[Matplotlib-users] suspect memory leak in Agg backend
Hi all guys, I'm experiencing a problem with automatic generation of .png figure using Agg backend. What i do is opening, saving and closing figure in a for statement without showing them up. Let's say approximatively 400 figures for a total of 160 MB disk space. I do not use an interactive shell. Sometimes (not always) i get an error message saying that is impossible to allocate new memory. So, can it be a memory leak problem in Agg backend ? I use Python 2.3 and maptplotlib 0.87.6 on a Linux HPC5 2.6.9-42.0.2.ELhugemem #1 SMP Thu Aug 17 18:22:52 EDT 2006 i686 athlon i386 GNU/Linux -- -- Emanuele Passera - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Problems with auto scaling with infinite values
Hi all, If I try to plot a graph with some y-values as -inf (which is very common in physical sciences as we often take log10 of amplitude values which can be zero), then matplotlib raises an exception: /usr/lib/python2.5/site-packages/matplotlib/ticker.py in scale_range(vmin, vmax, n, threshold) 814 offset = 10**ex 815 else: -- 816 ex = divmod(math.log10(-meanv), 1)[0] 817 offset = -10**ex 818 ex = divmod(math.log10(dv/n), 1)[0] type 'exceptions.OverflowError': math range error It is clear where the problem is, matplotlib takes log10 of the mean y-range (in this case infinity) to auto scale the y-axis. I know I can modify my input values to get around this problem, but it is so common to want to plot data (some of which may be zero) in say a decibel scale, that having a workaround for the case of -inf input would be nice. I tried to look into writing one myself, but got quickly lost. If someone could point me at the files/functions I should look at I will have a go. Hope somebody can help! Best regards, John Travers - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] suspect memory leak in Agg backend
On 7/13/07, Emanuele Passera [EMAIL PROTECTED] wrote: Hi all guys, I'm experiencing a problem with automatic generation of .png figure using Agg backend. What i do is opening, saving and closing figure in a for statement without showing them up. Let's say approximatively 400 figures for a total of 160 MB disk space. I do not use an interactive shell. Sometimes (not always) i get an error message saying that is impossible to allocate new memory. So, can it be a memory leak problem in Agg backend ? Take a look at unit/memleak_hawaii3.py. Does it leak on your system? If not (and it does not appear to be on ourson ours), maybe you can compare what is different and try and isolate the part that is leaking. http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/trunk/matplotlib/unit/memleak_hawaii3.py?view=markup JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] memory leak in Agg backend
Hi all, a few hours ago I have wtitten for a possible memory leak in Agg backend. It was my fault. It was a bad placement of matplotlibrc file. Sorry for the raised alarm. Instead i am glad to say that I have checked for the Agg backend with a for statement of opening a figure, drawing, saving and closing and a real time monitoring of machine memory used and I can say that has not a memory leak. -- -- Emanuele Passera - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problems with auto scaling with infinite values
On Friday 13 July 2007 09:13:03 am John Travers wrote: Hi all, If I try to plot a graph with some y-values as -inf (which is very common in physical sciences as we often take log10 of amplitude values which can be zero), then matplotlib raises an exception: /usr/lib/python2.5/site-packages/matplotlib/ticker.py in scale_range(vmin, vmax, n, threshold) 814 offset = 10**ex 815 else: -- 816 ex = divmod(math.log10(-meanv), 1)[0] 817 offset = -10**ex 818 ex = divmod(math.log10(dv/n), 1)[0] type 'exceptions.OverflowError': math range error It is clear where the problem is, matplotlib takes log10 of the mean y-range (in this case infinity) to auto scale the y-axis. I know I can modify my input values to get around this problem, but it is so common to want to plot data (some of which may be zero) in say a decibel scale, that having a workaround for the case of -inf input would be nice. I tried to look into writing one myself, but got quickly lost. If someone could point me at the files/functions I should look at I will have a go. I think this might trace back to Interval.get_bounds() in src/_transforms.h. Maybe we could consider an additional Interval method like Interval.get_finite_bounds(), which could do something like numpy's isfinite function to filter values that can not be plotted. But I'm not an expert on mpl's transforms, so perhaps someone more knowledgeable can comment. Darren - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] suspect memory leak in Agg backend
I'm been looking at a lot of memory leaks as of late, but have not come across any in the Agg backend. Can you send a snippet of code that reproduces your error? Perhaps there is some particular operation or set of operations that triggers a leak. Cheers, Mike Emanuele Passera wrote: Hi all guys, I'm experiencing a problem with automatic generation of .png figure using Agg backend. What i do is opening, saving and closing figure in a for statement without showing them up. Let's say approximatively 400 figures for a total of 160 MB disk space. I do not use an interactive shell. Sometimes (not always) i get an error message saying that is impossible to allocate new memory. So, can it be a memory leak problem in Agg backend ? I use Python 2.3 and maptplotlib 0.87.6 on a Linux HPC5 2.6.9-42.0.2.ELhugemem #1 SMP Thu Aug 17 18:22:52 EDT 2006 i686 athlon i386 GNU/Linux - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problems with auto scaling with infinite values
