Re: [Matplotlib-users] XKCD style graphs?

2012-10-05 Thread Matthias BUSSONNIER 

Le 4 oct. 2012 à 23:09, Juergen Hasch a écrit :

> Here is my take on it as an IPython notebook, based on Damon's code:
> http://nbviewer.ipython.org/3835181/
> 
> I took the engineering approach and filtered the random function instead of 
> doing some fft/ifft magic.
> Also, X and Y of the functions are affected now, giving them a more "natural" 
> look in the slopes.
> 
>   Juergen

If anyone have time to make some examples and a right side thumbnail
I can make it as featured notebook in the front page of nbviewer.

You can even make a direct PR agains nbviewer and I would then just have 
to merge and deploy.

To be fair, notebook should also give some explanation of the code, 
link to this discussion, maybe show one "original" xkcd graph.

Please take your time, and if there is several submission,
we'll sort out how to choose the best(s).

-- 
Matthias

> 
> 
> Am 04.10.2012 18:09, schrieb Pierre Haessig:
>> Le 04/10/2012 16:35, Pierre Haessig a écrit :
>>> So I think this code indeed resamples the rastered plot image on a
>>> shaken coordinate grid. I kind of understand that the noise on
>>> coordinates is spatially smoothed by a 10px Gaussian Point Spread
>>> Function (if I understand correctly...)
>> I've implemented this processing in a tiny "image_shake" script.
>> https://gist.github.com/3834536
>> A nice occasion to learn how to use some scipy image processing functions...
>> 
>> I've attached the before/after images because I didn't manage to put
>> them in the Gist (it's not a plot image but gives the idea of line shaking).
>> 
>> Now, I think it's unfortunately outside the frame of Fernando's
>> challenge, because this script uses zero matplotlib methods!!
>> 
>> Best,
>> Pierre
> 
> 
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Re: [Matplotlib-users] XKCD style graphs?

2012-10-05 Thread Damon McDougall 
On Fri, Oct 5, 2012 at 10:13 AM, Matthias BUSSONNIER
 wrote:
>
> Le 4 oct. 2012 à 23:09, Juergen Hasch a écrit :
>
>> Here is my take on it as an IPython notebook, based on Damon's code:
>> http://nbviewer.ipython.org/3835181/
>>
>> I took the engineering approach and filtered the random function instead of 
>> doing some fft/ifft magic.
>> Also, X and Y of the functions are affected now, giving them a more 
>> "natural" look in the slopes.
>>
>>   Juergen
>
> If anyone have time to make some examples and a right side thumbnail
> I can make it as featured notebook in the front page of nbviewer.
>
> You can even make a direct PR agains nbviewer and I would then just have
> to merge and deploy.
>
> To be fair, notebook should also give some explanation of the code,
> link to this discussion, maybe show one "original" xkcd graph.
>
> Please take your time, and if there is several submission,
> we'll sort out how to choose the best(s).
>
> --
> Matthias
>
>>
>>
>> Am 04.10.2012 18:09, schrieb Pierre Haessig:
>>> Le 04/10/2012 16:35, Pierre Haessig a écrit :
 So I think this code indeed resamples the rastered plot image on a
 shaken coordinate grid. I kind of understand that the noise on
 coordinates is spatially smoothed by a 10px Gaussian Point Spread
 Function (if I understand correctly...)
>>> I've implemented this processing in a tiny "image_shake" script.
>>> https://gist.github.com/3834536
>>> A nice occasion to learn how to use some scipy image processing functions...
>>>
>>> I've attached the before/after images because I didn't manage to put
>>> them in the Gist (it's not a plot image but gives the idea of line shaking).
>>>
>>> Now, I think it's unfortunately outside the frame of Fernando's
>>> challenge, because this script uses zero matplotlib methods!!
>>>
>>> Best,
>>> Pierre

This thread has made my week.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

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Re: [Matplotlib-users] EMF output: too many values to unpack error

2012-10-05 Thread Usjes 
Benjamin Root-2 wrote
> On Thu, Jun 9, 2011 at 12:40 PM, Klonuo Umom <

> klonuo@

> > wrote:
> 
> I set up pull requests to fix this problem, so the v1.0.x-maint branch and
> the master branch should soon have the fixes commited to them.  You can
> get
> the latest bugfixed branch for v1.0.1 at
> https://github.com/matplotlib/matplotlib/tree/v1.0.x-maint, although that
> would mean having to build from source.  You could also just edit your
> copy
> of the file C:\Python26\lib\site-
> packages\matplotlib\backends\backend_emf.py so that [:3] is added to the
> end
> of lines 69 and 105.  This page should show you what changes you need:
> https://github.com/WeatherGod/matplotlib/commit/bf8d9d6f7cea1546c736d3897387698e6ae5e5b3
> 
> I hope that helps!
> 
> Ben Root

Hi, 

I am having the same problem when trying to save a figure to a .emf file via
pylab.savefig(). 
I have tried updating backend_emf.py as suggested but this does not fix the
problem, it still has a problem with the updated code(see below).
The only difference I can see with the original poster is that I am using
backend_qt4agg.py rather than backend_wxagg.py in the original posters code.
This shouldn't change the fix, should it ?


pylab.savefig('nrg.emf')
Traceback (most recent call last):
  File "", line 1, in 
  File "C:\Python26\lib\site-packages\matplotlib\pyplot.py", line 363, in
savefig
return fig.savefig(*args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\figure.py", line 1084, in
savefig
self.canvas.print_figure(*args, **kwargs)
  File
"C:\Python26\lib\site-packages\matplotlib\backends\backend_qt4agg.py", line
144, in print_figure
FigureCanvasAgg.print_figure(self, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\backend_bases.py", line
1923, in print_figure
**kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\backend_bases.py", line
1723, in print_emf
return emf.print_emf(*args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 717, in print_emf
self.figure.draw(renderer)
  File "C:\Python26\lib\site-packages\matplotlib\artist.py", line 55, in
draw_wrapper
draw(artist, renderer, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\figure.py", line 738, in
draw
if self.frameon: self.patch.draw(renderer)
  File "C:\Python26\lib\site-packages\matplotlib\artist.py", line 55, in
draw_wrapper
draw(artist, renderer, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\patches.py", line 411, in
draw
renderer.draw_path(gc, tpath, affine, rgbFace)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 258, in draw_path
self.select_brush(rgbFace)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 565, in select_brush
brush=EMFBrush(self.emf,rgb)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 105, in __init__
r,g,b=rgb[:3]
ValueError: too many values to unpack




