Re: [Matplotlib-users] import pylab produces rounding error
If you cannot open the display, most likely it is because either you are running as root (bad, bad) or you are running over a remot connection (ssh) and do not have X11 forwarding properly enabled or configures. If you want to use mpl with an interactive window, you will need to have access to the display. The fact that you see this error only on the first time you import pylab is typical of exceptions that are thrown at module import time -- python only tries to import once so you see the exception only once. To solve this, trying running as a normal user rather than root or sudo, and if you are on a remote machine, try using ssh -X to enable X11 forwarding. We will need to know more about exactly what you are doing to help. For remote access you also need to allow the remote machine to access the display via xhost +name on the local machine. Well, I can assure you that I am neither working as root, I might be a newbie to matplotlib but not to linux, nor have any problem with the display. This problem is happening in both machines, remote (ssh -X, for sure, I've tested several times) and local, so no ssh conection. Anyway, I'm going to test a few more things and will let you know what happens. AR - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] animated hexbin plot
Chee Sing Lee wrote: Hello, I'm pretty new to matplotlib, so please bear with me. I am writing an application that includes a hexagonally binned scatter plot that updates periodically, up to a couple times a second. My current approach is clearing axes.collections, calling hexbin() with the updated data, and then calling canvas.draw(). It works, but it is entirely too slow. I would like to implement the blitting animation technique shown in the matplotlib cookbook, but the collection object returned by hexbin() doesn't seem to have any sort of set_data method to update the data. Any suggestions? My guess is that the entire hexbin method is fundamentally slow. Among other things, it is looping through all input values in python. In addition, the rendering, using a poly collection, is similar to pcolor, and that is also slow when the number of polygons is large. Profiling a run of hexbin might show whether there are obvious opportunities to speed it up. Eric I am using the wxPython GUI tookit, and FigureCanvasWxAgg. Thanks, Chee Sing Lee - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] ocean profile
I'd love to see it included to -- I believe the problem is finding a good code that is BSD compatible. Yes. Some examples on plotting data using spatial interpolation would be very nice. One with the delauny package: see below at: http://scipy.org/scipy/scikits/ And one with griddata: http://code.google.com/p/griddata-python/ We could use the accepted data sets from http://www.itc.nl/personal/rossiter/teach/lecnotes.html#l6 I have tested the griddata package but didn't reach very far due to other task to be accomplished earlier. Kind regards, Timmie - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] import pylab produces rounding error
On Thu, Jul 17, 2008 at 1:22 AM, Angela Rivera Campos [EMAIL PROTECTED] wrote: Well, I can assure you that I am neither working as root, I might be a newbie to matplotlib but not to linux, nor have any problem with the display. This problem is happening in both machines, remote (ssh -X, for sure, I've tested several times) and local, so no ssh conection. Anyway, I'm going to test a few more things and will let you know what happens. Very strange indeed -- the error clear indicates you cannot connect to the display. You should see the same in the same nvironment if you simply import gtk as the first line. Do you? JDH - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Error when running multiple jobs utilizing the Tex utilities in matplotlib
On Wednesday 16 July 2008 07:20:59 am Ian Harry wrote:
[EMAIL PROTECTED] 07:14 AM matplotlib]$ diff texmanager.py
/usr/lib64/python2.4/site-packages/matplotlib/texmanager.py
248c248
fh = file(outfile,'a')
---
fh = file(outfile)
252,254c252
else:
try: verbose.report(fh.read(), 'debug')
except: pass
---
else: verbose.report(fh.read(), 'debug')
259,261c257,258
else:
try: os.remove(fname)
except: pass
---
else: os.remove(fname)
280c277
fh = file(outfile,'a')
---
fh = file(outfile)
285,287c282
else:
try: verbose.report(fh.read(), 'debug')
except: pass
---
else: verbose.report(fh.read(), 'debug')
289,290c284
try: os.remove(outfile)
except: pass
---
os.remove(outfile)
314c308
# else: verbose.report(fh.read(), 'debug')
---
else: verbose.report(fh.read(), 'debug')
--snip--
I took a different approach:
Index: lib/matplotlib/texmanager.py
===
--- lib/matplotlib/texmanager.py(revision 5771)
+++ lib/matplotlib/texmanager.py(working copy)
@@ -273,16 +273,22 @@
%(os.path.split(texfile)[-1], outfile))
mpl.verbose.report(command, 'debug')
exit_status = os.system(command)
-fh = file(outfile)
+try:
+fh = file(outfile)
+report = fh.read()
+fh.close()
+except IOError:
+report = 'No latex error report available.'
