Re: [Matplotlib-users] dpi
Jae-Joon Lee lee.j.joon-re5jqeeqqe8avxtiumw...@public.gmane.org writes: On Fri, Oct 12, 2012 at 3:39 AM, Nikolaus Rath nikolaus-bth8mxji...@public.gmane.org wrote: matplotlib actually rescales the raw imshow data when saving to a vector format? Why is that? I think it should embed the bitmap with full resolution in the vector file and rely on the consumer of the vector file to scale it to whatever resolution is supported by the display device. imshow supports interpolation and that's why rasterization comes in. If you turn off interpolation (w/ interpolation=none), the original image will be embedded. Of course dpi has no meaning in this case. However, I agree with you that dpi should be a property of the backend only, not the figure. But I am not sure if this can be fixed soon. It will be difficult and will take lots of effort I think. Yeah, that's what I feared. But in the mean time, are there any best practices to minimize undesired effects like the one above? For example, are there any other functions that need special parameters to not raster their output when writing to a vector format? And is there a way to get a figure on the screen with the right size when I don't know what dpi the monitor is running with? Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] dpi
Hello, I'm confused by the dpi property of figures that can be set in matplotlibrc or passed to pyplot.figure(). It seems to me that dpi is really a property of the backend, not the figure, and the only place to specify it ought to be when saving into a bitmap file. For example, when showing a figure on the screen, I really want matplotlib to use the physical dpi of the monitor rather than any default value. When saving the figure in some vector graphics format, I don't see what the meaning of the dpi is at all. Am I missing something? Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] dpi
Damon McDougall damon.mcdougall-re5jqeeqqe8avxtiumw...@public.gmane.org writes: On Thu, Oct 11, 2012 at 4:00 PM, Nikolaus Rath nikolaus-bth8mxji...@public.gmane.org wrote: When saving the figure in some vector graphics format, I don't see what the meaning of the dpi is at all. Sure, I use `dpi=` all the time for vector formats. Purely because when you make calls to `imshow`, you get a rasterised image embedded in a figure with vector text and tickmarks and labels, for example. matplotlib actually rescales the raw imshow data when saving to a vector format? Why is that? I think it should embed the bitmap with full resolution in the vector file and rely on the consumer of the vector file to scale it to whatever resolution is supported by the display device. Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Corrupted percent signs in labels
Benjamin Root ben.root-grryuj3d...@public.gmane.org writes:
For some reason, my matplotlib isn't able to print percent signs ('%')
properly:
[1] inspiron:~/tmp# cat mplbug.py
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
print matplotlib.__version__
plt.plot(np.arange(10), np.arange(10)**2)
plt.xlabel('Percent [%]')
plt.savefig('mplbug.pdf')
[0] inspiron:~/tmp# python mplbug.py
1.1.1rc2
I have attached the resulting PDF. For some reason, the slash in the
percent sign becomes a triangle that partially covers the upper left
circle.
Known bug? Any workarounds that don't require upgrading (I'd like to
stick with the Debian package)?
I'm using the AGG backend and saving to a png file without any
problems, but I'm using the current git master branch. I'll try to see
if I can recreate on 1.1.1rc2. Watch this space.
No dice. I still can't recreate your problem on OS X 10.7.4 with
matplotlib version 1.1.1-rc2.
What are your font/tex specifications in the matplotlib.rcParams
dictionary?
For me the problem occurs with PDF files, not PNG files. Or was that
just a typo?
Font specifications are all default.
# python -c 'import matplotlib; import pprint;
# pprint.pprint(matplotlib.rcParams)' | egrep 'tex'
'legend.handletextpad': 0.8,
'mathtext.bf': 'serif:bold',
'mathtext.cal': 'cursive',
'mathtext.default': 'it',
'mathtext.fallback_to_cm': True,
'mathtext.fontset': 'cm',
'mathtext.it': 'serif:italic',
'mathtext.rm': 'serif',
'mathtext.sf': 'sans\\-serif',
'mathtext.tt': 'monospace',
'text.antialiased': True,
'text.color': 'k',
'text.dvipnghack': None,
'text.hinting': True,
'text.latex.preamble': [''],
'text.latex.preview': False,
'text.latex.unicode': False,
'text.usetex': False,
I think I know why this is happening. Iirc, we recently took on a patch to
allow string formatting for labels. For most cases, it shouldn't effect
anybody, but if there is a lonely percent sign, I would imagine it could
cause issues. As a test, try a double percent sign '%%'. If that works,
the my theory might be right.