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Re: [Matplotlib-users] EMF output: too many values to unpack error

2012-10-05 Thread Benjamin Root 
On Fri, Oct 5, 2012 at 6:38 AM, Usjes  wrote:

> Benjamin Root-2 wrote
> > On Thu, Jun 9, 2011 at 12:40 PM, Klonuo Umom <
>
> > klonuo@
>
> > > wrote:
> >
> > I set up pull requests to fix this problem, so the v1.0.x-maint branch
> and
> > the master branch should soon have the fixes commited to them.  You can
> > get
> > the latest bugfixed branch for v1.0.1 at
> > https://github.com/matplotlib/matplotlib/tree/v1.0.x-maint, although
> that
> > would mean having to build from source.  You could also just edit your
> > copy
> > of the file C:\Python26\lib\site-
> > packages\matplotlib\backends\backend_emf.py so that [:3] is added to the
> > end
> > of lines 69 and 105.  This page should show you what changes you need:
> >
> https://github.com/WeatherGod/matplotlib/commit/bf8d9d6f7cea1546c736d3897387698e6ae5e5b3
> >
> > I hope that helps!
> >
> > Ben Root
>
> Hi,
>
> I am having the same problem when trying to save a figure to a .emf file
> via
> pylab.savefig().
> I have tried updating backend_emf.py as suggested but this does not fix the
> problem, it still has a problem with the updated code(see below).
> The only difference I can see with the original poster is that I am using
> backend_qt4agg.py rather than backend_wxagg.py in the original posters
> code.
> This shouldn't change the fix, should it ?
>
>
Does it fail for the example I originally gave?

from pylab import *
plot([1, 2, 3])
savefig("foobar.emf")


Ben Root
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Jianbao Tao 
I think that is a great idea. I think it is worthwhile to put a highlighted
spot, or whatever, that shows matplotlib plots in academic publications.
Additionally, it is good for enlarging the matplotlib user base to ask
people to acknowledge matplotlib in their papers if they use matplotlib to
make plots, and share links of their publications. Of course,
matplotlib.orgshould provide some sort of platform for people to share
that kind of
information, such as a public email address. Such acknowledgement is not a
hard thing to do, and I think most people, if not all, that benefit from
matplotlib would be more than happy to do so. :-)

Jianbao

Message: 4
> Date: Thu, 4 Oct 2012 22:31:34 -0600
> From: G?khan Sever 
> Subject: [Matplotlib-users] Matplotlib produced plots in academic
> journal articles
> To: matplotlib-users@lists.sourceforge.net
> Message-ID:
>  xekryyys9kf5zw9q7yigziaketio...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> Is there any collection of articles that shows academic articles using
> matplotlib produced plots? I have come across a few recent articles in my
> field with plots produced by matplotlib. Though, the mpl page shows some
> nice examples of publication quality plots, it would be nice to have a
> discipline specific collection of academic paper citations/links (hopefully
> mostly open-access titles) to raise awareness of mpl usage in academia by
> attracting other language users.
>
> What do you think?
>
> --
> G?khan
>
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Michael Droettboom 
This is a great idea.  Anything to raise the level of perceived 
"legitimacy" in the academic community would be great. We can definitely 
add content like this to the documentation and/or website.


Mike

On 10/05/2012 09:43 AM, Jianbao Tao wrote:
I think that is a great idea. I think it is worthwhile to put a 
highlighted spot, or whatever, that shows matplotlib plots in academic 
publications. Additionally, it is good for enlarging the matplotlib 
user base to ask people to acknowledge matplotlib in their papers if 
they use matplotlib to make plots, and share links of their 
publications. Of course, matplotlib.org  should 
provide some sort of platform for people to share that kind of 
information, such as a public email address. Such acknowledgement is 
not a hard thing to do, and I think most people, if not all, that 
benefit from matplotlib would be more than happy to do so. :-)


Jianbao

Message: 4
Date: Thu, 4 Oct 2012 22:31:34 -0600
From: G?khan Sever mailto:gokhanse...@gmail.com>>
Subject: [Matplotlib-users] Matplotlib produced plots in academic
journal articles
To: matplotlib-users@lists.sourceforge.net

Message-ID:
   
mailto:xekryyys9kf5zw9q7yigziaketio...@mail.gmail.com>>

Content-Type: text/plain; charset="utf-8"

Hello,

Is there any collection of articles that shows academic articles using
matplotlib produced plots? I have come across a few recent
articles in my
field with plots produced by matplotlib. Though, the mpl page
shows some
nice examples of publication quality plots, it would be nice to have a
discipline specific collection of academic paper citations/links
(hopefully
mostly open-access titles) to raise awareness of mpl usage in
academia by
attracting other language users.

What do you think?

