.1.0 from
the sourceforge site and installed in this manner:
$ export CFLAGS=-arch i386 -arch x86_64 -I/usr/X11/include
-I/usr/X11/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk
$ export LDFLAGS=-Wall -undefined dynamic_lookup -bundle -arch i386 -arch
x86_64 -L/usr/X11/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk
$ export FFLAGS=-arch i386 -arch x86_64
$ tar -xf matplotlib-1.1.0.tar.gz
$ cd matplotlib-1.1.0
$ python setup.py build
$ python setup.py install
$
$ python
import matplotlib as mpl
mpl.test(1)
...EEE
==
ERROR: Failure: AttributeError ('module' object has no attribute
'test_backend_svg')
--
Traceback (most recent call last):
File /private/tmp/test/lib/python2.6/site-packages/nose/loader.py, line
379, in loadTestsFromName
module = resolve_name(addr.module)
File /private/tmp/test/lib/python2.6/site-packages/nose/util.py, line
331, in resolve_name
obj = getattr(obj, part)
AttributeError: 'module' object has no attribute 'test_backend_svg'
(etc.)
#
The failure is for all modules in matplotlib.tests except for test_agg,
test_cbook, test_mlab, and test_transform.
Is the sourceforge achive incomplete?
-Dave
--
David Welch
david.m.we...@gmail.com
--
Dept. of Psychiatry
Dept. of Biomedical Engineering
University of Iowa
--
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[Matplotlib-users] Matplotlib.tests sub-modules missing
Hello,
I am installing matplotlib on Snow Leopard 10.6. I downloaded v1.1.0 from the
sourceforge site and installed in this manner:
$ export CFLAGS=-arch i386 -arch x86_64 -I/usr/X11/include
-I/usr/X11/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk
$ export LDFLAGS=-Wall -undefined dynamic_lookup -bundle -arch i386 -arch
x86_64 -L/usr/X11/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk
$ export FFLAGS=-arch i386 -arch x86_64
$ tar -xf matplotlib-1.1.0.tar.gz
$ cd matplotlib-1.1.0
$ python setup.py build
$ python setup.py install
$
$ python
import matplotlib as mpl
mpl.test(1)
...EEE
==
ERROR: Failure: AttributeError ('module' object has no attribute
'test_backend_svg')
--
Traceback (most recent call last):
File /private/tmp/test/lib/python2.6/site-packages/nose/loader.py, line
379, in loadTestsFromName
module = resolve_name(addr.module)
File /private/tmp/test/lib/python2.6/site-packages/nose/util.py, line 331,
in resolve_name
obj = getattr(obj, part)
AttributeError: 'module' object has no attribute 'test_backend_svg'
(etc.)
#
The failure is for all modules in matplotlib.tests except for test_agg,
test_cbook, test_mlab, and test_transform.
Is the sourceforge achive incomplete?
-Dave
--
David Welch
david.m.we...@gmail.com
--
RSA(R) Conference 2012
Save $700 by Nov 18
Register now
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Re: [Matplotlib-users] how would you do this (animated bargraph) (Neal Becker)
Neal, I do something similar to this where data that I'm plotting in a 2D line plot comes from a UDP socket and some memory mapped files. To accomplish the live updating I have a mix of your #2 and #3. I have a main GUI thread that displays the plots, then I have a second thread that gets data from a python generator and signals the GUI thread when that new data has arrived. Inside the generator is where I have socket communications and select calls. Hope this helps. -Dave On 9/30/11 9:10 AM, matplotlib-users-requ...@lists.sourceforge.net wrote: Message: 4 Date: Fri, 30 Sep 2011 07:37:49 -0400 From: Neal Beckerndbeck...@gmail.com Subject: [Matplotlib-users] how would you do this (animated bargraph) To:matplotlib-users@lists.sourceforge.net Message-ID:j649me$ug4$1...@dough.gmane.org Content-Type: text/plain; charset=ISO-8859-1 I just put together an animated bargraph to show results from a realtime process. I used this as an example: http://matplotlib.sourceforge.net/examples/animation/animation_blit_qt4.html The tricky part for me was that in the original design, there was a realtime process running. I have to write some information to my hardware (at a rate of about 1/360ms). To do this, I have a kernel driver that uses 'read' to tell the user space when an interrupt has occurred, which is when the user space should write new information to the hardware. So I don't know how or if this could be hooked into qt event processing. Just for a quick-and-dirty demo, I just removed the realtime processing from the user-space and put it in the kernel driver, so now my bargraph display can simply update on a periodic timer, and the userspace code has no realtime requirement. But this is just a kludge. So I wonder how other's would solve this? I'm thinking it would be either: 1) multi-process 2) multi-thread 3) 1 process, but somehow hook my realtime events into qt's event loop. For #3, my device driver has a filedescriptor, that could use select to detect the interrupt (rather than blocking read call). #1 and #2 seem complicated. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] OS X 10.6.8 macports python2.6 64bit , Installing matplotlib fails.