Nope, using '%%' just results in two corrupted signs in the PDF.
Best,
-Nikolaus
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Re: [Matplotlib-users] Corrupted percent signs in labels
Michael Droettboom mdroe-pfb3ainihtehxe+lvdl...@public.gmane.org writes:
For some reason, my matplotlib isn't able to print percent signs ('%')
properly:
It's a known bug, fixed since 1.1.1.
https://github.com/matplotlib/matplotlib/issues/1211
Indeed. Luckily 1.2.0~rc2-1 is in experimental, and upgrading fixed the
problem. Thanks!
Now the only question that remains is: why doesn't github find this
issue when I search for '%'?
BTW: If you're running the Debian package, how come the version is a
release candidate? (1.1.1rc2)
Not sure what you mean, why shouldn't it?
Best,
-Nikolaus
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[Matplotlib-users] Corrupted percent signs in labels
Hello,
For some reason, my matplotlib isn't able to print percent signs ('%')
properly:
[1] inspiron:~/tmp# cat mplbug.py
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
print matplotlib.__version__
plt.plot(np.arange(10), np.arange(10)**2)
plt.xlabel('Percent [%]')
plt.savefig('mplbug.pdf')
[0] inspiron:~/tmp# python mplbug.py
1.1.1rc2
I have attached the resulting PDF. For some reason, the slash in the
percent sign becomes a triangle that partially covers the upper left
circle.
Known bug? Any workarounds that don't require upgrading (I'd like to
stick with the Debian package)?
Thanks,
-Nikolaus
--
»Time flies like an arrow, fruit flies like a Banana.«
PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C
mplbug.pdf
Description: Adobe PDF document
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Re: [Matplotlib-users] Corrupted percent signs in labels
Damon McDougall damon.mcdougall-re5jqeeqqe8avxtiumw...@public.gmane.org
writes:
On Tue, Oct 9, 2012 at 10:56 PM, Damon McDougall
damon.mcdougall-re5jqeeqqe8avxtiumw...@public.gmane.org wrote:
On Tue, Oct 9, 2012 at 10:32 PM, Nikolaus Rath
nikolaus-bth8mxji...@public.gmane.org wrote:
Hello,
For some reason, my matplotlib isn't able to print percent signs ('%')
properly:
[1] inspiron:~/tmp# cat mplbug.py
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
print matplotlib.__version__
plt.plot(np.arange(10), np.arange(10)**2)
plt.xlabel('Percent [%]')
plt.savefig('mplbug.pdf')
[0] inspiron:~/tmp# python mplbug.py
1.1.1rc2
I have attached the resulting PDF. For some reason, the slash in the
percent sign becomes a triangle that partially covers the upper left
circle.
Known bug? Any workarounds that don't require upgrading (I'd like to
stick with the Debian package)?
I'm using the AGG backend and saving to a png file without any
problems, but I'm using the current git master branch. I'll try to see
if I can recreate on 1.1.1rc2. Watch this space.
No dice. I still can't recreate your problem on OS X 10.7.4 with
matplotlib version 1.1.1-rc2.
What are your font/tex specifications in the matplotlib.rcParams dictionary?
For me the problem occurs with PDF files, not PNG files. Or was that
just a typo?
Font specifications are all default.
# python -c 'import matplotlib; import pprint;
# pprint.pprint(matplotlib.rcParams)' | egrep 'tex'
'legend.handletextpad': 0.8,
'mathtext.bf': 'serif:bold',
'mathtext.cal': 'cursive',
'mathtext.default': 'it',
'mathtext.fallback_to_cm': True,
'mathtext.fontset': 'cm',
'mathtext.it': 'serif:italic',
'mathtext.rm': 'serif',
'mathtext.sf': 'sans\\-serif',
'mathtext.tt': 'monospace',
'text.antialiased': True,
'text.color': 'k',
'text.dvipnghack': None,
'text.hinting': True,
'text.latex.preamble': [''],
'text.latex.preview': False,
'text.latex.unicode': False,
'text.usetex': False,
Best,
-Nikolaus
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[Matplotlib-users] Using object oriented interface in interactive mode?