--
G?khan



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Re: [Matplotlib-users] EMF output: too many values to unpack error

2012-10-05 Thread Usjes 
Benjamin Root-2 wrote
> On Fri, Oct 5, 2012 at 6:38 AM, Usjes <

> oisin_nz@.co

> > wrote:
> 
> Does it fail for the example I originally gave?
> 
> from pylab import *
> plot([1, 2, 3])
> savefig("foobar.emf")
> 
> 
> Ben Root

Yes, it fails even with the simple plot suggested; see log below. I am new
to Python but I did also try inserting the command:
print rgb 
preceding the offending line, to get an idea of what the dimensions of 'rgb'
are but the print statement also fails due to 'too many values to unpack'

savefig("foobar.emf")
Traceback (most recent call last):
  File "", line 1, in 
  File "C:\Python26\lib\site-packages\matplotlib\pyplot.py", line 363, in
savefig
return fig.savefig(*args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\figure.py", line 1084, in
savefig
self.canvas.print_figure(*args, **kwargs)
  File
"C:\Python26\lib\site-packages\matplotlib\backends\backend_qt4agg.py", line
144, in print_figure
FigureCanvasAgg.print_figure(self, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\backend_bases.py", line
1923, in print_figure
**kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\backend_bases.py", line
1723, in print_emf
return emf.print_emf(*args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 717, in print_emf
self.figure.draw(renderer)
  File "C:\Python26\lib\site-packages\matplotlib\artist.py", line 55, in
draw_wrapper
draw(artist, renderer, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\figure.py", line 738, in
draw
if self.frameon: self.patch.draw(renderer)
  File "C:\Python26\lib\site-packages\matplotlib\artist.py", line 55, in
draw_wrapper
draw(artist, renderer, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\patches.py", line 411, in
draw
renderer.draw_path(gc, tpath, affine, rgbFace)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 258, in draw_path
self.select_brush(rgbFace)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 565, in select_brush
brush=EMFBrush(self.emf,rgb)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_emf.py",
line 105, in __init__
r,g,b=rgb[:3]
ValueError: too many values to unpack



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Re: [Matplotlib-users] EMF output: too many values to unpack error

2012-10-05 Thread Benjamin Root 
On Fri, Oct 5, 2012 at 10:47 AM, Usjes  wrote:

> Benjamin Root-2 wrote
> > On Fri, Oct 5, 2012 at 6:38 AM, Usjes <
>
> > oisin_nz@.co
>
> > > wrote:
> >
> > Does it fail for the example I originally gave?
> >
> > from pylab import *
> > plot([1, 2, 3])
> > savefig("foobar.emf")
> >
> >
> > Ben Root
>
> Yes, it fails even with the simple plot suggested; see log below. I am new
> to Python but I did also try inserting the command:
> print rgb
> preceding the offending line, to get an idea of what the dimensions of
> 'rgb'
> are but the print statement also fails due to 'too many values to unpack'
>
>
Actually, that is very telling...  Did you restart python after editing the
.py file?  Python will only load a source file once in a session (unless
explicitly forced to do a reload, but that is not intended for newbies).
So, any changes to any source .py file will not take effect until you
restart your python session.  This is different from other languages like
Matlab.

Ben Root

P.S. - The way I am able to deduce this is that when an exception occurs,
the "compiled" code will tell python which lines it came from in the
original source file so that python can display the traceback.  If you edit
the source file to add a line before the line that triggers a traceback, it
can look like the wrong line is triggering the error because the compiled
code doesn't know that its source has been updated.
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Re: [Matplotlib-users] EMF output: too many values to unpack error

2012-10-05 Thread Usjes 
Benjamin Root-2 wrote
> Actually, that is very telling...  Did you restart python after editing
> the
> .py file?  Python will only load a source file once in a session (unless
> explicitly forced to do a reload, but that is not intended for newbies).
> So, any changes to any source .py file will not take effect until you
> restart your python session.  This is different from other languages like
> Matlab.
> 
> Ben Root
> 
> P.S. - The way I am able to deduce this is that when an exception occurs,
> the "compiled" code will tell python which lines it came from in the
> original source file so that python can display the traceback.  If you
> edit
> the source file to add a line before the line that triggers a traceback,
> it
> can look like the wrong line is triggering the error because the compiled
> code doesn't know that its source has been updated.

Yes, it now works for me , thanks. 
I didn't think a restart was necessary as I could see my '[:3]' edit in the
error msg, it hadn't occurred to me that it would source the code for the
error msg from the updated file even though it was out of sync with the
'compiled' version.

Usjes 





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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Fernando Perez 
On Fri, Oct 5, 2012 at 6:52 AM, Michael Droettboom  wrote:
> This is a great idea.  Anything to raise the level of perceived "legitimacy"
> in the academic community would be great. We can definitely add content like
> this to the documentation and/or website.

Our strategy:

- Prominent display on the main page of a citation request, along with
links on our top nav-bar:
http://ipython.org/#citing-ipython

- A copy/paste ready citation entry: http://ipython.org/citing.html

Matplotlib has a 'canonical' paper back in the same CISE issue that
can be used, here's the bibtex entry for it (should probably be
trimmed only to the main fields):

@Article{Hunter:2007,
  Author = {Hunter, J. D.},
  Title  = {Matplotlib: A 2D graphics environment},
  Journal= {Computing In Science \& Engineering},
  Volume = {9},
  Number = {3},
  Pages  = {90--95},
  abstract   = {Matplotlib is a 2D graphics package used for Python
   for application development, interactive scripting, and
   publication-quality image generation across user
   interfaces and operating systems.},
  address= {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,
   CA 90720-1314 USA},
  bdsk-url-1 =
{http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019},
  date-added = {2010-09-23 12:22:10 -0700},
  date-modified  = {2010-09-23 12:22:10 -0700},
  isi= {000245668100019},
  isi-recid  = {155389429},
  month  = may # "/" # jun,
  publisher  = {IEEE COMPUTER SOC},
  year   = 2007
}


Cheers,

f

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[Matplotlib-users] Problem with shared axis

2012-10-05 Thread Jianbao Tao 
Hi,

I am working on a time-series data browser based on matplotlib. In general,
it shows a N_row x 1_col stack of axes, which share the x axis, the time
axis. It is nice that matplotlib offers the sharex option so that the data
can be zoomed simultaneously in time. However, one problem with the sharex
option is that it not only shares the axis range (or limits, if you will),
but also the axis appearance, which is not always desirable. In my case, I
want the tick labels to be shown only on the bottom subplot. However, that
doesn't seem to be achievable with sharex.