I eventually got it to mostly work using: ³sudo port install py26-matplotlib @1.0.1 +gtk2² It doesn't match the correct egg format it seems, but it does work. On 8/10/11 11:01 AM, David Just just.da...@mayo.edu wrote: Hello, I¹ve been trying to install matplotlib correctly for the past couple of days. I¹m using a macports python2.6 built with +universal on. If I install with the the downloadable .egg file I end up with a message that states that _path.so has problems. (built for 32bit I guess) ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2 .6/site-packages/matplotlib-1.0.1_r0-py2.6.egg/matplotlib/_path.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site -packages/matplotlib-1.0.1_r0-py2.6.egg/matplotlib/_path.so: no matching architecture in universal wrapper If I install with easy_install-2.6 matplotlib from source I get the following: Best match: matplotlib 0.91.1 src/_image.cpp:952: error: png_infopp_NULL¹ was not declared in this scope error: Setup script exited with error: command '/usr/bin/gcc-4.2' failed with exit status 1 If I install with port install matplotlib it fails because the install in not the correct path structure in the site-packages folder. I¹ve tried searching the web and have found some indications that I need to install 32bit python 2.6 but cannot find how to do that, and all of my production machinese have 64bit python installed on them. Any help at this point would be appreciated. Thanks. -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Best way to cycle through numpy images using scroll?
I have an array of images stored as an array of numpy arrays. I need to be able to efficiently scroll through that set of images. My first attempt at doing this goes something like this: --init-- self.ax = pyplot.imshow(imgdta[0], interpolation='spline36', cmap=cm.gray, picker=True) # draw the plot @UndefinedVariable pyplot.axes().set_axis_off() self.fig = self.ax.get_figure() self.canvas = FigureCanvasGTKAgg(self.fig) --onscroll-- self.ax.set_array(imdta[n]) # 0 n num_images self.canvas.draw() This method of changing the image data does not seem to be very preferment. It takes ~.25 seconds to go from one image to the next. Can anybody suggest a faster way? This also ends up in a canvas that¹s much larger than I need, is there a better way to define my view area? Thank you, Dave. -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] OS X 10.6.8 macports python2.6 64bit , Installing matplotlib fails.
Hello, I¹ve been trying to install matplotlib correctly for the past couple of days. I¹m using a macports python2.6 built with +universal on. If I install with the the downloadable .egg file I end up with a message that states that _path.so has problems. (built for 32bit I guess) ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pytho n2.6/site-packages/matplotlib-1.0.1_r0-py2.6.egg/matplotlib/_path.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/matplotlib-1.0.1_r0-py2.6.egg/matplotlib/_path.so: no matching architecture in universal wrapper If I install with easy_install-2.6 matplotlib from source I get the following: Best match: matplotlib 0.91.1 src/_image.cpp:952: error: png_infopp_NULL¹ was not declared in this scope error: Setup script exited with error: command '/usr/bin/gcc-4.2' failed with exit status 1 If I install with port install matplotlib it fails because the install in not the correct path structure in the site-packages folder. I¹ve tried searching the web and have found some indications that I need to install 32bit python 2.6 but cannot find how to do that, and all of my production machinese have 64bit python installed on them. Any help at this point would be appreciated. Thanks. -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Forcing the size of a figure
Now that I¹m pre-building all my enlarged interpolated images to scroll through, I¹m having trouble forcing the figure/FigureCanvas to be the size I want. I¹m trying: fig.set_size_inches(768 / 72.0, 768 / 72.0), but it ends up the same size as the default plot. Thanks, Dave -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-dev2dev___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Best way to cycle through numpy images
Sorry if this get¹s re-posted, my earlier e-mail didn¹t seem to go through. I have an array of images stored as an array of numpy arrays. I need to be able to efficiently scroll through that set of images. My first attempt at doing this goes something like this: --init-- self.ax = pyplot.imshow(imgdta[0], interpolation='spline36', cmap=cm.gray, picker=True) # draw the plot @UndefinedVariable pyplot.axes().set_axis_off() self.fig = self.ax.get_figure() self.canvas = FigureCanvasGTKAgg(self.fig) --onscroll-- self.ax.set_array(imdta[n]) # 0 n num_images self.canvas.draw() This method ends up re-interpolating the image on each scroll event (which takes SIGNIFICANT time). What I¹d like to do is pre-build the images and then just change what image is displayed on the canvas on each scroll event. I cannot seem to figure out how to do this. Can anybody give me a pointer in the right direction. Thanks, Dave. -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-dev2dev___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