Hello, The following code shows the plot right away as expected: # python Python 2.7.3rc2 (default, Apr 22 2012, 22:30:17) [GCC 4.6.3] on linux2 Type help, copyright, credits or license for more information. import matplotlib matplotlib.__version__ '1.1.1rc2' import matplotlib.pyplot as plt plt.interactive(True) plt.plot(range(10)) [matplotlib.lines.Line2D object at 0x2ce7790] This, however, opens a window but the graph never shows up: # python Python 2.7.3rc2 (default, Apr 22 2012, 22:30:17) [GCC 4.6.3] on linux2 Type help, copyright, credits or license for more information. import matplotlib.pyplot as plt plt.interactive(True) fig = plt.figure() ax = fig.add_subplot(1,1,1) ax.plot(range(10)) [matplotlib.lines.Line2D object at 0x3055d90] Does interactive mode only apply to the plot commands in pyplot? Is there a method I can call in this case to refresh the window and show the plot? For seem reason, calling plt.axes() has the desired effect, but this is probably a side effect that I really should not rely on, right? Thanks! -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- 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] Using object oriented interface in interactive mode?
Benjamin Root ben.root-grryuj3d...@public.gmane.org writes: On Sunday, August 5, 2012, Nikolaus Rath wrote: Hello, The following code shows the plot right away as expected: # python Python 2.7.3rc2 (default, Apr 22 2012, 22:30:17) [GCC 4.6.3] on linux2 Type help, copyright, credits or license for more information. import matplotlib matplotlib.__version__ '1.1.1rc2' import matplotlib.pyplot as plt plt.interactive(True) plt.plot(range(10)) [matplotlib.lines.Line2D object at 0x2ce7790] This, however, opens a window but the graph never shows up: # python Python 2.7.3rc2 (default, Apr 22 2012, 22:30:17) [GCC 4.6.3] on linux2 Type help, copyright, credits or license for more information. import matplotlib.pyplot as plt plt.interactive(True) fig = plt.figure() ax = fig.add_subplot(1,1,1) ax.plot(range(10)) [matplotlib.lines.Line2D object at 0x3055d90] Does interactive mode only apply to the plot commands in pyplot? Is there a method I can call in this case to refresh the window and show the plot? For seem reason, calling plt.axes() has the desired effect, but this is probably a side effect that I really should not rely on, right? Correct, I think you want plt.draw(). Thanks, that works! But why is it necessary? Does interactive mode only apply to direct pyplot.* commands? Thanks, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- 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] How to remove vertical lines when plotting rotating phase
Hello, I'm plotting a rotating phase: # ipython --pylab x1 = linspace(0, 2*pi, 30) x = concatenate((x1,x1,x1,x1)) plot(x) The resulting plot has ugly vertical lines whenever x wraps from 2*pi back to zero. Does someone have a nice, general way to get to get rid of such lines? (the actual data is of course less predictable and regular than the example above). Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Setting tick labels for matshow
Stan West stan.west-qqjzlxdiqip5oiiguju...@public.gmane.org writes: From: Nikolaus Rath [mailto:nikolaus-bth8mxji...@public.gmane.org] Sent: Tuesday, November 02, 2010 21:38 In [16]: matplotlib.__version__ Out[16]: '1.0.0' I attached the result of fig.savefig(). Let's see if it makes it through the list. The bug in question was fixed at revision 8652, after 1.0.0 was released. The distinction between the x and y axes in your case is because the y axis is inverted. You can work around the bug by avoiding the Axes.set_xticks() and set_yticks() [...] I hope that helps. It does, thanks! -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- The Next 800 Companies to Lead America's Growth: New Video Whitepaper David G. Thomson, author of the best-selling book Blueprint to a Billion shares his insights and actions to help propel your business during the next growth cycle. Listen Now! http://p.sf.net/sfu/SAP-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Shadowed Text?
