Re: [Matplotlib-users] Colorbar not working with specgram
Thanks Eric for pointing out this. However i've found that psd and specgram plot 10*log10*(Pxx/max(Pxx)), so i'll have a range from 0 db down. Anyway, what do you mean by should not be axes method? Do you mean using the array output of specgram and psd and plotting that result by myself? Cheers Davide On Tue, 2009-07-21 at 09:12 -1000, Eric Firing wrote: davide lasagna wrote: Hello everybody, this is my first post in this list. I'm plotting a spectrogram with Pxx, freqs, bins, im = specgram(y, nfft=256, f_sampling=12000) and i want to add a colorbar with colorbar() The problem is that the color scale seems to be wrong with respect to the data in Pxx, i.e. Pxx is of the order of 1e-2 while in the colorbar i have tick values spanning from -20 to -180. What is the problem?? specgram and psd plot power in decibels: 10*log10(Pxx). Because they involve heavy computation and application-specific choices, like the decibel scale, they really should not be axes methods. You can make a function plot the spectrogram however you like by looking at the source code in the Axes.specgram method (the pyplot specgram function is just a thin wrapper for this method), which is using mlab.specgram to do the calculation and is then just scaling and plotting. Eric Thanks in advance! Davide -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Colorbar not working with specgram
davide lasagna wrote: Thanks Eric for pointing out this. However i've found that psd and specgram plot 10*log10*(Pxx/max(Pxx)), so i'll have a range from 0 db down. Aha, I wasn't looking closely enough! Anyway, what do you mean by should not be axes method? That was a side remark about what the Axes class should do or not do. I would prefer that it stick to plotting. For example, at present it does not have a method for empirical orthogonal functions, or for wavelets--and that's good, it shouldn't. Numerical code (usually in numpy or scipy) should do the calculations, and then the result should be plotted using Axes methods or pyplot functions for line plotting, contouring, making images, etc. So getting back to the specgram, I would prefer that it be given as an example--a script combining the calculation with the plotting--rather than having calculation and plotting done in an Axes method. Do you mean using the array output of specgram and psd and plotting that result by myself? The calculations are being done by functions in the matplotlib.mlab module, so yes, I suggest using those functions directly (not the pyplot functions that wrap the Axes methods that call the mlab functions and then plot the result) and then doing your own scaling and plotting. The Axes specgram method might guide you in the latter (giving an example of how to use imshow, for example), but if you write your own function you can make it do exactly what you want instead of accepting the scaling choice imposed by the Axes method. Eric Cheers Davide On Tue, 2009-07-21 at 09:12 -1000, Eric Firing wrote: davide lasagna wrote: Hello everybody, this is my first post in this list. I'm plotting a spectrogram with Pxx, freqs, bins, im = specgram(y, nfft=256, f_sampling=12000) and i want to add a colorbar with colorbar() The problem is that the color scale seems to be wrong with respect to the data in Pxx, i.e. Pxx is of the order of 1e-2 while in the colorbar i have tick values spanning from -20 to -180. What is the problem?? specgram and psd plot power in decibels: 10*log10(Pxx). Because they involve heavy computation and application-specific choices, like the decibel scale, they really should not be axes methods. You can make a function plot the spectrogram however you like by looking at the source code in the Axes.specgram method (the pyplot specgram function is just a thin wrapper for this method), which is using mlab.specgram to do the calculation and is then just scaling and plotting. Eric Thanks in advance! Davide -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] I really can't get into hist() barstacked
Sandro Tosi ha scritto:
On Wed, Jul 22, 2009 at 10:25, msdeviceran...@gmail.com wrote:
Sandro Tosi ha scritto:
Hi all,
I'd like to do a histogram with barstacked style. Well, I'm not able
to make it in any way :(
- what is the format of the the data to pass?
- what's the value of bins? (related to the above question, I suppose)
for example, let's say I want to plot this series
s1 = 2,3,6,3,1
s2 = 1,2,2,4,1
s3 = 4,1,0,3,7
what's the format of data to pass to hist() ? by row? by column?
Thanks a lot in advance,
I think hist() *computes* histograms ; you can find information here:
http://matplotlib.sourceforge.net/api/pyplot_api.html
and infact I want a barstacked histogram
So you want to
1) compute your histogram from your series of values and then
2) display the several histograms as a stacked bar graph
or just
1) display already-calculated histogram values as a stacked bar graph
These are two different things. Since it seems you want to pass directly
s1,s2,s3, it seems that they are your already calculated histogram
values. In this case hist() is of no utility for you.
It seems from your example that you already have the histogram computed
no, I just have a series of lists to plot, I didn't compute anything.
Ok, so you want a bar graph and not to compute a histogram.
and that you want to plot the bar graph; in this case you should look to
bar()
In the page linked above you find also the example on how to do a
barstacked graph.
sure, for 2 data sets might be fine: but what for 10 ? how to use the
bottom argument in that case?
Ehm, it seems pretty straighforward to me.