if exit_status:
raise RuntimeError(('LaTeX was not able to process the
following \
-string:\n%s\nHere is the full report generated by LaTeX: \n\n'% repr(tex)) +
fh.read())
-else: mpl.verbose.report(fh.read(), 'debug')
-fh.close()
+string:\n%s\nHere is the full report generated by LaTeX: \n\n'% repr(tex)) +
report)
+else: mpl.verbose.report(report, 'debug')
for fname in glob.glob(basefile+'*'):
if fname.endswith('dvi'): pass
elif fname.endswith('tex'): pass
-else: os.remove(fname)
+else:
+try: os.remove(fname)
+except OSError: pass
return dvifile
@@ -305,14 +311,19 @@
os.path.split(dvifile)[-1], outfile))
mpl.verbose.report(command, 'debug')
exit_status = os.system(command)
-fh = file(outfile)
+try:
+fh = file(outfile)
+report = fh.read()
+fh.close()
+except IOError:
+report = 'No dvipng error report available.'
if exit_status:
raise RuntimeError('dvipng was not able to \
process the flowing file:\n%s\nHere is the full report generated by dvipng: \
-\n\n'% dvifile + fh.read())
-else: mpl.verbose.report(fh.read(), 'debug')
-fh.close()
-os.remove(outfile)
+\n\n'% dvifile + report)
+else: mpl.verbose.report(report, 'debug')
+try: os.remove(outfile)
+except OSError: pass
return pngfile
Would you update from svn and see if it works for you?
Thanks,
Darren
-
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Re: [Matplotlib-users] ocean profile
On Wed, Jul 16, 2008 at 6:59 PM, Alan G Isaac [EMAIL PROTECTED] wrote: I assume you know of Robert Kern's code? URL:http://cours-info.iut-bm.univ-fcomte.fr/docs/python/scipy/scipy.sandbox.delaunay-module.html I was aware of the project but always assumed he was relying on some GPL/LGPL code since it wasn't in scipy proper, but I now see this is not the case. I just talked with Jeff Whitaker who wrote the griddata functionality on top of NCAR's natgrid (GPL), and he expressed a willingness to port his code to use Robert's code, which we could include in mpl. Robert, what is the reason this hasn't gone into scipy proper, and do you see any problems with us folding it into mpl for use by griddata? Thanks, JDH - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] twinx memory leak
Anyone have any thoughts on this? It seems like it's serious enough to try to resolve before the next bugfix release. Cheers, Mike Michael Droettboom wrote: Yes, it should be. I'm further puzzled that removing del Gcf.figs[num] prevents the memory leak. There is some side effect that happens when all of the figures have been closed (I think it shuts down the GUI mainloop), that keeping at least one figure around at all times avoids. But I haven't been able to get to the bottom of that, just a half-supported theory at this point. Cheers, Mike laurent oget wrote: I am puzzled. Wasn't the whole point of close() to avoid memory leaks? Laurent 2008/7/15 Michael Droettboom [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Yes, as of r5747 twinx (well, shared axes specifically) no longer leaks. Manuel has discovered a seemingly generic leak that occurs when pyplot.close() is called and running a GUI backend. I can confirm his results with the script he last sent. Cheers, Mike Manuel Metz wrote: John Hunter wrote: On Mon, Jul 14, 2008 at 3:05 PM, Michael Droettboom [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: I can confirm this. Commenting out del Gcf.figs[num] in Gcf.destroy (in _pylab_helpers.py) also seems to resolve the leak. But I have no idea why, so I won't commit it just yet. I don't have much time to look deeper now. Does anyone (who probably understands figure management better than me) have an idea what might cause this? Can you post the script you are using to test -- I am a little confused from reading this thread by whether or not twinx is implicated. Also, I saw that you committed some changes vis-a-vis the twinx leak r5747 | mdboom | 2008-07-11 13:21:53 -0500 (Fri, 11 Jul 2008) | 2 lines Fix memory leak when using shared axes. so I thought that part was resolved already... JDH I use a modified version of the script Laurent Oget posted (see attachment). Here is the output if I don't comment out