Hello, I am placing a text object in a place where the background is sometimes dark and sometimes light, so the text is hard to see. Adding a background to the text object itself looks a bit ugly, so I am wondering if there is a way to add a shadow to the text itself. What's the best way to do this? I thought about redrawing the same text just offset by a fraction of the text size, but I can't quite figure out how to do the placement properly. My rough idea is the get the position of the text in pixel coordinates, add an offset to it and then position it with display coordinates as well. But how do I get the display coordinates of something that I placed in axes coordinates? And how to I determine how many pixels I need to offset without knowing the dpi? Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Achieve Improved Network Security with IP and DNS Reputation. Defend against bad network traffic, including botnets, malware, phishing sites, and compromised hosts - saving your company time, money, and embarrassment. Learn More! http://p.sf.net/sfu/hpdev2dev-nov ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Setting tick labels for matshow
Hello, I am trying to set tick labels for a matshow plot. This works just fine if I only work on the X axis: res = np.diag(np.arange(10)) # dummy data modes = [ (x+1, 0) for x in range(5) ] # dummy data fig = plt.figure() ax = fig.add_subplot(111) cs = ax.matshow(res) fig.colorbar(cs, ticks=np.arange(0,-10,-1), shrink=0.8) ax.set_xticklabels(['%d/%d' % (x[1], x[0]) for x in modes]) ax.set_xticks(2*np.arange(len(modes))+0.5) but if I try to do the same think with the Y axis, everything looks messed up (e.g. the matrix is no longer square): ax.set_yticklabels(['%d/%d' % (x[1], x[0]) for x in modes]) ax.set_yticks(2*np.arange(len(modes))+0.5) What am I doing wrong? Thanks, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Trouble with contour plot
Benjamin Root ben.root-grryuj3d...@public.gmane.org writes:
On Thu, Oct 28, 2010 at 3:31 PM, Nikolaus Rath
nikolaus-bth8mxji...@public.gmane.org wrote:
Hello,
I'm having a weird problem with a contour plot. Consider the following
plots:
import cPickle as pickle
import matplotlib.pyplot as plt
(Theta, Phi, Bnormal) = pickle.load(open('trouble.pickle', 'rb'))
plt.figure(0)
for i in [0, 300]:
plt.plot(Theta, Bnormal[:, i], label='Bnormal at Phi=%.3g' % Phi[i])
plt.ylabel('Theta')
plt.legend()
plt.savefig('figure0.png')
plt.figure(1)
plt.contourf(Phi, Theta, Bnormal)
plt.xlabel('Phi')
plt.ylabel('Theta')
plt.colorbar()
plt.savefig('figure1.png')
The 'trouble.pickle' file is available on
http://www.rath.org/trouble.pickle. At Phi=0 the contour plot agrees
with the crossection (both show an n=7 oscillation), but at Phi=1.68 the
contour plot shows a uniform value while the crossection shows a phase
shifted version of oscillation at Phi=0.
It seems to me that this is a blatant contradiction.
I have also uploaded the two figures at http://www.rath.org/figure1.png
and http://www.rath.org/figure0.png.
Am I missing something, or is this a bug?
$ python --version
Python 2.6.5
$ python -c 'import matplotlib; print matplotlib.__version__'
1.0.0
Thanks,
-Nikolaus
Nikolaus,
What might be happening is that the Theta variable isn't monotonic. It
first goes from zero to pi, then from -pi to 0. This also explains the odd
lines that appear in the line plots at the top and bottom. Try reforming
your arrays so that the domain is monotonic (note that you will have to
adjust the Phi and the Bnormal arrays as well because they were arranged
assuming a certain domain from Theta.
Indeed, this was the problem. Thank you very much!
However, it seems to me that this is quite a serious bug. The contour
documentation on
http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.contour
does not mention this requirement, and obviously the contour method
itself does not even bother to check if its arguments are monotonically
increasing. Instead, it just *silently* produces garbage that in some
cases even looks like plausible data(!).
Am I missing something here? Otherwise I'll report this on the bug
tracker. I think this should be documented and contour() should check
its input and raise a ValueError if it's not monotonic.