I attach the same example of the webpage but extended with three bar
graphs stacked. I admit that the fact the example used tuples for the
values made it unnecessarily awkward; using numpy arrays everything goes
to place:
#!/usr/bin/env python
# a stacked bar plot with errorbars
import numpy as np
import matplotlib.pyplot as plt
N = 5
menMeans = np.array([20, 35, 30, 35, 27])
womenMeans = np.array([25, 32, 34, 20, 25])
xMeans = np.array([17, 11, 43, 5, 18])
menStd = (2, 3, 4, 1, 2)
womenStd = (3, 5, 2, 3, 3)
ind = np.arange(N)# the x locations for the groups
width = 0.35 # the width of the bars: can also be len(x) sequence
p1 = plt.bar(ind, menMeans, width, color='r', yerr=womenStd)
p2 = plt.bar(ind, womenMeans, width, color='y',
bottom=menMeans, yerr=menStd)
p3 = plt.bar(ind, xMeans, width, color='b', bottom=womenMeans+menMeans)
plt.ylabel('Scores')
plt.title('Scores by group and gender')
plt.xticks(ind+width/2., ('G1', 'G2', 'G3', 'G4', 'G5') )
plt.yticks(np.arange(0,81,10))
plt.legend( (p1[0], p2[0], p3[0]), ('Men', 'Women','Aliens') )
plt.show()
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Re: [Matplotlib-users] centering axis ticks labels
hello, anyone has an idea about how to get this right? thanks a lot in advance, Johann Johann Cohen-Tanugi wrote: hi there, I stumbled into yet another problem, see script attached. Now there are 10 pixels and 10 label values on each axis, but I get only half the ticks, and as a result half the labels get discarded... How can I specify the number of ticks it uses? Note that I could use plt.pcolor(np.array(EMINS),np.array(ROIS),d) and at least the labelling would be correct, but the pixels are now more or less wide depending on the interval between values, which was not intended thanks a lot in advance for your help, Johann Johann Cohen-Tanugi wrote: Hello, how can I center axis tick labels, so that the labels ends up at the center between 2 ticks. thanks in advance, Johann -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] I really can't get into hist() barstacked
Sandro Tosi ha scritto: I got only data values, nothing already computed (for whatever you mean by that), and I want to plot stacked bars with those values (either by row or by column). Ok, I see. It seems from your example that you already have the histogram computed no, I just have a series of lists to plot, I didn't compute anything. Ok, so you want a bar graph and not to compute a histogram. what is the difference? maybe I didn't get it right ;) Oh, sorry, I thought it was common knowledge. That's why I didn't understand at beginning :) A histogram is a *statistical technique* which takes a vector of data, classifies them into bins (usually magnitude intervals), counts the number of data points into each bin and returns another vector with the number of data points for each bin. It is a technique to get an approximation of the distribution underlying your data; it is not the only one (for example I am a big fan of kernel density estimation, which is, roughly speaking, the continuous extension of the histogram) A bar graph is a representation of data as bars of different heights. Usually people display histograms with bar graphs, each bar being a bin, and for this reason they often confuse the two things :) But they're two different and quite unrelated things: there's nothing intrinsically wrong in plotting histograms as line or scatter plots, for example, and you can do bar graphs of things which are not histograms. So it seems you want a bar graph :),and that's why hist() is of little help for you. In the page linked above you find also the example on how to do a barstacked graph. sure, for 2 data sets might be fine: but what for 10 ? how to use the bottom argument in that case? Ehm, it seems pretty straighforward to me. ... p3 = plt.bar(ind, xMeans, width, color='b', bottom=womenMeans+menMeans) do you really expect it to be straightforward for 10, 100 or for any other dynamically generated data? let's imagine today I get 15 sets of data, tomorrow 20, the next day 7. I cannot do that by hand, and I want some general way to get stacked by dynamically adaptable to more columns with more blocks in them. I didn't try, but isn't it easily done with a for cycle? Instead of having p1,p2,p3 you have a vector pN=[...] where you append the bars, and the bottom is the sum of the previous values of your bars. Not counting the fact that if you have 100 data sets, maybe a stacked bar graph begins to be confusing ;) but hey, that's your choice! :D m. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problems with autofmt_xdate()
Hi there, I've upgraded to python 2.6, install all packages I need for that version (using matplotlib windows installer with gtk support found here: http://www.lfd.uci.edu/~gohlke/#pythonlibs ) and now everything seems to be ok. Thanks again. 2009/7/22 Domenico Nappo domenico.na...@gmail.com 2009/7/21 John Hunter jdh2...@gmail.com I have the suspect that matplotlib windows support simply doesn't exist:) I'll try prepackaged windows distributions like EPD or Python(x,y) and hope this will solve this issue... I'm pretty sure they do not package mpl with the gtk backend, but Christoph Gohlke has a version that does http://www.lfd.uci.edu/~gohlke/#pythonlibshttp://www.lfd.uci.edu/%7Egohlke/#pythonlibs Oh, finally...we have found a package with gtk support. Thanks. I will try it. Even if I've already downloaded 240 MB of EDP and I'd like to try it as well. Thank you very much to you two! -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] imshow background and/or colour to alpha