PL.close(1). ~/python/test$ python looptest.py -dGTK 0 GC 69354 69354 0 13854 100 GC 84354 150 0 15163 200 GC 99354 150 0 16306 300 GC 114354 150 0 17364 400 GC 129354 150 0 18576 ~/python/test$ python looptest.py -dTK 0 GC 69521 69521 0 14065 100 GC 84521 150 0 15444 200 GC 99521 150 0 16581 300 GC 114521 150 0 17719 400 GC 129521 150 0 18715 ~/python/test$ python looptest.py -dPS 0 GC 59307 59307 0 7705 100 GC 59307 0 0 8037 200 GC 59307 0 0 8038 300 GC 59307 0 0 8038 400 GC 59307 0 0 8038 (so for the window-less backend PS no objects are left) And now I commented out the line PL.close(1): ~/python/test$ python looptest.py -dGTK 0 GC 69379 69379 0 13855 100 GC 69379 0 0 14253 200 GC 69379 0 0 14253 300 GC 69379 0 0 14253 400 GC 69379 0 0 14252 Manuel -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net mailto:Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] twinx memory leak
On Thu, Jul 17, 2008 at 12:42 PM, Michael Droettboom [EMAIL PROTECTED] wrote: Anyone have any thoughts on this? It seems like it's serious enough to try to resolve before the next bugfix release. I think what we are seeing here is the known GUI figure canvas leak (Michael, I think our offlist conversation about mainquit was a red herring since removing that call doesn't help). We have found in the past that creation of gtk canvases and tk canvases leak and this is outside mpl. The reason that commenting out del Gcf.figs[num] fixes the leak because it causes pyplot to simply reuse the figure rather than re-call new_figure_manager. The chain of logic _pylab_helpers.Gcf: def get_fig_manager(num): figManager = Gcf.figs.get(num, None) if figManager is not None: Gcf.set_active(figManager) return figManager pyplot.figure figManager = _pylab_helpers.Gcf.get_fig_manager(num) if figManager is None: if get_backend().lower() == 'ps': dpi = 72 figManager = new_figure_manager(num, figsize=figsize, dpi=dpi, facecolor=facecolor, edgecolor=edgecolor, frameon=frameon, FigureClass=FigureClass, **kwargs) so when you do not del the figure number, the manager still lives in the dictionary in Gcf and is returned by _pylab_helpers.Gcf.get_fig_manager(num), and so subsequent calls to new_figure_manager are not triggered (so the figure is not really closed...) So there is a bug here, but I am not sure it is in mpl -- I think it is more likely to be in the GUI toolkits themselves, as we do not see them in any of the mpl image backends. I don't think we need to hold a release on this, since it is a known and existing problem with no obvious mpl solution, though getting a reproducible test case that just used the GUI code for submission to pygtk, tkinter, etc... would be useful. JDH Michael and I just talked through this offlist, and it appears that what is happening is that form any of the interactive backends, the trigger to stop the GUI mainloop is when all the figures have been closed. The typical use case in a script is to raise several GUI figures and the program exits when all of them have been closed. pylab otherwise doesn't know when to quit and return the shell prompt. The backend first checks to see if you are in interactive mode, and does not call main quit if you are, so this doesn't affect folks using mpl in an ipython shell or other interactive sessions. The only use case where it should arise is like the one in looptest, where a script creates a GUI figure and then closes it in non-interactive mode. Although there is a use case where this makes sense (eg if we had a blocking show) where one would create a figure, raise it, block, close it, rinse and repeat, this mode is not currently supported in pylab (show would need to be smarter, though with our new blocking input functions we might be able to attempt this). This also does not affect applications since the close/destroy handling is a pyplot construct. Michael pointed out that the twinx problem was separate (and fixed) so is unrelated to the close bug and can be removed from the looptest test script. There is a workaround for those who really need this functionality, although it is unsupported currently, and that is simply to wrap the close call in ion/ioff function calls to turn interaction on. The interactive backends won't attempt to call mainquit if interactive mode is on, so PL.ion() PL.close(1) PL.ioff() blocks this leak - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] small scatter plot color bug