Best,
-Nikolaus
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Re: [Matplotlib-users] Trouble with contour plot
Benjamin Root ben.root-grryuj3d...@public.gmane.org writes: However, it seems to me that this is quite a serious bug. The contour documentation on http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.contour does not mention this requirement, and obviously the contour method itself does not even bother to check if its arguments are monotonically increasing. Instead, it just *silently* produces garbage that in some cases even looks like plausible data(!). Am I missing something here? Otherwise I'll report this on the bug tracker. I think this should be documented and contour() should check its input and raise a ValueError if it's not monotonic. You are right, the documentation is seriously lacking and woefully out-of-date. It still claims that it can not handle internal regions correctly with masked arrays (I am pretty sure that is fixed) and it says nothing of any characteristics of X and Y. I see. I added this issue to the bug tracker so that it doesn't get forgotten. I don't know if there are any strict requirement on monotonicity for X and Y, or if there are any cases where the plot is still valid even if that property is violated. If it is a requirement, then I agree that there should be a check. How can it not be a requirement if the output is wrong in some cases? It does not matter if there are also cases where it works - you would never be able to trust any plot you generate. P.S. - I find that in many cases, contourf() is the wrong function to use for such plots, and find pcolor() (or one of its variants) to be better suited. Don't know what is better for you in your case, but it might be something to investigate. Thanks for the hint, looks interesting. I looked at the documentation, but I don't really understand the difference between pcolor and pcolormesh. Could you elaborate on that? Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Trouble with contour plot
Eric Firing efiring-msmayosy5ky3upmlikx...@public.gmane.org writes: I don't know if there are any strict requirement on monotonicity for X and Y, or if there are any cases where the plot is still valid even if that property is violated. If it is a requirement, then I agree that there should be a check. For sensible output, it is a requirement. Contour and contourf (like imshow, pcolor, and pcolormesh) work with gridded data. Gridding is the responsibility of the user. It can be done in many different ways, so it makes sense to keep the gridding separate from the display of the gridded data. If there is a check--and I am not convinced there should be--it should provide only a warning. It is perfectly reasonable for a person to take a dataset and contour it even if the grid is not monotonic. Sometimes one wants to get a quick look at raw input, complete with errors. I don't quite understand your last point. In my example, the single jump from pi to -pi makes half of the plot constant while in truth it is oscillatory. I would not say that this reflects the raw input in any way, and I am not sure what one could learn from this plot with a quick (or even prolonged) look. Am I missing something? Is there some obvious connection between the jump in Theta, the data, and the resulting plot? To me the plot looks like unpredictable garbage, so I really don't understand how anyone could want to do something like that... Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Trouble with contour plot
Hello,
I'm having a weird problem with a contour plot. Consider the following
plots:
import cPickle as pickle
import matplotlib.pyplot as plt
(Theta, Phi, Bnormal) = pickle.load(open('trouble.pickle', 'rb'))
plt.figure(0)
for i in [0, 300]:
plt.plot(Theta, Bnormal[:, i], label='Bnormal at Phi=%.3g' % Phi[i])
plt.ylabel('Theta')
plt.legend()
plt.savefig('figure0.png')
plt.figure(1)
plt.contourf(Phi, Theta, Bnormal)
plt.xlabel('Phi')
plt.ylabel('Theta')
plt.colorbar()
plt.savefig('figure1.png')
The 'trouble.pickle' file is available on
http://www.rath.org/trouble.pickle. At Phi=0 the contour plot agrees
with the crossection (both show an n=7 oscillation), but at Phi=1.68 the
contour plot shows a uniform value while the crossection shows a phase
shifted version of oscillation at Phi=0.
It seems to me that this is a blatant contradiction.
I have also uploaded the two figures at http://www.rath.org/figure1.png
and http://www.rath.org/figure0.png.
Am I missing something, or is this a bug?
$ python --version
Python 2.6.5
$ python -c 'import matplotlib; print matplotlib.__version__'
1.0.0
Thanks,
-Nikolaus
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[Matplotlib-users] GridSpec Index Order
Hello, I just noticed that in order to get a 3 row by 4 column grid, I have to do import matplotlib.pyplot as plt from matplotlib.gridspec import GridSpec def make_ticklabels_invisible(fig): for i, ax in enumerate(fig.axes): ax.text(0.5, 0.5, ax%d % (i+1), va=center, ha=center) for tl in ax.get_xticklabels() + ax.get_yticklabels(): tl.set_visible(False) plt.figure() gs = GridSpec(3, 4) for i in range(4): for j in range(3): plt.subplot(gs[i, j]) plt.suptitle(GridSpec) make_ticklabels_invisible(plt.gcf()) plt.show() So I have to instantiate GridSpec with a (rows, column), but when I index the grid I have to use (column, row). Is there any reason for this counterintuitive behaviour? Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] GridSpec Index Order
On 10/25/2010 11:18 AM, Jae-Joon Lee wrote: On Mon, Oct 25, 2010 at 10:45 PM, Nikolaus Rath nikol...@rath.org wrote: So I have to instantiate GridSpec with a (rows, column), but when I index the grid I have to use (column, row). Is there any reason for this counterintuitive behaviour? This is not an intended behavior but a bug which affects a grid of non-square shape. This has been fixed in the svn version. Meanwhile, you may use 1-d indexing. e.g., import matplotlib.pyplot as plt from matplotlib.gridspec import GridSpec gs = GridSpec(3, 4) for irow in range(3): for icol in range(4): ax = plt.subplot(gs[irow*4+icol]) I see, thanks. Is there also a way to use this workaround for slices? I want a subplot in column 4 that spans all rows... Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] GridSpec for Figure objects?