The follow snippet demonstrates my example:
#- code 
import matplotlib.pyplot as plt
fig = plt.figure()
ax1 = fig.add_subplot(211)
ax2 = fig.add_subplot(212, sharex=ax1)

ax1.get_xaxis().set_ticklabels([]) # This also suppresses x tick labels of
ax2.
fig.canvas.draw()
#-- end of code 

Is there a workaround, hopefully simple and straightforward, to share range
(or limits) only among axes? Better yet, can this feature be added, like a
keyword sharexrange, in the future, if it is not already there? Of course,
the situation should be similar for y axis, too.

Thank you very much.

Jianbao
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Re: [Matplotlib-users] Problem with shared axis

2012-10-05 Thread Damon McDougall 
On Fri, Oct 5, 2012 at 5:44 PM, Jianbao Tao  wrote:
> Hi,
>
> I am working on a time-series data browser based on matplotlib. In general,
> it shows a N_row x 1_col stack of axes, which share the x axis, the time
> axis. It is nice that matplotlib offers the sharex option so that the data
> can be zoomed simultaneously in time. However, one problem with the sharex
> option is that it not only shares the axis range (or limits, if you will),
> but also the axis appearance, which is not always desirable. In my case, I
> want the tick labels to be shown only on the bottom subplot. However, that
> doesn't seem to be achievable with sharex.
>
> The follow snippet demonstrates my example:
> #- code 
> import matplotlib.pyplot as plt
> fig = plt.figure()
> ax1 = fig.add_subplot(211)
> ax2 = fig.add_subplot(212, sharex=ax1)
>
> ax1.get_xaxis().set_ticklabels([]) # This also suppresses x tick labels of
> ax2.
> fig.canvas.draw()
> #-- end of code 
>
> Is there a workaround, hopefully simple and straightforward, to share range
> (or limits) only among axes? Better yet, can this feature be added, like a
> keyword sharexrange, in the future, if it is not already there? Of course,
> the situation should be similar for y axis, too.
>
> Thank you very much.
>
> Jianbao

This was the first hit in a google search:
http://stackoverflow.com/questions/4209467/matplotlib-share-x-axis-but-dont-show-x-axis-tick-labels-for-both-just-one

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Gökhan Sever 
On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez wrote:

>
> @Article{Hunter:2007,
>   Author = {Hunter, J. D.},
>   Title  = {Matplotlib: A 2D graphics environment},
>   Journal= {Computing In Science \& Engineering},
>   Volume = {9},
>   Number = {3},
>   Pages  = {90--95},
>   abstract   = {Matplotlib is a 2D graphics package used for Python
>for application development, interactive scripting, and
>publication-quality image generation across user
>interfaces and operating systems.},
>   address= {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,
>CA 90720-1314 USA},
>   bdsk-url-1 =
> {
> http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019
> },
>   date-added = {2010-09-23 12:22:10 -0700},
>   date-modified  = {2010-09-23 12:22:10 -0700},
>   isi= {000245668100019},
>   isi-recid  = {155389429},
>   month  = may # "/" # jun,
>   publisher  = {IEEE COMPUTER SOC},
>   year   = 2007
> }
>

That wos link is useful, however I see only a paper listed following the
"Time Cited" link in the atmospheric science field. A few papers I have
seen mentions mpl in acknowledgement section, but some not, though the
plots in them are obviously produced by mpl.

Should we list some articles here, as a base for a section that would go to
mpl website?

-- 
Gökhan
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Re: [Matplotlib-users] Problem with shared axis

2012-10-05 Thread Jianbao Tao 
Works like a charm. :-)

Thank you so much, Damon.

Jianbao

On Fri, Oct 5, 2012 at 10:53 AM, Damon McDougall
wrote:

> On Fri, Oct 5, 2012 at 5:44 PM, Jianbao Tao  wrote:
> > Hi,
> >
> > I am working on a time-series data browser based on matplotlib. In
> general,
> > it shows a N_row x 1_col stack of axes, which share the x axis, the time
> > axis. It is nice that matplotlib offers the sharex option so that the
> data
> > can be zoomed simultaneously in time. However, one problem with the
> sharex
> > option is that it not only shares the axis range (or limits, if you
> will),
> > but also the axis appearance, which is not always desirable. In my case,
> I
> > want the tick labels to be shown only on the bottom subplot. However,
> that
> > doesn't seem to be achievable with sharex.
> >
> > The follow snippet demonstrates my example:
> > #- code
> 
> > import matplotlib.pyplot as plt
> > fig = plt.figure()
> > ax1 = fig.add_subplot(211)
> > ax2 = fig.add_subplot(212, sharex=ax1)
> >
> > ax1.get_xaxis().set_ticklabels([]) # This also suppresses x tick labels
> of
> > ax2.
> > fig.canvas.draw()
> > #-- end of code
> 
> >
> > Is there a workaround, hopefully simple and straightforward, to share
> range
> > (or limits) only among axes? Better yet, can this feature be added, like
> a
> > keyword sharexrange, in the future, if it is not already there? Of
> course,
> > the situation should be similar for y axis, too.
> >
> > Thank you very much.
> >
> > Jianbao
>
> This was the first hit in a google search:
>
> http://stackoverflow.com/questions/4209467/matplotlib-share-x-axis-but-dont-show-x-axis-tick-labels-for-both-just-one
>
> --
> Damon McDougall
> http://www.damon-is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Damon McDougall 
On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever  wrote:
>
>
> On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
> wrote:
>>
>>
>> @Article{Hunter:2007,
>>   Author = {Hunter, J. D.},
>>   Title  = {Matplotlib: A 2D graphics environment},
>>   Journal= {Computing In Science \& Engineering},
>>   Volume = {9},
>>   Number = {3},
>>   Pages  = {90--95},
>>   abstract   = {Matplotlib is a 2D graphics package used for Python
>>for application development, interactive scripting, and
>>publication-quality image generation across user
>>interfaces and operating systems.},
>>   address= {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,
>>CA 90720-1314 USA},
>>   bdsk-url-1 =
>>
>> {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019},
>>   date-added = {2010-09-23 12:22:10 -0700},
>>   date-modified  = {2010-09-23 12:22:10 -0700},
>>   isi= {000245668100019},
>>   isi-recid  = {155389429},
>>   month  = may # "/" # jun,
>>   publisher  = {IEEE COMPUTER SOC},
>>   year   = 2007
>> }
>
>
> That wos link is useful, however I see only a paper listed following the
> "Time Cited" link in the atmospheric science field. A few papers I have seen
> mentions mpl in acknowledgement section, but some not, though the plots in
> them are obviously produced by mpl.
>
> Should we list some articles here, as a base for a section that would go to
> mpl website?
>
> --
> Gökhan