Hi, I am trying to do a plot where small images are used as markers at definite coordinate positions (just to make myself clear: I am trying to see how the shape of a polymer changes with different parameters, so I want little icons of the polymer placed at the x,y of the parameters). Doing that with imshow() , putting images as sub-matrixes etc. seems doable. However problem is my images have a black background, and correspondingly it seems that the RGB 0,0,0 value of the matrix is shown -kinda correctly- as black (a zeros filled canvas is shown as black). I wonder: Is there a default way to tell imshow() that I want a certain colour (in this case, black) , and that colour only, to be alpha? Or do I have to manually change the matrix? Thanks! m. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] problem with svn install
Hi all, I have a problem with an svn install. I've followed the instruciont on mpl website, that is: $ svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/matplotlib matplotlib $ cd matplotlib $ python setupegg.py develop Please note that i've run the last command with sudo as i'm explicitly asked to do so. Then if i run this simple test script: from pylab import * plot([1,2,3]) show() from the command line as python test.py --verbose-helpful i get thise output: dav...@davide-desktop:~$ python test.py --verbose-helpful $HOME=/home/davide CONFIGDIR=/home/davide/.matplotlib matplotlib data path /home/davide/partizione/matplotlib/lib/matplotlib/mpl-data loaded rc file /home/davide/partizione/matplotlib/lib/matplotlib/mpl-data/matplotlibrc matplotlib version 0.98.6svn verbose.level helpful interactive is False units is False platform is linux2 Traceback (most recent call last): File mio, line 1, in module from pylab import * File /home/davide/partizione/matplotlib/lib/pylab.py, line 1, in module from matplotlib.pylab import * File /home/davide/partizione/matplotlib/lib/matplotlib/pylab.py, line 206, in module from matplotlib import mpl # pulls in most modules File /home/davide/partizione/matplotlib/lib/matplotlib/mpl.py, line 1, in module from matplotlib import artist File /home/davide/partizione/matplotlib/lib/matplotlib/artist.py, line 5, in module from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath File /home/davide/partizione/matplotlib/lib/matplotlib/transforms.py, line 34, in module from matplotlib._path import affine_transform ImportError: /home/davide/partizione/matplotlib/lib/matplotlib/_path.so: failed to map segment from shared object: Operation not permitted Could it be that i've installed in the wrong directory? If yes how can i cope with this? Thanks in advance for any help. Davide -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] animate histogram
Animating a line plot is well covered in the Cookbook: http://www.scipy.org/Cookbook/Matplotlib/Animations Can anyone offer a hint or two for animating a histogram? Thanks, Alan Isaac -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] problem with svn install
On Wed, Jul 22, 2009 at 11:47 AM, Jouni K. Seppänen j...@iki.fi wrote: davide lasagna lasagnadav...@gmail.com writes: ImportError: /home/davide/partizione/matplotlib/lib/matplotlib/_path.so: failed to map segment from shared object: Operation not permitted Could it be that i've installed in the wrong directory? If yes how can i cope with this? Apparently this could be caused by SELinux (good luck with configuring that correctly), or perhaps your /home filesystem is mounted with the noexec option to prevent users from running their own code. Ask your system administrator how to install libraries so that Python can call dlopen on them. -- Jouni K. Seppänen http://www.iki.fi/jks -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users I also have been bitten by SELinux a couple times. On my personal Fedora 11 laptop, and previously on FC10 my resolution was to completely disable SELinux to eliminate installation and running issues. Fortunately, I have not dealt with administrative restrictions on our machines that sit in the lab. Once I heard of a complain in this regard sys-admin will be the first to know after me :) -- Gökhan -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] PDF backend errors out; PNG works fine
Thank you for your response. Your response made me wonder how the script would operate in a non-graphic environment--I had tested it on a login node but not on a computing node. It appears that even though I have no need for any graphic display, the modules I am loading expect to have it nonetheless. I invoke matplotlib using the standard import matplotlib.pyplot as plt line. Here is the output when run on a compute node: - [ac.jkere...@n123 pygraph]$ ./run_pygraph.py png Creating Top 100 V/C ratios graph... Traceback (most recent call last): File ./run_pygraph.py, line 566, in module GraphTop100VC (Top100VCFilename) File ./run_pygraph.py, line 326, in GraphTop100VC fig=plt.figure() File /soft/python/lib/python2.6/site-packages/matplotlib/pyplot.py, line 251, in figure **kwargs) File /soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_tkagg.py, line 90, in new_figure_manager window = Tk.Tk() File /soft/python/lib/python2.6/lib-tk/Tkinter.py, line 1643, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable - Can anyone advise if there another way to invoke matplotlib that does not require graphic support? With respect to your suggestion that I run python setup.py build, I don't seem to have the necessary permissions but the sysadmin is very helpful and once I have a little more information on the new problem I'll get his help again. Thanks again, John Kerenyi -Original Message- From: Jouni K. Seppänen [mailto:j...@iki.fi] Sent: Wednesday, July 22, 2009 9:38 AM To: matplotlib-users@lists.sourceforge.net Subject: Re: [Matplotlib-users] PDF backend errors out; PNG works fine John Kerenyi jo...@moval.org writes: File /soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_ pd f.py, line 44, in module from matplotlib import ttconv ImportError: /soft/python/lib/python2.6/site-packages/matplotlib/ttconv.so: undefined symbol: _ZTVSt19basic_ostringstreamIcSt11char_traitsIcESaIcEE Sounds like a mismatch between C++ libraries on the system where matplotlib was built and where it is being used. You mentioned a cluster; perhaps your sysadmin compiled matplotlib on a special node that has more libraries installed than the computation nodes. I don't know how to fix this, but as a first step you could try compiling matplotlib on a computation node (submit something like python setup.py build as a job the same way you would submit another task on the cluster) and seeing if that gives more clues about what is missing. -- Jouni K. Seppänen http://www.iki.fi/jks -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] PDF backend errors out; PNG works fine