Hello, I would like to create subplots with different sizes using the object oriented API. However, it seems that the subplot2grid() method exists only in pyplot, but not as a Figure instance method. Am I looking in the wrong place? How do I use subplot2grid with an existing Figure object? Thanks, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Same X and Y scale
Ryan May rmay31-re5jqeeqqe8avxtiumw...@public.gmane.org writes:
On Jul 30, 2010, at 14:34, Nikolaus Rath
nikolaus-bth8mxji...@public.gmane.org wrote:
Hi,
Consider this:
X = np.linspace(0.70, 1.1, 100)
Y = np.linspace(-1.19, 1.19, 70)
(Xs, Ys) = np.meshgrid(X, Y)
Z = np.sqrt((Xs-0.9)**2 + Ys**2) - 0.10
fig = plt.figure()
ax = fig.add_subplot(111)
ax.contour(X, Y, Z)
fig.show()
This works, but gives the y axis a different scale than the x axis so
the ellipses look like circles.
How can I get the same scale for the x- and y-axis?
I tried to set ax.set_autoscale_on(False), but that resulted in a
totally different part of the coordinate system being
Try:
ax.set_aspect('equal')
Works perfectly, thanks!
-Nikolaus
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Re: [Matplotlib-users] Contour plot of non-uniformly sampled data
Jeff Whitaker jswhit-97jfqw80gc6171pxa8y...@public.gmane.org writes: On 7/28/10 8:32 PM, Nikolaus Rath wrote: Hello, What is the best way to generate a contour plot from a set of non-uniformly sampled data (i.e., the datapoints do not lie on the points of a rectangular grid but are randomly distributed)? Thanks, -Nikolaus Nikolaus: You can either use mlab.griddata to interpolate the data to a regular grid, or use pyplot.tricontour to perform a delaunay triangulation and contour the resulting triangle values. Fantastic, thanks! Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Contour plot of non-uniformly sampled data
Hello, What is the best way to generate a contour plot from a set of non-uniformly sampled data (i.e., the datapoints do not lie on the points of a rectangular grid but are randomly distributed)? Thanks, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Contour plots with same color mapping
Hello, I would like to draw a couple of contour plots. The plots are on separate figures, but they should all have exactly the same color mapping (i.e, the same Z value should correspond to the same color in all plots). What's the best way to achieve this? From the documentation I gather that I should use the norm and extend keyword arguments, but I wasn't really able to figure out what values I have to pass and how the matplotlib.colors.Normalize instance works. Thanks, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Plotting irregular 2d data
Hi, I have a 1d array Z that unfortunately contains information about a two dimensional surface. The mapping is nontrivial (i.e. Z is not just a sequence of column or row information that I could reshape) but homogenous (i.e. there is a rectangular grid and Z contains data for each vertex). The x and y coordinates for each datapoint in Z are contained in separate arrays X and Y. A simple pyplot.contour(X, Y, Z) refuses to plot the data because Z is not 2d (TypeError: Input z must be a 2D array). What's the best way to plot this data? Is there an easy way to reshuffle the elements of Z so that they are in either row-column or column-row order? Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Plotting 2d fourier amplitudes
Hello,
I have 2d array with fourier amplitudes that I would like to plot. I
found two options: contourf and imshow. This is my code:
omega = np.fft.rfftn(b_field, axes=(1, 0))
omega = np.abs(np.fft.fftshift(omega, axes=(1,)))
fig = plt.figure()
ax = fig.add_subplot(111)
M = omega.shape[0]
N = omega.shape[1]
ax.set_title('Spectrum')
ax.set_ylabel(r'Poloidal Mode Number m')
ax.set_xlabel(r'Toroidal Mode Number n')
ax.grid(True)
# Get rid of normalization
omega /= np.prod(omega.shape)
The problem with contourf is that I can't seem to stop it from
strongly interpolating the data, which obscures the discrete nature:
(see www.rath.org/contourf.png)
ctr = ax.contourf(np.arange(-N / 2, N / 2),
np.arange(0, M),
omega * 1, 100, cmap=cm.YlOrRd,
interpolation='nearest')
fig.colorbar(ctr)
ax.set_xlim(xmin= -(N - 1) / 2, xmax=(N - 1) / 2)
ax.set_ylim(ymin=0, ymax=M - 1)
fig.show()
Apparently contourf does not accept the interpolation='nearest' option.
