Re: [Matplotlib-users] Unknown projection '3d' even with svn version?
Ok problem(s) solved, thanks a lot for the efficient help (this also taught me how to go through the code more thoroughly) * for the record: I had a pylab.py in the site-packages directory, probably a left-over from some other installation, which was interfering with the pylab.py which should be the one under matplotlib/. I just removed it now and it works well. * and you were right, the funny "try this" was a left over of many tests I had done to track down the problem (mea culpa on that one) thanks again, all works beautifully (and consistently) now. cheers Eric -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Matplotlib-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] colorbar settings with a object oriented approach (or mixed pyplot)
Folks, I was trying to use an object oriented approach to creating
colorbars, but I could manage to make it work. Currently I have close
to what I am trying to achieve, but the last bits are missing. The
outstanding issues are:
1) I only need one colorbar, how would I create a single colorbar on
the right that spanned across all axes? (ie. same height as the stack)
2) is there a way to place the colorbar in the bottom middle of my
panels (if I end up with more than one)?
3) How can I customize the tick labels of the colorbar?
4) Is this a 'pythonic' approach to begin with?
Here's my code, and a fake class that should provide the data needed
to use the example:
#!/usr/bin/env python
"""
Demo to help understand plotting tools
"""
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
class Fun(object):
""" Dummy class for testing
"""
class body:
pass
def __init__(self):
body = Fun.body
body.time = np.arange(1000)
body.alt = np.sin(body.time)
body.A = 360*np.random.random_sample(1000)-180
body.B = 180*np.random.random_sample(1000)-90
body.C = 90*np.random.random_sample(1000)-45
def plot_angles(F):
""" Plots the angles of body """
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
# Set up plotting environment colors
Nc = np.arange(-180,181,1)
norm = mpl.colors.normalize(Nc.min(),Nc.max())
fig, (ax1, ax2, ax3) = plt.subplots(3, sharex=True, sharey=True)
ax1.scatter(F.body.time,F.body.alt,c=F.body.A,norm=norm,label='A',edgecolor='none')
ax2.scatter(F.body.time,F.body.alt,c=F.body.B,norm=norm,label='B',edgecolor='none')
ax3.scatter(F.body.time,F.body.alt,c=F.body.C,norm=norm,label='C',edgecolor='none')
# Fine-tune figure; make subplots close to each other and hide x ticks for
# all but bottom plot.
fig.subplots_adjust(hspace=0)
plt.setp([a.get_xticklabels() for a in fig.axes[:-1]], visible=False)
for a in fig.axes:
ia = inset_axes(a,width="20%", height="5%", loc=4)
a.set_xlim(F.body.time[0],F.body.time[-1])
fig.add_subplot(a)
plt.colorbar(a.collections[0],cax=ia,orientation='horizontal')
ia.xaxis.set_ticks_position("top")
plt.draw()
return fig
def demo():
F = Fun()
plot_angles(F)
if __name__ == "__main__":
fig = demo()
plt.show()
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[Matplotlib-users] date plot with two y axes...and some other things
Goals: date plot with two y axes (plotting completely different things) point picking and point labeling As many lines as user wants, all colored differently. Having some problems with this. (matplotlib 0.98.5) 1) There is a known bug with twinx() and plot_date: http://sourceforge.net/tracker/index.php?func=detail&aid=3046812&group_id=80706&atid=560720 But I can get it to work if I change ONE OF the plot_date() calls (the one for the values plotted to the right-hand y axis) to just plot(). Is that going to introduce problems? Is there a better workaround? (The ones on that page don't work for me). 2) How can I get the lines belonging to different axes to cycle through colors such that the same color is not used for any lines shown in the plot? (that is, I don't want to hard code a color to any line, I want it to auto-cycle). 3) My point picking is not working with the two axes. In my routine, I label the picked point and to do that I have to make reference to its axis and call plot_date(). How can I know which axis the picked point came from, so that I can label it appropriately? Sorry this is a little stirred together, but hoping I can get some hints to allow me to work it into shape. Thanks, Che -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Matplotlib-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Possible memory leak?