You can use the Agg or PDF backends to run matplotlib without display support: import matplotlib matplotlib.use(PDF) Cheers, Mike John Kerenyi wrote: Thank you for your response. Your response made me wonder how the script would operate in a non-graphic environment--I had tested it on a login node but not on a computing node. It appears that even though I have no need for any graphic display, the modules I am loading expect to have it nonetheless. I invoke matplotlib using the standard import matplotlib.pyplot as plt line. Here is the output when run on a compute node: - [ac.jkere...@n123 pygraph]$ ./run_pygraph.py png Creating Top 100 V/C ratios graph... Traceback (most recent call last): File ./run_pygraph.py, line 566, in module GraphTop100VC (Top100VCFilename) File ./run_pygraph.py, line 326, in GraphTop100VC fig=plt.figure() File /soft/python/lib/python2.6/site-packages/matplotlib/pyplot.py, line 251, in figure **kwargs) File /soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_tkagg.py, line 90, in new_figure_manager window = Tk.Tk() File /soft/python/lib/python2.6/lib-tk/Tkinter.py, line 1643, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable - Can anyone advise if there another way to invoke matplotlib that does not require graphic support? With respect to your suggestion that I run python setup.py build, I don't seem to have the necessary permissions but the sysadmin is very helpful and once I have a little more information on the new problem I'll get his help again. Thanks again, John Kerenyi -Original Message- From: Jouni K. Seppänen [mailto:j...@iki.fi] Sent: Wednesday, July 22, 2009 9:38 AM To: matplotlib-users@lists.sourceforge.net Subject: Re: [Matplotlib-users] PDF backend errors out; PNG works fine John Kerenyi jo...@moval.org writes: File /soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_ pd f.py, line 44, in module from matplotlib import ttconv ImportError: /soft/python/lib/python2.6/site-packages/matplotlib/ttconv.so: undefined symbol: _ZTVSt19basic_ostringstreamIcSt11char_traitsIcESaIcEE Sounds like a mismatch between C++ libraries on the system where matplotlib was built and where it is being used. You mentioned a cluster; perhaps your sysadmin compiled matplotlib on a special node that has more libraries installed than the computation nodes. I don't know how to fix this, but as a first step you could try compiling matplotlib on a computation node (submit something like python setup.py build as a job the same way you would submit another task on the cluster) and seeing if that gives more clues about what is missing. -- Jouni K. Seppänen http://www.iki.fi/jks -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list 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 -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] SourceForge is telling me that there are no mirrors for the windows installer
Is anyone else having this problem? Is there another website that I can try? -mike w. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] problem with svn install (Davide Lasagna)
Well, actually i'm using Ubuntu at work on a virtual machine, and the svn copy is in a partition mounted at boot by a line in /etc/fstab. If i remember correctly this filesystem is mounted with options users. I'm at home now, i'll try with the exec option tomorrow. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] SourceForge is telling me that there are no mirrors for the windows installer
Never mind I found a mirror at http://www.lfd.uci.edu/~gohlke/download/matplotlib-0.98.5.3.win32-py2.6.zip -mike w. Mike Waters wrote: Is anyone else having this problem? Is there another website that I can try? -mike w. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Turning off the timezone (and more) in AutoDateFormatter
Hi all,
I'm passing in None for the timezone in AutoDateFormatter.
What I am getting is UTC, but what I want is nothing.
Looking at the code, I see lines like:
self._formatter = DateFormatter(%H:%M:%S %Z, self._tz)
so my None is getting passed through. Then in DateFormatter, I see:
if tz is None: tz = _get_rc_timezone()
Which looks like it's getting a timezone from an rc parameter. This
strikes me as not such a good idea. Far too easy to get the timezone
wrong -- I'm not sure there should be such a thing as a default time zone.
However, the issue at hand is that I want to not show the timezone at
all. I would have thought that None would be a good way to spell that,
but it's taken already to mean default.
So that means editing/overriding AutoDateFormatter. The way it's
written, I pretty much have to re-write the entire thing, which isn't so
bad, but it might be nicer if we could make it easier to override just
part of it.
One idea:
Some say that the right way to spell case/switch in Python is a
dict, rather than a collection of if--elifs. So in this case, we could
make a dict of format strings, something like below.
I've tried this, and I can now easily override the formatting for a
particular time range, like so:
Formatter = mpl.dates.AutoDateFormatter(locator, tz=None)
# edit the format strings to remove the TZ spec
# this only works with my custom version of AutoDateLocator
Formatter.format_strings[1.0/24.0] = %H:%M:%S
I do agree with the comments that there are other ways to improve this,
but maybe this is a start.
