Re: [Matplotlib-users] Colorbar not working with specgram

[davide lasagna]

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 
> >  
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> 


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Re: [Matplotlib-users] Problems with autofmt_xdate()

[Domenico Nappo]

2009/7/21 John Hunter 

>
> > 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/#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!
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Re: [Matplotlib-users] Colorbar not working with specgram

[Eric Firing]

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 
>>>  
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> 
> 
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Re: [Matplotlib-users] I really can't get into hist() barstacked

[Sandro Tosi]

On Tue, Jul 21, 2009 at 18:00, Sandro Tosi wrote:
> 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?

Just to clarify: from the above lists of values, I'm expecting to draw
something like:

  |
  s3  | s3[1]  s3[2]  s3[3]  ...
  s2  ->  | s2[1]  s2[2]  s2[3]  ...
  s1  | s1[1]  s1[2]  s1[3]  ...
--+---
  |

or

|  .........
| s1[3]  s2[3]  s3[3]
| s1[2]  s2[2]  s3[2]
 s1 s2 s3   ->  | s1[1]  s2[1]  s3[1]
  --+--
|

Either are fine (once I get how to do, I'll adapt data to that),
simply I don't know how to do that :)

Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi

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Re: [Matplotlib-users] I really can't get into hist() barstacked

[ms]

Sandro Tosi ha scritto:
> On Wed, Jul 22, 2009 at 10:25, ms 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

[Johann Cohen-Tanugi]

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
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>>   
> 
>
> --
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> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize  
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Re: [Matplotlib-users] I really can't get into hist() barstacked

[ms]

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.


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Re: [Matplotlib-users] Problems with autofmt_xdate()

[Domenico Nappo]

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 

>
>
> 2009/7/21 John Hunter 
>
>>
>> > 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/#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!
>
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[Matplotlib-users] PDF backend errors out; PNG works fine

[John Kerenyi]

Hello all,
 
I am a relatively new user of matplotlib but have come a long way in
these last couple months. I developed some Python graph scripts on my
Windows machine, which reports matplotlib version 0.98.5.2 (installed
via Python(x,y)). These scripts write either .png or .pdf files,
depending on how called; and they work fine in this environment.
 
Now that my scripts are suitable for running unattended, I've asked a
Linux system administrator to install matplotlib on a Linux cluster
which I use for my main application, and he did so from source. The
version that is reported is 0.98.5.3.
 
When I run the script in the Linux environment, png files are written as
intended, with no errors, but attempting to create pdf graphs generates
the following error for the first occurrence of savefig:
 
---
 
[ac.jkere...@l01 pygraph]$ ./run_pygraph.py pdf
Creating Top 100 V/C ratios graph...
MaxVCRatios.pdf
Traceback (most recent call last):
  File "./run_pygraph.py", line 566, in 
GraphTop100VC (Top100VCFilename)
  File "./run_pygraph.py", line 369, in GraphTop100VC
fig.savefig("MaxVCRatios"+OutputImageType,format="pdf")
  File "/soft/python/lib/python2.6/site-packages/matplotlib/figure.py",
line 990, in savefig
self.canvas.print_figure(*args, **kwargs)
  File
"/soft/python/lib/python2.6/site-packages/matplotlib/backend_bases.py",
line 1419, in print_figure
**kwargs)
  File
"/soft/python/lib/python2.6/site-packages/matplotlib/backend_bases.py",
line 1311, in print_pdf
from backends.backend_pdf import FigureCanvasPdf # lazy import
  File
"/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_pd
f.py", line 44, in 
from matplotlib import ttconv
ImportError:
/soft/python/lib/python2.6/site-packages/matplotlib/ttconv.so: undefined
symbol: _ZTVSt19basic_ostringstreamIcSt11char_traitsIcESaIcEE

-
 
The expression "MaxVCRatios"+OutputImageType resolves to the string
"MaxVCRatios.pdf" (confirmed by the second output line of the script,
which was printed for testing purposes). I played with providing or
omitting the format="pdf" parameter and it made no difference. I've also
searched for others with a similar issue and found none so I'm posting
to this list to see if anyone can help. I need to know if this is a
problem with my script, or if it's something the system administrator
needs to fix. Let me know if there's any additional information you
would like me to provide.
 
Thanks,
 
John K.
 
John Kerenyi, P.E. 
Senior Traffic Engineer 
City of Moreno Valley 
14177 Frederick Street
P.O. Box 88005
Moreno Valley, CA  92552-0805
(951) 413-3199
(951) 413-3141 fax 
jo...@moval.org
 
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[Matplotlib-users] imshow background and/or colour to alpha

[massimo sandal]

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.