Matplotlib Users:
It seems matplotlib plotting has a relatively small memory leak. My
experiments suggest it leaks between 5K and 8K bytes of RAM for ever plot
redraw. For example, in one experiment, plotting the same buffer (so as to
not
allocate new memory) every second for a period of about 12 hours resulted in
memory usage (physical RAM) increasing by approximately 223MB, which is
about
5.3K per replot. The plotting code is:
class PlotPanel(wx.Panel):
def __init__(self, parent):
wx.Panel.__init__(self, parent, wx.ID_ANY,
style=wx.BORDER_THEME|wx.TAB_TRAVERSAL)
self._figure = MplFigure(dpi=None)
self._canvas = MplCanvas(self, -1, self._figure)
self._axes = self._figure.add_subplot(1,1,1)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self._canvas, 1, wx.EXPAND|wx.TOP, 5)
self.SetSizer(sizer)
def draw(self, channel, seconds):
self._axes.clear()
self._axes.plot(channel, seconds)
self._canvas.draw()
`draw()` is called every second with the same `channels` and `seconds`
numpy.array buffers.
In my case, this leak, though relatively small, becomes a serious issue
since
my software often runs for long periods of time (days) plotting data
streamed
from a data acquisition unit.
Any suggestions will help. Am I miss understanding something here? Maybe I
need to call some obscure function to free memory, or something?
My testing environment:
* Windws XP SP3, Intel Core 2 Duo @ 2.33GHz, 1.96 GB RAM
* Python 2.6.6 (r266:84297, Aug 24 2010, 18:46:32) [MSC v.1500 32 bit
(Intel)] on win32
* matplotlib version 1.0.0
* numpy 1.4.1
* wxPython version 2.8.11.0
The complete test program follows.
Thanks,
Caleb
from random import random
from datetime import datetime
import os
import time
import win32api
import win32con
import win32process
import wx
import numpy
import matplotlib as mpl
from matplotlib.figure import Figure as MplFigure
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as MplCanvas
def get_process_memory_info(process_id):
memory = {}
process = None
try:
process = win32api.OpenProcess(
win32con.PROCESS_QUERY_INFORMATION|win32con.PROCESS_VM_READ,
False, process_id);
if process is not None:
return win32process.GetProcessMemoryInfo(process)
finally:
if process:
win32api.CloseHandle(process)
return memory
meg = 1024.0 * 1024.0
class PlotPanel(wx.Panel):
def __init__(self, parent):
wx.Panel.__init__(self, parent, wx.ID_ANY,
style=wx.BORDER_THEME|wx.TAB_TRAVERSAL)
self._figure = MplFigure(dpi=None)
self._canvas = MplCanvas(self, -1, self._figure)
self._axes = self._figure.add_subplot(1,1,1)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self._canvas, 1, wx.EXPAND|wx.TOP, 5)
self.SetSizer(sizer)
def draw(self, channel, seconds):
self._axes.clear()
self._axes.plot(channel, seconds)
self._canvas.draw()
class TestFrame(wx.Frame):
def __init__(self, parent, id, title):
wx.Frame.__init__(
self, parent, id, title, wx.DefaultPosition, (600, 400))
self.testDuration = 60 * 60 * 24
self.startTime = 0
self.channel = numpy.sin(numpy.arange(1000) * random())
self.seconds = numpy.arange(len(self.channel))
self.plotPanel = PlotPanel(self)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.plotPanel, 1 ,wx.EXPAND)
self.SetSizer(sizer)
self._timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self._onTimer, self._timer)
self._timer.Start(1000)
print "starting memory: ",\
get_process_memory_info(os.getpid())["WorkingSetSize"]/meg
def _onTimer(self, evt):
if self.startTime == 0:
self.startTime = time.time()
if (time.time() - self.startTime) >= self.testDuration:
self._timer.Stop()
self.plotPanel.draw(self.channel, self.seconds)
t = datetime.now()
memory = get_process_memory_info(os.getpid())
print "time: {0}, working: {1:f}".format(
t, memory["WorkingSetSize"]/meg)
class MyApp(wx.App):
def OnInit(self):
frame = TestFrame(None, wx.ID_ANY, "Memory Leak")
self.SetTopWindow(frame)
frame.Show(True)
return True
if __name__ == '__main__':
app = MyApp(0)
app.MainLoop()
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Re: [Matplotlib-users] Possible memory leak?