Short version:
I think this is a good idea.

Long version:
I think a 'Who uses matplotlib?' section in the website would provide
good solid academic backing, too. I know the Met Office
(PHIL) and some of the guys in the PECOS group at ICES
use it.

Actual papers is great, but probably rather drab? I think if we want
to show it off, we should include sample images from citations, rather
than just citations. After all, how many people are going to chase a
citation to see sample output when we have a gallery section? Better
still would be to have an 'academic gallery' section. Perhaps this
could be part of the gallery re-work someone was going to do (was it
Tony? I forget).

I don't know. I think the idea is good, but I think there needs to be
some thought and consensus regarding the *best* way to get people to
*visually* judge matplotlib's capabilities in the academic realm.

This is just my two.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Floris van Breugel 
That citation should be *much* more prominent on the matplotlib homepage. I
regret to say that I was unaware of that paper I should have cited in my
last paper which made heavy use of matplotlib generated plots with lots of
customizations. Next time I'll be sure to include the proper citation!

I think including a gallery of published examples would be great, however,
there will be some serious challenges with regards to copyright. It would
be great to show MPL being used in high impact journals (which it is), but
getting permission from them to show the plots on the MPL website may
require some paperwork. So, a list of citations might be a good place to
start. Here's mine: http://jeb.biologists.org/content/215/11/1783.full

- Floris


On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall
wrote:

> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever 
> wrote:
> >
> >
> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
> > wrote:
> >>
> >>
> >> @Article{Hunter:2007,
> >>   Author = {Hunter, J. D.},
> >>   Title  = {Matplotlib: A 2D graphics environment},
> >>   Journal= {Computing In Science \& Engineering},
> >>   Volume = {9},
> >>   Number = {3},
> >>   Pages  = {90--95},
> >>   abstract   = {Matplotlib is a 2D graphics package used for Python
> >>for application development, interactive scripting,
> and
> >>publication-quality image generation across user
> >>interfaces and operating systems.},
> >>   address= {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS
> ALAMITOS,
> >>CA 90720-1314 USA},
> >>   bdsk-url-1 =
> >>
> >> {
> http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019
> },
> >>   date-added = {2010-09-23 12:22:10 -0700},
> >>   date-modified  = {2010-09-23 12:22:10 -0700},
> >>   isi= {000245668100019},
> >>   isi-recid  = {155389429},
> >>   month  = may # "/" # jun,
> >>   publisher  = {IEEE COMPUTER SOC},
> >>   year   = 2007
> >> }
> >
> >
> > That wos link is useful, however I see only a paper listed following the
> > "Time Cited" link in the atmospheric science field. A few papers I have
> seen
> > mentions mpl in acknowledgement section, but some not, though the plots
> in
> > them are obviously produced by mpl.
> >
> > Should we list some articles here, as a base for a section that would go
> to
> > mpl website?
> >
> > --
> > Gökhan
>
> Short version:
> I think this is a good idea.
>
> Long version:
> I think a 'Who uses matplotlib?' section in the website would provide
> good solid academic backing, too. I know the Met Office
> (PHIL) and some of the guys in the PECOS group at ICES
> use it.
>
> Actual papers is great, but probably rather drab? I think if we want
> to show it off, we should include sample images from citations, rather
> than just citations. After all, how many people are going to chase a
> citation to see sample output when we have a gallery section? Better
> still would be to have an 'academic gallery' section. Perhaps this
> could be part of the gallery re-work someone was going to do (was it
> Tony? I forget).
>
> I don't know. I think the idea is good, but I think there needs to be
> some thought and consensus regarding the *best* way to get people to
> *visually* judge matplotlib's capabilities in the academic realm.
>
> This is just my two.
>
> --
> Damon McDougall
> http://www.damon-is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>
>
> --
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
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(925) 963 8280

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Re: [Matplotlib-users] Saving animations