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[Matplotlib-users] problem with svn install

[davide lasagna]

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 
from pylab import *
  File "/home/davide/partizione/matplotlib/lib/pylab.py", line 1, in 
from matplotlib.pylab import *
  File "/home/davide/partizione/matplotlib/lib/matplotlib/pylab.py", line 206, 
in 
from matplotlib import mpl  # pulls in most modules
  File "/home/davide/partizione/matplotlib/lib/matplotlib/mpl.py", line 1, in 

from matplotlib import artist
  File "/home/davide/partizione/matplotlib/lib/matplotlib/artist.py", line 5, 
in 
from transforms import Bbox, IdentityTransform, TransformedBbox, 
TransformedPath
  File "/home/davide/partizione/matplotlib/lib/matplotlib/transforms.py", line 
34, in 
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








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Re: [Matplotlib-users] PDF backend errors out; PNG works fine

[Jouni K . Seppänen]

"John Kerenyi"  writes:

>   File
> "/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_pd
> f.py", line 44, in 
> 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


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Re: [Matplotlib-users] problem with svn install

[Jouni K . Seppänen]

davide lasagna  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.

-- 
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[Matplotlib-users] animate histogram

[Alan G Isaac]

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

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Re: [Matplotlib-users] problem with svn install

[Gökhan SEVER]

On Wed, Jul 22, 2009 at 11:47 AM, Jouni K. Seppänen  wrote:

> davide lasagna  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
>
>
>
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>


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
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Re: [Matplotlib-users] PDF backend errors out; PNG works fine

[John Kerenyi]

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 
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"  writes:

>   File
> "/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_
> pd
> f.py", line 44, in 
> 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


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Re: [Matplotlib-users] PDF backend errors out; PNG works fine

[Michael Droettboom]

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 
> 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"  writes:
>
>   
>>   File
>> "/soft/python/lib/python2.6/site-packages/matplotlib/backends/backend_
>> pd
>> f.py", line 44, in 
>> 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
>
>
> --
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>
> --
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>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA


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[Matplotlib-users] SourceForge is telling me that there are no mirrors for the windows installer

[Mike Waters]

Is anyone else having this problem? Is there another website that I can 
try?

-mike w.

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Re: [Matplotlib-users] problem with svn install (Davide Lasagna)

[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.
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Re: [Matplotlib-users] SourceForge is telling me that there are no mirrors for the windows installer

[Mike Waters]

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.
>
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>
>   


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[Matplotlib-users] Turning off the timezone (and more) in AutoDateFormatter

[Christopher Barker]

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
NOAA/NOS/OR&R(206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115   (206) 526-6317   main reception

chris.bar...@noaa.gov

-- 
Christopher Barker, Ph.D.
Oceanographer

Emergency Response Division
NOAA/NOS/OR&R(206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115   (206) 526-6317   main reception

chris.bar...@noaa.gov

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[Matplotlib-users] Two different definitions of autocorrelation?

[Michael Lerner]

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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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [Matplotlib-users] griddata returns nan

[Jeff Whitaker]

plankton wrote:
> Greetings all,
>
> I rotate a vector field and than I tried to interpolate it to a new grid
> using griddata. 
>
> CODE:
>
> x_grid_unique = unique(x_grid)
> y_grid_unique = unique(y_grid)
> x_meshgrid,  y_meshgrid =   meshgrid(x_grid_unique, y_grid_unique)
> x_rot_meshgrid = reshape(x_rot,  [ len(x_meshgrid[:, 0]),
> len(x_meshgrid[0, :])] )
> y_rot_meshgrid = reshape(y_rot,  [ len(x_meshgrid[:, 0]),
> len(x_meshgrid[0, :])] )
> u_rot_meshgrid = reshape(u_rot,  [ len(x_meshgrid[:, 0]),
> len(x_meshgrid[0, :])] )
> v_rot_meshgrid = reshape(v_rot,  [ len(x_meshgrid[:, 0]),
> len(x_meshgrid[0, :])] )
> u_interpolate = griddata(x_rot,  y_rot, u_rot,  x_rot_meshgrid, 
> y_rot_meshgrid)
> v_interpolate = griddata(x_rot,  y_rot, v_rot,  x_rot_meshgrid, 
> y_rot_meshgrid)
>
>
>
> I unfortunately griddata returns some nan (It seems that there are multiple
> occurrences of the same [X,Y] pair in the data). In matlab you can use
> griddata with additional options  e.g. ru =
> griddata(nx,ny,nu,rx,ry,'linear', {'QJ'}) to fix this, but this seems to be
> not possible using the griddata function in matplotlib. Is there any other
> way to avoid a return of nan?
>
> For any help many thanks in advance
>
> Andreas
>
>
>
>   
Andreas:  Can you provide a standalone script that I can run which 
demonstrates the problem?  Otherwise, it's hard to know what's going on.