On Thu, Nov 18, 2010 at 1:11 PM, Caleb Constantine wrote:
> Matplotlib Users:
>
> It seems matplotlib plotting has a relatively small memory leak. My
> experiments suggest it leaks between 5K and 8K bytes of RAM for ever plot
> redraw. For example, in one experiment, plotting the same buffer (so as to
> not
> allocate new memory) every second for a period of about 12 hours resulted
> in
> memory usage (physical RAM) increasing by approximately 223MB, which is
> about
> 5.3K per replot. The plotting code is:
>
> class PlotPanel(wx.Panel):
> def __init__(self, parent):
> wx.Panel.__init__(self, parent, wx.ID_ANY,
> style=wx.BORDER_THEME|wx.TAB_TRAVERSAL)
> self._figure = MplFigure(dpi=None)
> self._canvas = MplCanvas(self, -1, self._figure)
> self._axes = self._figure.add_subplot(1,1,1)
>
> sizer = wx.BoxSizer(wx.VERTICAL)
> sizer.Add(self._canvas, 1, wx.EXPAND|wx.TOP, 5)
> self.SetSizer(sizer)
>
> def draw(self, channel, seconds):
> self._axes.clear()
> self._axes.plot(channel, seconds)
> self._canvas.draw()
>
>
> `draw()` is called every second with the same `channels` and `seconds`
> numpy.array buffers.
>
> In my case, this leak, though relatively small, becomes a serious issue
> since
> my software often runs for long periods of time (days) plotting data
> streamed
> from a data acquisition unit.
>
> Any suggestions will help. Am I miss understanding something here? Maybe I
> need to call some obscure function to free memory, or something?
>
> My testing environment:
>
> * Windws XP SP3, Intel Core 2 Duo @ 2.33GHz, 1.96 GB RAM
> * Python 2.6.6 (r266:84297, Aug 24 2010, 18:46:32) [MSC v.1500 32 bit
> (Intel)] on win32
> * matplotlib version 1.0.0
> * numpy 1.4.1
> * wxPython version 2.8.11.0
>
> The complete test program follows.
>
> Thanks,
>
> Caleb
>
>
> from random import random
> from datetime import datetime
> import os
> import time
> import win32api
> import win32con
> import win32process
>
> import wx
> import numpy
>
> import matplotlib as mpl
> from matplotlib.figure import Figure as MplFigure
> from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as
> MplCanvas
>
> def get_process_memory_info(process_id):
> memory = {}
> process = None
> try:
> process = win32api.OpenProcess(
> win32con.PROCESS_QUERY_INFORMATION|win32con.PROCESS_VM_READ,
> False, process_id);
> if process is not None:
> return win32process.GetProcessMemoryInfo(process)
> finally:
> if process:
> win32api.CloseHandle(process)
> return memory
>
> meg = 1024.0 * 1024.0
>
> class PlotPanel(wx.Panel):
> def __init__(self, parent):
> wx.Panel.__init__(self, parent, wx.ID_ANY,
> style=wx.BORDER_THEME|wx.TAB_TRAVERSAL)
> self._figure = MplFigure(dpi=None)
> self._canvas = MplCanvas(self, -1, self._figure)
> self._axes = self._figure.add_subplot(1,1,1)
>
> sizer = wx.BoxSizer(wx.VERTICAL)
> sizer.Add(self._canvas, 1, wx.EXPAND|wx.TOP, 5)
> self.SetSizer(sizer)
>
> def draw(self, channel, seconds):
> self._axes.clear()
> self._axes.plot(channel, seconds)
> self._canvas.draw()
>
> class TestFrame(wx.Frame):
> def __init__(self, parent, id, title):
> wx.Frame.__init__(
> self, parent, id, title, wx.DefaultPosition, (600, 400))
>
> self.testDuration = 60 * 60 * 24
> self.startTime = 0
>
> self.channel = numpy.sin(numpy.arange(1000) * random())
> self.seconds = numpy.arange(len(self.channel))
>
> self.plotPanel = PlotPanel(self)
>
> sizer = wx.BoxSizer(wx.VERTICAL)
> sizer.Add(self.plotPanel, 1 ,wx.EXPAND)
> self.SetSizer(sizer)
>
> self._timer = wx.Timer(self)
> self.Bind(wx.EVT_TIMER, self._onTimer, self._timer)
> self._timer.Start(1000)
> print "starting memory: ",\
> get_process_memory_info(os.getpid())["WorkingSetSize"]/meg
>
> def _onTimer(self, evt):
> if self.startTime == 0:
> self.startTime = time.time()
>
> if (time.time() - self.startTime) >= self.testDuration:
> self._timer.Stop()
>
> self.plotPanel.draw(self.channel, self.seconds)
>
> t = datetime.now()
> memory = get_process_memory_info(os.getpid())
> print "time: {0}, working: {1:f}".format(
> t, memory["WorkingSetSize"]/meg)
>
> class MyApp(wx.App):
> def OnInit(self):
> frame = TestFrame(None, wx.ID_ANY, "Memory Leak")
> self.SetTopWindow(frame)
> frame.Show(True)
> return True
>
> if __name__ == '__main__':
> app = MyApp(0)
> app.MainLoop()
>
>
>
Caleb,
Interesting analysis. One possible source of a leak would be some sort of
dangling refere
Re: [Matplotlib-users] Possible memory leak?