-Chris
class AutoDateFormatter(ticker.Formatter):
This class attempts to figure out the best format to use. This is
most useful when used with the :class:`AutoDateLocator`.
# This can be improved by providing some user-level direction on
# how to choose the best format (precedence, etc...)
# Perhaps a 'struct' that has a field for each time-type where a
# zero would indicate don't show and a number would indicate
# show with some sort of priority. Same priorities could mean
# show all with the same priority.
# Or more simply, perhaps just a format string for each
# possibility...
def __init__(self, locator, tz=None):
self._locator = locator
self._formatter = DateFormatter(%b %d %Y %H:%M:%S %Z, tz)
self._tz = tz
self.format_strings = { 365.0 : %Y,
30.0 : %b %Y,
1.0 : %b %d %Y,
7.0 : %b %d %Y,
1.0/24.0 : %H:%M:%S %Z,
1.0/(24*60) : %H:%M:%S %Z,
1.0/(24*3600) : %H:%M:%S %Z,
}
self.fallback_format = %b %d %Y %H:%M:%S %Z
def __call__(self, x, pos=0):
scale = float( self._locator._get_unit() )
f_string = self.format_strings.get(scale, self.fallback_format)
self._formatter = DateFormatter(f_string, self._tz)
return self._formatter(x, pos)
--
Christopher Barker, Ph.D.
Oceanographer
Emergency Response Division
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7600 Sand Point Way NE (206) 526-6329 fax
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Emergency Response Division
NOAA/NOS/ORR(206) 526-6959 voice
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[Matplotlib-users] Two different definitions of autocorrelation?
Hi,
I'm used to the following definition of autocorrelation:
R(\tau) = \frac{(X_t - \mu)(X_{t+\tau}-\mu)}{\sigma^2}
However, it looks like acorr is just giving me
R(\tau) = \sum{X_t*X_{t+\tau}}
Just specifying normed=True doesn't get the first formula. Is there some
trivial option that I've missed?
Here's what I did:
It's easy enough to subtract \mu from my timeseries, but when I ask acorr to
normalize things for me, I get the whole timeseries normalized by the value
of R(0):
if normed: c/= np.dot(x,x)
I really do want the formula I gave, which requires each point of the
autocorrelation to be averaged separately. So, I modified my local version
of acorr to say
if normed:
nrm = arange(len(x))
nrm = hstack((nrm,nrm[:-1][::-1]))*std(x)**2
c /= nrm
Thanks,
-michael
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[Matplotlib-users] log plots do not work when using base 2
I've written a python gui to matplotlib which allows the user to plot either cartesian, semi-log, or log-log plots. Log plots can be generated for typical base values except for base 2. Is this a bug, or is there some reason that matplotlib does not do log plots using base 2? Using base 2, the log-log plot error is: -- begin snippet - Exception in Tkinter callback Traceback (most recent call last): File C:\python251_102507\lib\lib-tk\Tkinter.py, line 1403, in __call__ return self.func(*args) File C:\python251_102507\lib\site-packages\matplotlib\backends\backend_tkagg. py, line 211, in resize self.show() File C:\python251_102507\lib\site-packages\matplotlib\backends\backend_tkagg. py, line 214, in draw FigureCanvasAgg.draw(self) File C:\python251_102507\lib\site-packages\matplotlib\backends\backend_agg.py , line 261, in draw self.figure.draw(self.renderer) File C:\python251_102507\lib\site-packages\matplotlib\figure.py, line 759, i n draw for a in self.axes: a.draw(renderer) File C:\python251_102507\lib\site-packages\matplotlib\axes.py, line 1523, in draw a.draw(renderer) File C:\python251_102507\lib\site-packages\matplotlib\axis.py, line 712, in draw for tick, loc, label in self.iter_ticks(): File C:\python251_102507\lib\site-packages\matplotlib\axis.py, line 659, in iter_ticks minorLocs = self.minor.locator() File C:\python251_102507\lib\site-packages\matplotlib\ticker.py, line 1026, in __call__ if len(subs) 1 or subs[0] != 1.0: IndexError: index out of bounds - end snippet - -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] waitfor/uiwait for show figure - wait until figure is closed - show next figure - wait until figure is closed - ...?
Hi, basically I'm looking for something like 'waitfor' or 'uiwait' from the Matlab. I want to achieve is the following behavior: - show a figure with several subplot/images to the user - let the user click on some stuff to get coordinates, handles, ... - wait until the user has closed the window - based on the returned data, show a new figure and let the user select some more stuff - repeat What is the best way to do something similar in matplotlib? I tried to use pylab.show() several times in the same script but then soon found out that this is not recommend / does not work. Right now a combination of ion() and waitforbuttonpress seems to be the only way to achieve something similar to what i want to do, but i was wondering if there are other ways. Any ideas? Thanks, Jan -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] ipython --pylab without namespace pollution?