2012-10-05 Thread Andreas Mueller 
On 10/05/2012 02:49 AM, Ryan May wrote:
> On Thu, Oct 4, 2012 at 12:38 PM, Andreas Mueller
>  wrote:
>> On 10/04/2012 03:51 PM, Benjamin Root wrote:
>> On Thu, Oct 4, 2012 at 10:02 AM, Andreas Mueller 
>> wrote:
>>> Hi everybody.
>>> I have been trying to save some animations I made and I encountered the
>>> problem mentioned here.
>>> I am using current master.
>>> To be precise, when I use
>>> anim.save("file.mp4", fps=10, extra_args=['-vcodec', 'libx264'])
>>> I get "RuntimeError: Error writing to file" from the agg backend.
>>> If I don't use the extra_args, it works, but I get very, very bad
>>> quality that can not be redeemed using bitrate.
>>> I have ffmpeg and libx264 installed. I also tried the mencoder by passing
>>> MencoderWriter() to save, but that resulted in a video where all frames
>>> are identical.
>>>
>>> Any help on this would be appreciated. Is there an easy way to just dump
>>> the frames? I can do the mencoder bit myself.
>>>
>>> Thanks,
>>> Andy
>>>
>> Exactly which version of mpl are you using, and what is your platform?  This
>> will help us diagnose what is going on.
>>
>>
>>> Thanks for the quick answer.
>>> I am not on the box but I used master from yesterday, so
>>> 89482b21c8582d49a2ddc2865e472eb404fd07e2, I guess.
>>> The platform is Ubuntu Precise (with loads of random Python packages, but
>>> that seems somewhat unrelated).
> I'm on Ubuntu Precise (12.04) here as well. No problems with/without,
> but I'm noticing the extra_args aren't being used (which I think is a
> known bug I need to fix.) Can you run with --verbose-debug and post
> the relevant output? (Or just compress and attach.)
Thanks for the tip. I didn't know about ``--verbose-debug``.
It told me Unknown encoder 'libx264'.
I found out I need to install libavcodec-extra-53 for it to work.
Not everything is going smoothly.

It would be great if the docs could be updated with how to specify
a codec btw. I only found out by chance.

Thanks for your help, andy

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Nelle Varoquaux 
>
> I think including a gallery of published examples would be great, however,
> there will be some serious challenges with regards to copyright. It would
> be great to show MPL being used in high impact journals (which it is), but
> getting permission from them to show the plots on the MPL website may
> require some paperwork. So, a list of citations might be a good place to
> start. Here's mine: http://jeb.biologists.org/content/215/11/1783.full
>

I just came back from a bioinformatics workshop: I was suprised by the
amound of people using matplotlib to display results.
I think it wouldn't be too hard to gather images and published them on
matplotlib's website if the authors are OK with it. Also, in cancer
research, publications and/or plots are often available publicly.

I don't think citations would be as efficient: I personnally wouldn't
bother looking at those.
Here is an example on circos' website of how they advertise the use of
their plotting library in research: http://circos.ca/intro/published_images/

Cheers,
N


>
> - Floris
>
>
> On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall <
> damon.mcdoug...@gmail.com> wrote:
>
>> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever 
>> wrote:
>> >
>> >
>> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
>> > wrote:
>> >>
>> >>
>> >> @Article{Hunter:2007,
>> >>   Author = {Hunter, J. D.},
>> >>   Title  = {Matplotlib: A 2D graphics environment},
>> >>   Journal= {Computing In Science \& Engineering},
>> >>   Volume = {9},
>> >>   Number = {3},
>> >>   Pages  = {90--95},
>> >>   abstract   = {Matplotlib is a 2D graphics package used for Python
>> >>for application development, interactive scripting,
>> and
>> >>publication-quality image generation across user
>> >>interfaces and operating systems.},
>> >>   address= {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS
>> ALAMITOS,
>> >>CA 90720-1314 USA},
>> >>   bdsk-url-1 =
>> >>
>> >> {
>> http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019
>> },
>> >>   date-added = {2010-09-23 12:22:10 -0700},
>> >>   date-modified  = {2010-09-23 12:22:10 -0700},
>> >>   isi= {000245668100019},
>> >>   isi-recid  = {155389429},
>> >>   month  = may # "/" # jun,
>> >>   publisher  = {IEEE COMPUTER SOC},
>> >>   year   = 2007
>> >> }
>> >
>> >
>> > That wos link is useful, however I see only a paper listed following the
>> > "Time Cited" link in the atmospheric science field. A few papers I have
>> seen
>> > mentions mpl in acknowledgement section, but some not, though the plots
>> in
>> > them are obviously produced by mpl.
>> >
>> > Should we list some articles here, as a base for a section that would
>> go to
>> > mpl website?
>> >
>> > --
>> > Gökhan
>>
>> Short version:
>> I think this is a good idea.
>>
>> Long version:
>> I think a 'Who uses matplotlib?' section in the website would provide
>> good solid academic backing, too. I know the Met Office
>> (PHIL) and some of the guys in the PECOS group at ICES
>> use it.
>>
>> Actual papers is great, but probably rather drab? I think if we want
>> to show it off, we should include sample images from citations, rather
>> than just citations. After all, how many people are going to chase a
>> citation to see sample output when we have a gallery section? Better
>> still would be to have an 'academic gallery' section. Perhaps this
>> could be part of the gallery re-work someone was going to do (was it
>> Tony? I forget).
>>
>> I don't know. I think the idea is good, but I think there needs to be
>> some thought and consensus regarding the *best* way to get people to
>> *visually* judge matplotlib's capabilities in the academic realm.
>>
>> This is just my two.
>>
>> --
>> Damon McDougall
>> http://www.damon-is-a-geek.com
>> B2.39
>> Mathematics Institute
>> University of Warwick
>> Coventry
>> West Midlands
>> CV4 7AL
>> United Kingdom
>>
>>
>> --
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>> ___
>> Matplotlib-users mailing list
>> Matplotlib-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
>
> --
> Floris van Breugel
> PhD Candidate at Caltech
> Control and Dynamical Systems
> (925) 963 8280
>
> Wildlife and Landscape Photographer
> Galleries: http://www.ArtInNaturePhotography.com/
> Blog: http://www.ArtInNaturePhotography.com/wordpress/
>
>

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Steven Boada 
The idea of pulling key (and sexy) figures from papers is an awesome 
idea. I know when I am trying to make figures, I often search around 
looking at the different styles that people use to present similar 
data. There is also something different about publication level plots 
than the simple examples that MPL has on the gallery page now. Sure 
some of them are neat, but more importantly, they show you how to do 
something. Pulling figures from papers show you how to convey 
information and look good doing it.

I'll certainly cite MPL and ipython as I have used those a lot to both 
develop and present my results. Sadly, most of us in astronomy are 
still using IDL for all of the figure making.