On Thu, Nov 18, 2010 at 2:20 PM, Benjamin Root wrote: > Interesting analysis. One possible source of a leak would be some sort of > dangling reference that still hangs around even though the plot objects have > been cleared. By the time of the matplotlib 1.0.0 release, we did seem to > clear out pretty much all of these, but it is possible there are still some > lurking about. We should probably run your script against the latest svn to > see how the results compare. In our experience, many of the GUI backends have some leak, and these are in the GUI and not in mpl. Caleb, can you see if you can replicate the leak with your example code using the agg backend (no GUI). If so, could you post the code that exposes the leak. if not, I'm afraid it is in wx and you might need to deal with the wx developers. JDH -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Matplotlib-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Possible memory leak?
On 11/18/10 5:05 PM, John Hunter wrote: > On Thu, Nov 18, 2010 at 2:20 PM, Benjamin Root wrote: > >> Interesting analysis. One possible source of a leak would be some sort of >> dangling reference that still hangs around even though the plot objects have >> been cleared. By the time of the matplotlib 1.0.0 release, we did seem to >> clear out pretty much all of these, but it is possible there are still some >> lurking about. We should probably run your script against the latest svn to >> see how the results compare. > > In our experience, many of the GUI backends have some leak, and these > are in the GUI and not in mpl. Caleb, can you see if you can > replicate the leak with your example code using the agg backend (no > GUI). If so, could you post the code that exposes the leak. if not, > I'm afraid it is in wx and you might need to deal with the wx > developers. Heh. Good timing! I just fixed a bug in Chaco involving a leaking cycle that the garbage collector could not clean up. The lesson of my tale of woe is that even if there is no leak when you run without wxPython, that doesn't mean that wxPython is the culprit. If any object in the connected graph containing a cycle (even if it does not directly participate in the cycle) has an __del__ method in pure Python, then the garbage collector will not clean up that cycle for safety reasons. Read the docs for the gc module for details. We use SWIG to wrap Agg and SWIG adds __del__ methods for all of its classes. wxPython uses SWIG and has the same problems. If there is a cycle which can reach a wxPython object, the cycle will leak. The actual cycle may be created by matplotlib, though. You can determine if this is the case pretty easily, though. Call gc.collect() then examine the list gc.garbage. This will contain all of those objects with a __del__ that prevented a cycle from being collected. I recommend using objgraph to diagram the graph of references to those objects. It's invaluable to actually see what's going on. http://pypi.python.org/pypi/objgraph -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Matplotlib-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] set font properties for colorbar
Hello, I see that for a legend you can do the following: ax = plt.scatter(x,y,label='test data') p_leg = mpl.font_manager.FontProperties(size='8') ax.legend(prop=p_leg) But, how do you do set font properties for the colorbar tick labels? Thanks! -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Matplotlib-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Control of thread/program not returning to ipython after creating a plot.
So I tried updating and rebuilding Matplotlib - no luck - something (at least on my system) is goofy with the GTK(Agg),WX(Agg), and Fltk(Agg) backends. But the TkAgg backend works great. So I will stick with that, but if anyone else sees this problem and it becomes an issue, I'd be happy to help debug it in any way I can. -C On Wed, 17 Nov 2010 19:46:34 -0600 Benjamin Root wrote: > On Wed, Nov 17, 2010 at 7:38 PM, Collin Day > wrote: > > > On Wed, 17 Nov 2010 19:00:54 -0600 > > Benjamin Root wrote: > > > > Another data point - > > > > I tried Qt4Agg - it also works interactively - ie it goes back to > > the ipython cmd line. I also noticed when I start ipython --pylab, > > the following error messages occur: > > > > ** Message: pygobject_register_sinkfunc is deprecated (GtkWindow) > > ** Message: pygobject_register_sinkfunc is deprecated (GtkInvisible) > > ** Message: pygobject_register_sinkfunc is deprecated (GtkObject) > > > > > Interesting. It is possible that the gtk backend might have been > compiled against gtk development libraries that do not match your > current gtk library. What have you updated recently, and how did you > do it? > > Ben Root -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Matplotlib-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/matplotlib-users