Is there a way to make it stop interpolating?
The problem with imshow is, that it rescales the data so the
colorbar does not show the correct amplitudes (see
www.rath.org/imshow.png):
ctr = ax.imshow(omega, cmap=cm.YlOrRd, aspect='equal',
interpolation='nearest',
origin='lower', extent=(-(N-1)/2, (N-1)/2, 0, M-1))
fig.colorbar(ctr)
ax.set_xlim(xmin= -(N - 1) / 2, xmax=(N - 1) / 2)
ax.set_ylim(ymin=0, ymax=M - 1)
fig.show()
Is there a way to get the proper amplitudes into the colorbar?
Thanks!
-Nikolaus
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Re: [Matplotlib-users] Plotting 2d fourier amplitudes
Hi, I want the colorbar to show the real fourier amplitudes, not the amplitudes after rescaling to 0..1. In other words: the colorbar created by imshow should have the same values as the one created by contourf. I am not sure how I can use vmin and vmax to achieve that effect. The scaling is done correctly, it's just that the colorbar should show the original, and not the rescaled values. Thanks, -Niko I did not try vmin and vmax, because On 04/26/2010 02:31 PM, Jae-Joon Lee wrote: Did you try to change vmin, vmax? http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.imshow If this is not what you want, please describe more explicitly why the colorbar is wrong. Regards, -JJ On Mon, Apr 26, 2010 at 11:37 AM, Nikolaus Rath nikol...@rath.org wrote: The problem with imshow is, that it rescales the data so the colorbar does not show the correct amplitudes (see www.rath.org/imshow.png): ctr = ax.imshow(omega, cmap=cm.YlOrRd, aspect='equal', interpolation='nearest', origin='lower', extent=(-(N-1)/2, (N-1)/2, 0, M-1)) fig.colorbar(ctr) ax.set_xlim(xmin= -(N - 1) / 2, xmax=(N - 1) / 2) ax.set_ylim(ymin=0, ymax=M - 1) fig.show() Is there a way to get the proper amplitudes into the colorbar? -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Plotting 2d fourier amplitudes
Hi, Believe it or not, the factor of 1 was my only problem all the time. Until you pointed it out I never noticed that it was missing in one of the calls. Thanks! Niko On 04/26/2010 03:26 PM, Jae-Joon Lee wrote: I think I'm lost. In other words: the colorbar created by imshow should have the same values as the one created by contourf. But, in your original post, your plotting two different image. with contourf, you're drawing omega*1, but with imshow, you're drawing omega. Are you saying that these two should have same colorbar, although there is a factor 1 difference? And, as far as I know, colorbar shows values of the original input. What is the min and max of omega, and what do you expect your colorbar show? If possible, please post a complete example so that others can test. Regards, -JJ I am not sure how I can use vmin and vmax to achieve that effect. The scaling is done correctly, it's just that the colorbar should show the original, and not the rescaled values. Thanks, -Niko I did not try vmin and vmax, because On 04/26/2010 02:31 PM, Jae-Joon Lee wrote: Did you try to change vmin, vmax? http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.imshow If this is not what you want, please describe more explicitly why the colorbar is wrong. Regards, -JJ On Mon, Apr 26, 2010 at 11:37 AM, Nikolaus Rath nikol...@rath.org wrote: The problem with imshow is, that it rescales the data so the colorbar does not show the correct amplitudes (see www.rath.org/imshow.png): ctr = ax.imshow(omega, cmap=cm.YlOrRd, aspect='equal', interpolation='nearest', origin='lower', extent=(-(N-1)/2, (N-1)/2, 0, M-1)) fig.colorbar(ctr) ax.set_xlim(xmin= -(N - 1) / 2, xmax=(N - 1) / 2) ax.set_ylim(ymin=0, ymax=M - 1) fig.show() Is there a way to get the proper amplitudes into the colorbar? -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] How to show interactive plot window from program