Steven

On Fri 05 Oct 2012 12:45:30 PM CDT, Nelle Varoquaux wrote:
>
>
> I think including a gallery of published examples would be great,
> however, there will be some serious challenges with regards to
> copyright. It would be great to show MPL being used in high impact
> journals (which it is), but getting permission from them to show
> the plots on the MPL website may require some paperwork. So, a
> list of citations might be a good place to start. Here's mine:
> http://jeb.biologists.org/content/215/11/1783.full
>
>
> I just came back from a bioinformatics workshop: I was suprised by the
> amound of people using matplotlib to display results.
> I think it wouldn't be too hard to gather images and published them on
> matplotlib's website if the authors are OK with it. Also, in cancer
> research, publications and/or plots are often available publicly.
>
> I don't think citations would be as efficient: I personnally wouldn't
> bother looking at those.
> Here is an example on circos' website of how they advertise the use of
> their plotting library in research:
> http://circos.ca/intro/published_images/
>
> Cheers,
> N
>
>
> - Floris
>
> On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall
> mailto:damon.mcdoug...@gmail.com>> wrote:
>
> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever
> mailto:gokhanse...@gmail.com>> wrote:
> >
> >
> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez
> mailto:fperez@gmail.com>>
> > wrote:
> >>
> >>
> >> @Article{Hunter:2007,
> >>   Author = {Hunter, J. D.},
> >>   Title  = {Matplotlib: A 2D graphics environment},
> >>   Journal= {Computing In Science \& Engineering},
> >>   Volume = {9},
> >>   Number = {3},
> >>   Pages  = {90--95},
> >>   abstract   = {Matplotlib is a 2D graphics package
> used for Python
> >>for application development, interactive
> scripting, and
> >>publication-quality image generation
> across user
> >>interfaces and operating systems.},
> >>   address= {10662 LOS VAQUEROS CIRCLE, PO BOX 3014
> , LOS ALAMITOS,
> >>CA 90720-1314 USA},
> >>   bdsk-url-1 =
> >>
> >>
> 
> {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019},
> >>   date-added = {2010-09-23 12:22:10 -0700},
> >>   date-modified  = {2010-09-23 12:22:10 -0700},
> >>   isi= {000245668100019},
> >>   isi-recid  = {155389429},
> >>   month  = may # "/" # jun,
> >>   publisher  = {IEEE COMPUTER SOC},
> >>   year   = 2007
> >> }
> >
> >
> > That wos link is useful, however I see only a paper listed
> following the
> > "Time Cited" link in the atmospheric science field. A few
> papers I have seen
> > mentions mpl in acknowledgement section, but some not,
> though the plots in
> > them are obviously produced by mpl.
> >
> > Should we list some articles here, as a base for a section
> that would go to
> > mpl website?
> >
> > --
> > Gökhan
>
> Short version:
> I think this is a good idea.
>
> Long version:
> I think a 'Who uses matplotlib?' section in the website would
> provide
> good solid academic backing, too. I know the Met Office
> (PHIL) and some of the guys in the PECOS group
> at ICES
> use it.
>
> Actual papers is great, but probably rather drab? I think if
> we want
> to show it off, we should include sample images from
> citations, rather
> than just citations. After all, how many people are going to
> chase a
> citation to see sample output when we have a gallery section?
> Better
> still would

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Floris van Breugel 
The problem is with many journals the content (including figures) is
copyright by the journal, not the author. But I imagine most journals would
grant permission, it's just an additional step that should be taken where
required.

The circos layout looks nice!

- Floris



On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
wrote:

>
>
>> I think including a gallery of published examples would be great,
>> however, there will be some serious challenges with regards to copyright.
>> It would be great to show MPL being used in high impact journals (which it
>> is), but getting permission from them to show the plots on the MPL website
>> may require some paperwork. So, a list of citations might be a good place
>> to start. Here's mine: http://jeb.biologists.org/content/215/11/1783.full
>>
>
> I just came back from a bioinformatics workshop: I was suprised by the
> amound of people using matplotlib to display results.
> I think it wouldn't be too hard to gather images and published them on
> matplotlib's website if the authors are OK with it. Also, in cancer
> research, publications and/or plots are often available publicly.
>
> I don't think citations would be as efficient: I personnally wouldn't
> bother looking at those.
> Here is an example on circos' website of how they advertise the use of
> their plotting library in research:
> http://circos.ca/intro/published_images/
>
> Cheers,
> N
>
>
>>
>> - Floris
>>
>>
>> On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall <
>> damon.mcdoug...@gmail.com> wrote:
>>
>>> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever 
>>> wrote:
>>> >
>>> >
>>> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
>>> > wrote:
>>> >>
>>> >>
>>> >> @Article{Hunter:2007,
>>> >>   Author = {Hunter, J. D.},
>>> >>   Title  = {Matplotlib: A 2D graphics environment},
>>> >>   Journal= {Computing In Science \& Engineering},
>>> >>   Volume = {9},
>>> >>   Number = {3},
>>> >>   Pages  = {90--95},
>>> >>   abstract   = {Matplotlib is a 2D graphics package used for
>>> Python
>>> >>for application development, interactive
>>> scripting, and
>>> >>publication-quality image generation across user
>>> >>interfaces and operating systems.},
>>> >>   address= {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS
>>> ALAMITOS,
>>> >>CA 90720-1314 USA},
>>> >>   bdsk-url-1 =
>>> >>
>>> >> {
>>> http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019
>>> },
>>> >>   date-added = {2010-09-23 12:22:10 -0700},
>>> >>   date-modified  = {2010-09-23 12:22:10 -0700},
>>> >>   isi= {000245668100019},
>>> >>   isi-recid  = {155389429},
>>> >>   month  = may # "/" # jun,
>>> >>   publisher  = {IEEE COMPUTER SOC},
>>> >>   year   = 2007
>>> >> }
>>> >
>>> >
>>> > That wos link is useful, however I see only a paper listed following
>>> the
>>> > "Time Cited" link in the atmospheric science field. A few papers I
>>> have seen
>>> > mentions mpl in acknowledgement section, but some not, though the
>>> plots in
>>> > them are obviously produced by mpl.
>>> >
>>> > Should we list some articles here, as a base for a section that would
>>> go to
>>> > mpl website?
>>> >
>>> > --
>>> > Gökhan
>>>
>>> Short version:
>>> I think this is a good idea.
>>>
>>> Long version:
>>> I think a 'Who uses matplotlib?' section in the website would provide
>>> good solid academic backing, too. I know the Met Office
>>> (PHIL) and some of the guys in the PECOS group at ICES
>>> use it.
>>>
>>> Actual papers is great, but probably rather drab? I think if we want
>>> to show it off, we should include sample images from citations, rather
>>> than just citations. After all, how many people are going to chase a
>>> citation to see sample output when we have a gallery section? Better
>>> still would be to have an 'academic gallery' section. Perhaps this
>>> could be part of the gallery re-work someone was going to do (was it
>>> Tony? I forget).
>>>
>>> I don't know. I think the idea is good, but I think there needs to be
>>> some thought and consensus regarding the *best* way to get people to
>>> *visually* judge matplotlib's capabilities in the academic realm.
>>>
>>> This is just my two.
>>>
>>> --
>>> Damon McDougall
>>> http://www.damon-is-a-geek.com
>>> B2.39
>>> Mathematics Institute
>>> University of Warwick
>>> Coventry
>>> West Midlands
>>> CV4 7AL
>>> United Kingdom
>>>
>>>
>>> --
>>> Don't let slow site performance ruin your business. Deploy New Relic APM
>>> Deploy New Relic app performance management and know exactly
>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>> http://p.sf.net