-Jeff

-- 
Jeffrey S. Whitaker Phone  : (303)497-6313
Meteorologist   FAX: (303)497-6449
NOAA/OAR/PSD  R/PSD1Email  : jeffrey.s.whita...@noaa.gov
325 BroadwayOffice : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web: http://tinyurl.com/5telg


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[Matplotlib-users] log plots do not work when using base 2

[Barnette, Daniel W]

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 -


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[Matplotlib-users] ipython --pylab without namespace pollution?

[Christopher Barker]

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?

I love ipython pylab mode, but like to use namespaces to keep things clean.

thanks,

-Chris



-- 
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Oceanographer

Emergency Response Division
NOAA/NOS/OR&R(206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115   (206) 526-6317   main reception

chris.bar...@noaa.gov

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[Matplotlib-users] waitfor/uiwait for "show figure -> wait until figure is closed -> show next figure -> wait until figure is closed -> ..."?

[Jan Müller]

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
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Re: [Matplotlib-users] ipython --pylab without namespace pollution?

[Robert Kern]

On 2009-07-22 18:09, Christopher Barker 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?
>
> I love ipython pylab mode, but like to use namespaces to keep things clean.

ipython -wthread

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth."
   -- Umberto Eco


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Re: [Matplotlib-users] ipython --pylab without namespace pollution?

[Ryan May]

On Wed, Jul 22, 2009 at 6:09 PM, Christopher Barker
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.

Ryan

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[Matplotlib-users] How to disable imshow blurring/interpolation

[Johan Carlin]

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
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[Matplotlib-users] log base 2 plots

[Barnette, Daniel W]

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?

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[Matplotlib-users] Help with plot_directive

[dpo]

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

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Re: [Matplotlib-users] memory leak with PyQt4 plus savefig or print_figure

[Alexander Baker]

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.

[Matplotlib-users] bar charts can't handle datetimes with less than a day between datapoints?

[Nick Seow]

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()

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[Matplotlib-users] log base 2 plots

[Barnette, Daniel W]

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?

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Re: [Matplotlib-users] ipython --pylab without namespace pollution?

[John Hunter]

On Wed, Jul 22, 2009 at 8:04 PM, Ryan May wrote:
> On Wed, Jul 22, 2009 at 6:09 PM, Christopher Barker 
> 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

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Re: [Matplotlib-users] How to disable imshow blurring/interpolation

[Eric Firing]

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
> 
> 
> 
> 
> --
> 
> 
> 
> 
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Re: [Matplotlib-users] ipython --pylab without namespace pollution?

[Ryan May]

On Wed, Jul 22, 2009 at 8:34 PM, John Hunter  wrote:

> On Wed, Jul 22, 2009 at 8:04 PM, Ryan May 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
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Re: [Matplotlib-users] ipython --pylab without namespace pollution?

[John Hunter]

On Wed, Jul 22, 2009 at 8:50 PM, Ryan May 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.

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Re: [Matplotlib-users] log base 2 plots

[John Hunter]

On Tue, Jul 21, 2009 at 3:32 PM, Barnette, Daniel W wrote:
> 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?

Can you post an example which shows your problem?  The following works for me:

  In [14]: x, y = np.random.rand(2, 100)

  In [15]: loglog(x, y, basex=2)
  Out[15]: []

JDH

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Re: [Matplotlib-users] bar charts can't handle datetimes with less than a day between datapoints?

[John Hunter]

On Tue, Jul 21, 2009 at 8:00 PM, Nick Seow wrote:
> 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

under the hood, mpl converts datetime objects to days since 1/1/,
using a floating point representation for fractions of a day.  So a
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

Perhaps bar should take a width=None arg and try to infer the ideal
with, eg assuming even spacing, but for now you need to specify the
width in fractional days when making bar plots with datetimes.

JDH

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[Matplotlib-users] plotting 2d or 3d normal distribution pdf

[per freem]

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.
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Re: [Matplotlib-users] bar charts can't handle datetimes with less than a day between datapoints?

[Nick Seow]

Ah, thanks!

On Thu, Jul 23, 2009 at 12:18 PM, John Hunter 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

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Re: [Matplotlib-users] problem with svn install

[davide lasagna]

Yes,
That did it. The partition had to be mounted with option
execin /etc/fstab!!
Thanks.

Cheers

Davide


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