On Friday 13 July 2007 10:32:15 am John Hunter wrote: On 7/13/07, Darren Dale [EMAIL PROTECTED] wrote: I think this might trace back to Interval.get_bounds() in src/_transforms.h. Maybe we could consider an additional Interval method like Interval.get_finite_bounds(), which could do something like numpy's isfinite function to filter values that can not be plotted. But I'm not an expert on mpl's transforms, so perhaps someone more knowledgeable can comment. I'm happy to do this, if someone can advise how to get a portable isinf. [...] I would be happy to import it from numpy (since we can now rely on it, woohoo) but am having trouble here too If we can figure out how to get it from numpy, we can use numpy's isnan as well, and drop that bit of extension code from mpl's sources. I see isfinite defined in umathmodule.c.src (and also in ufuncobject.h but only for _MSC_VER. If anyone can advise on how to get isinf or isfinite, pease do. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problems with auto scaling with infinite values
On 7/13/07, Darren Dale [EMAIL PROTECTED] wrote: I think this might trace back to Interval.get_bounds() in src/_transforms.h. Maybe we could consider an additional Interval method like Interval.get_finite_bounds(), which could do something like numpy's isfinite function to filter values that can not be plotted. But I'm not an expert on mpl's transforms, so perhaps someone more knowledgeable can comment. I'm happy to do this, if someone can advise how to get a portable isinf. I tried including math.h after reading http://www.google.com/url?sa=tct=rescd=1url=http%3A%2F%2Fwww.opengroup.org%2Fonlinepubs%2F009695399%2Ffunctions%2Fisinf.htmlei=wYqXRr7IAovwiwHolJn2Bwusg=AFQjCNGAlh-XN0EWgSuTSEsOLPLNCiTxNwsig2=KAxpuLGHMuqoeGtzTz85YQ but the symbol isn't found there on my system. I would be happy to import it from numpy (since we can now rely on it, woohoo) but am having trouble here too I see isfinite defined in umathmodule.c.src (and also in ufuncobject.h but only for _MSC_VER. If anyone can advise on how to get isinf or isfinite, pease do. JDH - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Properly aligned tick labels on the inside
For the archives (and further proof that programming done during the
witching hour between 4pm and 5pm should be avoided at all costs):
The solution is easy.
for tick in axes.yaxis.get_major_ticks():
tick.set_pad(-25)
tick.label2.set_horizontalalignment('right')
A
-Original Message-
From: Anthony M. Floyd
Sent: July 12, 2007 4:37 PM
To: matplotlib-users@lists.sourceforge.net
Subject: [Matplotlib-users] Properly aligned tick labels on the inside
Hi All,
I'm trying to plot tick labels on the inside (ie data side)
of a typical x-y plot. My setup is Python 2.5.1, matplotlib
0.90.0 on WinXP.
I've been able to accomplish this by adjusting the padding of
the individual ticks, but it doesn't quite accomplish what I want.
For example, imagine a typical x-y plot, except that the tick
labels are on the right-hand side (by setting
axes.yaxis.tick_right()). Adjusting the padding of the ticks
by doing:
for tick in axes.yaxis.get_major_ticks():
tick.set_pad(-25)
I'm able to get the numbers to appear about where I want.
The problem is that these numbers are left aligned. So, it
works fine for small numbers, but for large numbers, or when
my tick formatter switches over to using scientific notation
the numbers will overlap the axis. If my labels are on the
inside of the right-hand side, I want them to be
right-aligned and grow left towards the centre of the plot.
I thought about doing it by setting tick_left() and then
using a (large) computed pad, but then the tick lines are on
the wrong side.
So, my question is: can I get right-aligned tick labels on
the right-side of a plot? How?
I suspect I can do this by using
axis.set_offset_position('...'), but I've been unable to get
that to do anything in my tests using pylab.
I can post code if it'll be helpful.
Thanks,
Anthony.
--
Anthony Floyd, PhD
Convergent Manufacturing Technologies Inc.
6190 Agronomy Rd, Suite 403
Vancouver BC V6T 1Z3
CANADA
Email: [EMAIL PROTECTED] | Tel: 604-822-9682
WWW: http://www.convergent.ca| Fax: 604-822-9659
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Re: [Matplotlib-users] Problems with auto scaling with infinite values
Darren Dale wrote: If we can figure out how to get it from numpy, we can use numpy's isnan as well, and drop that bit of extension code from mpl's sources. Done in r3512. Hurray for inclusion instead of code duplication. (I originally copied that stuff from numarray, which inspired numpy's design of that stuff, but since back then would couldn't depend on either...) On Friday 13 July 2007 10:32:15 am John Hunter wrote: I'm happy to do this, if someone can advise how to get a portable isinf. Also in r3512, I inserted the definition of isfinite, copied from numpy's umathmodule.c.src at the top of _transforms.cpp. If it works for numpy, it should work for us. I'm slightly worried that this stuff will break on MSVC... Does anyone have the ability to test this svn revision sooner than later? -Andrew - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