On Wed, Jul 22, 2009 at 6:09 PM, Christopher Barker chris.bar...@noaa.govwrote: Hi folks, Does anyone know if there is a way to use ipython with the advantages of the -pylab option (separate gui thread, etc.), but without the whole pylab namespace getting sucked in? Put this in your ~/.ipython/ipythonrc: pylab_import_all 0 That gives you exactly what you want. In my case, I also made a profile that imports numpy as np and matplotlib.pyplot as plt, so that I can get the equivalent of the ease pylab without the pollution. Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma Sent from Norman, Oklahoma, United States -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] How to disable imshow blurring/interpolation
Hi all, I have just migrated from Matlab to Scipy. Matplotlib has been great so far. However, I have some trouble getting imshow to behave like Matlab's image function. If you do image(eye(8)) in matlab, you get this: http://www.flickr.com/photos/phineasgage/3746211714/ If you do imshow(eye(8)) in matplotlib, you get this: http://www.flickr.com/photos/phineasgage/3745417651/ How do I get matplotlib to stop interpolating or blurring the borders in the image? I have tried setting interpolation=None (the default behaviour), but this has no effect. I use matplotlib-0.98.5.2n2 as part of the Enthought distro on Red Hat 4 Linux. Any help would be greatly appreciated. Johan -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] log base 2 plots
I've written a python gui to matplotlib which allows the user to plot either cartesian, semi-log, or log-log plots. Log plots can be generated for typical base values except for base 2. Is this a bug, or is there some reason that matplotlib does not do log plots using base 2? -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Help with plot_directive
Hello, I am running Matplotlib 0.98.6svn compiled from source on OSX and Sphinx 0.6.2. I am trying the following example to test plot_directive .. plot:: from numpy import linspace, sin import matplotlib.pylab as plt x = linspace(0.01,25, 1) plt.plot(x, sin(x)/x) plt.show() When I 'make html', I get the warning messages: /Users/dpo/local/dev/pyorder/doc/source/pymc60.rst:: WARNING: image file not readable: build/plot_directive/inline/2d6f2be741.png /Users/dpo/local/dev/pyorder/doc/source/pymc60.rst:: WARNING: image file not readable: build/plot_directive/inline/2d6f2be741.pdf and the plot is not embedded in my html page. The links 'hires.png' and 'pdf' do point to (readable) images, though. From build/html: $ ls -l plot_directive/inline/ total 104 -rw-r--r-- 1 dpo dpo 41347 22 Jul 20:01 2d6f2be741.hires.png -rw-r--r-- 1 dpo dpo 7370 22 Jul 20:01 2d6f2be741.pdf Strangely, there is no 'png' link even though my conf.py specifies plot_formats = ['png', 'hires.png', 'pdf'] If I look at the generated html, I notice that the img tag wants the png, which doesn't exist. That is one problem. The other problem is that the img tag searches for the png file in build/plot_directive/inline/, which does not exist either. The same happens in the LaTeX output. When I 'make latex' followed by 'make all-pdf' from build/latex, I get the error message: LaTeX Warning: File `build/plot_directive/inline/2d6f2be741.pdf' not found on input line 499. !pdfTeX error: pdflatex (file build/plot_directive/inline/2d6f2be741.pdf): cannot find image file == Fatal error occurred, no output PDF file produced! Indeed, the image files are in plot_directive/inline/ and not in build/plot_directive/inline/. Changing the path in the .tex solves the problem. Thanks in advance, Dominique -- View this message in context: http://www.nabble.com/Help-with-plot_directive-tp24617359p24617359.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] memory leak with PyQt4 plus savefig or print_figure
Ralph,
Perhaps time to migrate to Chaco API from Enthought? not sure if there is
Ubuntu support yet however.
Alex Baker
http://code.enthought.com/chaco/
Ralf Gommers-2 wrote:
Hi,
I am working on a PyQt4 application with some embedded MPL figures, and am
also trying to save some figures as png's without displaying them. I am
observing huge memory increases (10s or 100s of Mb) the moment I try to
save
a png. I reproduced the issue by combining two mpl examples,
http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_qt4.htmland
http://matplotlib.sourceforge.net/examples/api/agg_oo.html. Full code is
attached. When pressing the save figure button, memory usage shoots up,
multiple clicks keep sending it higher (although not monotonically).
I tested on two different platforms
- Matplotlib 98.5.2 and Python 2.6.2 on Ubuntu.
- latest Enthought Python Distribution on Windows XP.
The function that does the png saving is:
def save_png():
Save an image as a png file
pngpath = 'test_mplsave.png'
fig = Figure()
canvas = FigureCanvas(fig)
ax = fig.add_subplot(111)
x = arange(5e3)
ax.plot(x, sin(x))
canvas.print_figure(pngpath)
## tried all things commented out below, all makes no difference ##
#fig.savefig(pngpath)
#del(fig)
#del(canvas)
#del(ax)
#import matplotlib.pyplot as plt
#plt.close(fig)
#import gc
#gc.collect()
Commenting out the canvas.print_figure line fixes the issue.
Am I doing something obviously wrong, or mixing two incompatible ways of
doing things?