It seems like this should be possible: ax.scatter(x, y, c=None) but axes chokes on the c=None parameter. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] small scatter plot color bug
On Thu, Jul 17, 2008 at 1:53 PM, Ben Axelrod [EMAIL PROTECTED] wrote: It seems like this should be possible: ax.scatter(x, y, c=None) Just use plot(x, y, 'o') or whatever marker you want, and set the markersize. scatter is meant for plots where either the marker size or marker color vary. plot handles homogeneous markers. JDH - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] difference between plot and scatter
It seems that axes.plot() handles 'None' values in the input arrays gracefully by just not plotting that point. But axes.scatter() bugs out. Can this be fixed? Thanks, -Ben - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] difference between plot and scatter
On Thu, Jul 17, 2008 at 2:35 PM, Ben Axelrod [EMAIL PROTECTED] wrote: It seems that axes.plot() handles 'None' values in the input arrays gracefully by just not plotting that point. But axes.scatter() bugs out. Can this be fixed? We try to support np.nan and np masked arrays to handle missing data. The fact that None works with plot is a fortuitous consequence of the fact that numpy converts None-NaN on a coercion to float, but it is not something we plan on trying to support explicitly. You can easily write your own none_to_nan function def none_to_nan(seq): return np.asarray(seq, float) and if nans are failing we'll treat it as a bug in mpl JDH - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] ploting a contour graph from data files
Michael Droettboom wrote: Oz Nahum wrote: I am mostly frustrated with documentation writers who write very nice tutorials describing how to plot completely unusfull graphs of spheres inside loops and a dolphin swimming in the middle. I'm sorry. I just couldn't resist writing a tutorial example for this. Please take it in the spirit of fun it was intended. That's freaking hilarious. Someone clearly has too much time on their hands. (Yeah right.) Goes to show the power of matplotlib though. Nice one. Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Can I update symbol positions and colors in a collection?
Eric Bruning wrote: I have scatterplots on several axes that are dynamically updated, and thus I need to keep track of each of the PolyCollection artists that represent the scattered data. I would like to keep the same PolyCollection object but update the positions, colors, etc. of the symbols, possibly changing their total number, something along the lines of Line.set_data. Did I miss a method that would do what I want? I have already looked at removing the collection from the axes and replotting, but for some reason my axis limits get reset when I do so. Guys, I helped Eric out with this offline, and obviously set_array is for the colors, but the only solution we could come up with was to directly reset the PolyCollection._offsets member. This seems a little hacky. Is there any reason that there is not an set_offsets() (or something like it)? Any reason why I shouldn't code up a patch? Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Can I update symbol positions and colors in a collection?
On Thu, Jul 17, 2008 at 10:28 PM, Ryan May [EMAIL PROTECTED] wrote: I helped Eric out with this offline, and obviously set_array is for the colors, but the only solution we could come up with was to directly reset the PolyCollection._offsets member. This seems a little hacky. Is there any reason that there is not an set_offsets() (or something like it)? Any reason why I shouldn't code up a patch? No, I can't thing of any reason why this attribute should not be publicly settable, so patch away. Thanks, JDH - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