Hello, When I'm calling the pyplot.plot function from ipython, I get a nice dialog in which I can zoom, pan save. How can I achieve the same thing from a non-interactive program? I tried fig = plt.figure() ax = fig.add_subplot(111) ax.contourf(stuff) fig.show() but this program terminates without showing anything. Is there a function that I can call that shows up the interactive window and only returns once I close the window? Thanks, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] ticks at 0 and 2pi
Hello,
I'm trying to plot something from 0 to 2pi:
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title('Radial Magnetic Field')
ax.set_ylabel(r'Poloidal Angle $\theta$')
ax.set_xlabel(r'Toroidal Angle $\phi$')
ax.set_xticks([0, 2 * math.pi])
ax.set_xticklabels(['0', r'$2\pi$'])
ax.set_yticklabels([r'$-\pi$', r'$\pi$'])
ax.set_yticks([-math.pi, math.pi])
ax.set_xlim(xmin=0, xmax=2 * math.pi)
ax.set_ylim(ymin= -math.pi, ymax=math.pi)
But unfortunately the ticks for x=2pi and y=pi are not shown. They do
show up if I move them a tiny bit:
ax.set_xticks([0, 2 * math.pi * 0.98])
ax.set_yticks([-math.pi, math.pi * 0.98])
But obviously this is ugly.
Is there a way to show the labels without moving the to the wrong
position and without extending the axis limits (since that introduces a
white border)?
Best,
-Nikolaus
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Re: [Matplotlib-users] ticks at 0 and 2pi
On 04/20/2010 10:29 AM, Ryan May wrote:
On Tue, Apr 20, 2010 at 8:58 AM, Nikolaus Rath nikol...@rath.org wrote:
Hello,
I'm trying to plot something from 0 to 2pi:
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title('Radial Magnetic Field')
ax.set_ylabel(r'Poloidal Angle $\theta$')
ax.set_xlabel(r'Toroidal Angle $\phi$')
ax.set_xticks([0, 2 * math.pi])
ax.set_xticklabels(['0', r'$2\pi$'])
ax.set_yticklabels([r'$-\pi$', r'$\pi$'])
ax.set_yticks([-math.pi, math.pi])
ax.set_xlim(xmin=0, xmax=2 * math.pi)
ax.set_ylim(ymin= -math.pi, ymax=math.pi)
I don't see the problem here, I get the ticks as specified. What
version of matplotlib are you using? What backend are you using?
Actually, now that I tried it again, it suddenly works. Strange... Sorry
for the pointless mail.
Best,
-Nikolaus
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[Matplotlib-users] How to make colormaps
Hello, Maybe my googling skills are deficient, but I wasn't able to find any information on how to define my own colormap. Can someone give me a pointer, or a basic example how to create a simple map that e.g. maps -1 to Red, 0 to White, and 1 to Blue? Thanks, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] How to make colormaps
On 04/20/2010 01:06 PM, Ryan May wrote: On Tue, Apr 20, 2010 at 11:40 AM, Jim Vickroy jim.vick...@noaa.gov wrote: Nikolaus Rath wrote: Hello, Maybe my googling skills are deficient, but I wasn't able to find any information on how to define my own colormap. Can someone give me a pointer, or a basic example how to create a simple map that e.g. maps -1 to Red, 0 to White, and 1 to Blue? http://lmgtfy.com/?q=matplotlib+colormaps That was a tad harsh, given that the first page of google results didn't really answer the question. (If you're going to be snarky, at least make sure you're right.) Don't worry, I'm usually worse myself. And his answer did help me. I actually googled the same query, but I skipped over the first two matches after reading the title since I thought they'd just lead me to examples/pylab_examples/show_colormaps.html (which I already found and deemed to be not helpful). Nick, this is a pretty good example: http://matplotlib.sourceforge.net/examples/api/colorbar_only.html If I understand correctly, this explains how to create a discrete colormap, which isn't quite what I want. But with the two links I can figure it out the rest, thanks to both of you! Best, -Nikolaus -- »Time flies like an arrow, fruit flies like a Banana.« PGP fingerprint: 5B93 61F8 4EA2 E279 ABF6 02CF A9AD B7F8 AE4E 425C -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