Cheers,
Ralf
#!/usr/bin/env python
# embedding_in_qt4.py --- Simple Qt4 application embedding matplotlib
canvases
#
# Copyright (C) 2005 Florent Rougon
# 2006 Darren Dale
#
# This file is an example program for matplotlib. It may be used and
# modified with no restriction; raw copies as well as modified versions
# may be distributed without limitation.
import sys, os, random
from PyQt4 import QtGui, QtCore
from numpy import arange, sin, pi
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as
FigureCanvas
from matplotlib.figure import Figure
class MyMplCanvas(FigureCanvas):
Ultimately, this is a QWidget (as well as a FigureCanvasAgg,
etc.).
def __init__(self, parent=None, width=5, height=4, dpi=100):
fig = Figure(figsize=(width, height), dpi=dpi)
self.axes = fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
FigureCanvas.__init__(self, fig)
self.setParent(parent)
FigureCanvas.setSizePolicy(self,
QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def compute_initial_figure(self):
pass
class MyStaticMplCanvas(MyMplCanvas):
Simple canvas with a sine plot.
def compute_initial_figure(self):
t = arange(0.0, 3.0, 0.01)
s = sin(2*pi*t)
self.axes.plot(t, s)
def save_png():
Save an image as a png file
pngpath = 'test_mplsave.png'
fig = Figure()
canvas = FigureCanvas(fig)
ax = fig.add_subplot(111)
x = arange(5e3)
ax.plot(x, sin(x))
#canvas.print_figure(pngpath)
## tried all things commented out below, all makes no difference ##
#fig.savefig(pngpath)
#del(fig)
#del(canvas)
#del(ax)
#import matplotlib.pyplot as plt
#plt.close(fig)
#import gc
#gc.collect()
class ApplicationWindow(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle(application main window)
self.file_menu = QtGui.QMenu('File', self)
self.file_menu.addAction('Quit', self.fileQuit,
QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
self.menuBar().addMenu(self.file_menu)
self.help_menu = QtGui.QMenu('Help', self)
self.main_widget = QtGui.QWidget(self)
l = QtGui.QVBoxLayout(self.main_widget)
sc = MyStaticMplCanvas(self.main_widget, width=5, height=4,
dpi=100)
dc = QtGui.QPushButton('Save image')
l.addWidget(sc)
l.addWidget(dc)
self.main_widget.setFocus()
self.setCentralWidget(self.main_widget)
self.statusBar().showMessage(All hail matplotlib!, 2000)
self.connect(dc, QtCore.SIGNAL(clicked()), save_png)
def fileQuit(self):
self.close()
def closeEvent(self, ce):
self.fileQuit()
qApp = QtGui.QApplication(sys.argv)
aw = ApplicationWindow()
aw.setWindowTitle(Try saving a simple png image)
aw.show()
sys.exit(qApp.exec_())
[Matplotlib-users] bar charts can't handle datetimes with less than a day between datapoints?
Hi, I'm worried that I'm doing something stupid, but can't quite spot it. testBarCharts() :- X axis in integers. Works fine. testBarChartsDTMonths() :- X axis in datetimes, 1 month between data points. Works fine testBarChartsDTHours() :- X axis in datetimes, 1 hour between data points. Bars seem to extend as far to the right as possible. When printing the list of patches returned from plotting, the widths are reported as 0.8, though. Am I screwing up or is this a matplotlib bug? Using matplotlib-0.98.5.3.win32-py2.6.exe and numpy-1.3.0-win32-superpack-python2.6.exe Many thanks, Nick import matplotlib.pyplot as plt import matplotlib.dates import datetime # This works fine def testBarCharts(): xs = [10,11,12,13] ys = [100,300,200,600] fig = plt.figure(figsize=(20,12)) # dims in inches ax1 = fig.add_subplot(111) ax1.set_ylabel(foo) rects = ax1.bar(xs,ys,color=(1,0,0)) # debugging print xs print ys for r in rects: print r.get_xy(),r.get_width(),x,r.get_height() fig.savefig(foo.png) plt.close(fig) # FIXME: This is all wonky def testBarChartsDTHours(): xs = [ \ datetime.datetime(2009,6,29,10), datetime.datetime(2009,6,29,11), datetime.datetime(2009,6,29,12), datetime.datetime(2009,6,29,13) ] ys = [100,300,200,600] fig = plt.figure(figsize=(20,12)) # dims in inches ax1 = fig.add_subplot(111) ax1.set_ylabel(foo) ax1.xaxis_date() min_x = min(xs) max_x = max(xs)+datetime.timedelta(0,2*60*60) rects = ax1.bar(xs,ys,color=(1,0,0)) # XXX note that all the rectangle dimensions look sane print xs print ys for r in rects: print r.get_xy(),r.get_width(),x,r.get_height() ax1.set_xbound(min_x,max_x) fig.savefig(foo1.png) plt.close(fig) # Works def testBarChartsDTMonths(): xs = [ \ datetime.datetime(2009,6,1), datetime.datetime(2009,7,1), datetime.datetime(2009,8,1), datetime.datetime(2009,9,1) ] ys = [100,300,200,600] fig = plt.figure(figsize=(20,12)) # dims in inches ax1 = fig.add_subplot(111) ax1.set_ylabel(foo) ax1.xaxis_date() min_x = min(xs) max_x = max(xs)+datetime.timedelta(1) rects = ax1.bar(xs,ys,color=(1,0,0)) # debugging print xs print ys for r in rects: print r.get_xy(),r.get_width(),x,r.get_height() ax1.set_xbound(min_x,max_x) fig.savefig(foo2.png) plt.close(fig) if __name__=='__main__': testBarCharts() testBarChartsDTMonths() testBarChartsDTHours() -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] log base 2 plots
I've written a python gui to matplotlib which allows the user to plot either cartesian, semi-log, or log-log plots. Log plots can be generated for typical base values except for base 2. Is this a bug, or is there some reason that matplotlib does not do log plots using base 2? -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] ipython --pylab without namespace pollution?
On Wed, Jul 22, 2009 at 8:04 PM, Ryan Mayrma...@gmail.com wrote: On Wed, Jul 22, 2009 at 6:09 PM, Christopher Barker chris.bar...@noaa.gov wrote: Hi folks, Does anyone know if there is a way to use ipython with the advantages of the -pylab option (separate gui thread, etc.), but without the whole pylab namespace getting sucked in? Put this in your ~/.ipython/ipythonrc: pylab_import_all 0 That gives you exactly what you want. In my case, I also made a profile that imports numpy as np and matplotlib.pyplot as plt, so that I can get the equivalent of the ease pylab without the pollution. Hey Ryan -- could you write up a sphinx/rest FAQ that describes all these steps in detail, eg how you create the profile and how you start ipython, so we can add it to the site docs? If you are uncomfortable with the docs, I can apply the patch. Thanks JDH -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] How to disable imshow blurring/interpolation
Johan Carlin wrote: Hi all, I have just migrated from Matlab to Scipy. Matplotlib has been great so far. However, I have some trouble getting imshow to behave like Matlab's image function. If you do image(eye(8)) in matlab, you get this: http://www.flickr.com/photos/phineasgage/3746211714/ If you do imshow(eye(8)) in matplotlib, you get this: http://www.flickr.com/photos/phineasgage/3745417651/ How do I get matplotlib to stop interpolating or blurring the borders in the image? I have tried setting interpolation=None (the default behaviour), but this has no effect. interpolation='nearest' Eric I use matplotlib-0.98.5.2n2 as part of the Enthought distro on Red Hat 4 Linux. Any help would be greatly appreciated. Johan -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] ipython --pylab without namespace pollution?
On Wed, Jul 22, 2009 at 8:34 PM, John Hunter jdh2...@gmail.com wrote: On Wed, Jul 22, 2009 at 8:04 PM, Ryan Mayrma...@gmail.com wrote: On Wed, Jul 22, 2009 at 6:09 PM, Christopher Barker chris.bar...@noaa.gov wrote: Hi folks, Does anyone know if there is a way to use ipython with the advantages of the -pylab option (separate gui thread, etc.), but without the whole pylab namespace getting sucked in? Put this in your ~/.ipython/ipythonrc: pylab_import_all 0 That gives you exactly what you want. In my case, I also made a profile that imports numpy as np and matplotlib.pyplot as plt, so that I can get the equivalent of the ease pylab without the pollution. Hey Ryan -- could you write up a sphinx/rest FAQ that describes all these steps in detail, eg how you create the profile and how you start ipython, so we can add it to the site docs? If you are uncomfortable with the docs, I can apply the patch. I'm willing to. However, I just noticed that with just the pylab_import_all 0, you get the import numpy as np and import matplotlib.pyplot as plt automatically. Also, nicely, these don't show up when you type 'whos'. This is with ipython 0.9.1. Should I just add the pylab_import_all 0 to the FAQ? Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma Sent from Norman, Oklahoma, United States -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] ipython --pylab without namespace pollution?
On Wed, Jul 22, 2009 at 8:50 PM, Ryan Mayrma...@gmail.com wrote: I'm willing to. However, I just noticed that with just the pylab_import_all 0, you get the import numpy as np and import matplotlib.pyplot as plt automatically. Also, nicely, these don't show up when you type 'whos'. This is with ipython 0.9.1. Should I just add the pylab_import_all 0 to the FAQ? Should be enough, but it would be nice to have a little bit on how to write a profile to add extra imports (eg scipy as sp) to an ipython profile and load it in the same FAQ. Yes, they could find it reading the ipython docs, but the easier it is to get the info the more useful it will be. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] plotting 2d or 3d normal distribution pdf
hi all, i'm trying to find the function for the pdf of a multivariate normal pdf. i know that multivariate_normal can be used to sample from the multivariate normal distribution, but i just want to get the pdf for a given vector of means and a covariance matrix. is there a function to do this? thank you. -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] bar charts can't handle datetimes with less than a day between datapoints?
Ah, thanks! On Thu, Jul 23, 2009 at 12:18 PM, John Hunterjdh2...@gmail.com wrote: bar width or 1.0 corresponds to 1 day. The default width to the bar command is 0.8, which is too thin for months, just right for days, and too wide for hours. Eg, for hours do bar(x, y, width=0.8*1/24.) # width is 0.8 hours for months, do something like bar(x, y, width=0.8*30/24.) # width approx 80% of a month It would be nice for the documentation to say something like width: the widths of the bars as a proportion of the width of 1 day instead of width: the widths of the bars Nick -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