Re: [Matplotlib-users] Saving animations

2012-10-05 Thread Ryan May 
On Fri, Oct 5, 2012 at 12:43 PM, Andreas Mueller
 wrote:
> Thanks for the tip. I didn't know about ``--verbose-debug``.
> It told me Unknown encoder 'libx264'.
> I found out I need to install libavcodec-extra-53 for it to work.
> Not everything is going smoothly.
>
> It would be great if the docs could be updated with how to specify
> a codec btw. I only found out by chance.
>
> Thanks for your help, andy

Glad to hear it.

It would be nice if there were good docs, period. But that requires a
lazy dev (me) to finish his Ph.D. first. :)

Ryan

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Graduate Research Assistant
School of Meteorology
University of Oklahoma

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Fernando Perez 
On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
 wrote:
> Here is an example on circos' website of how they advertise the use of their
> plotting library in research: http://circos.ca/intro/published_images/

Wow, that is one hell of a visually spiffy site.  Can't find any links
to development repositories, but in terms of targeting end users, the
author (because it looks like a single-person job, given the many "I"
references) has done a solid job.

Sites like this remind me that we really should put a bit more effort
into the 'marketing' aspect of our sites.  From what I can tell,
circos is very nice but has nowhere the technical depth,  complexity
and flexibility of matplotlib.  It's a fairly narrowly targeted tool.
But a site like that makes it really appealing to people.

Thanks for that link, Nelle!

Cheers,

f

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Gökhan Sever 
On Fri, Oct 5, 2012 at 11:45 AM, Nelle Varoquaux
wrote:

>
>
>> I think including a gallery of published examples would be great,
>> however, there will be some serious challenges with regards to copyright.
>> It would be great to show MPL being used in high impact journals (which it
>> is), but getting permission from them to show the plots on the MPL website
>> may require some paperwork. So, a list of citations might be a good place
>> to start. Here's mine: http://jeb.biologists.org/content/215/11/1783.full
>>
>
> I just came back from a bioinformatics workshop: I was suprised by the
> amound of people using matplotlib to display results.
> I think it wouldn't be too hard to gather images and published them on
> matplotlib's website if the authors are OK with it. Also, in cancer
> research, publications and/or plots are often available publicly.
>
> I don't think citations would be as efficient: I personnally wouldn't
> bother looking at those.
> Here is an example on circos' website of how they advertise the use of
> their plotting library in research:
> http://circos.ca/intro/published_images/
>
> Cheers,
> N
>

I think citation based discipline specific listing would make a good simple
start. For instance:

Atmospheric Science:

Article 1 citation [link1]
Article 2 citation [link2]


Bioinformatics:

Article 1 citation [link1]
Article 2 citation [link2]

etc...

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would
provide context to the use of plots rather that extracting figures and
putting them separately (dealing with copyright issues and such) on an
alternative gallery page. The figures you linked look shinny but not much
practical use in my field. Later, we can work on a more specific academic
gallery page, once citation gallery grows to a critical limit.


-- 
Gökhan
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Damon McDougall 
On Fri, Oct 5, 2012 at 7:42 PM, Fernando Perez  wrote:
> On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
>  wrote:
>> Here is an example on circos' website of how they advertise the use of their
>> plotting library in research: http://circos.ca/intro/published_images/
>
> Wow, that is one hell of a visually spiffy site.  Can't find any links
> to development repositories, but in terms of targeting end users, the
> author (because it looks like a single-person job, given the many "I"
> references) has done a solid job.
>
> Sites like this remind me that we really should put a bit more effort
> into the 'marketing' aspect of our sites.  From what I can tell,
> circos is very nice but has nowhere the technical depth,  complexity
> and flexibility of matplotlib.  It's a fairly narrowly targeted tool.
> But a site like that makes it really appealing to people.
>
> Thanks for that link, Nelle!

Yes, that site was *full* of eye-candy. It's maybe a bit over the top,
but it's certainly a good reference.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Fernando Perez 
On Fri, Oct 5, 2012 at 12:17 PM, Damon McDougall
 wrote:
> It's maybe a bit over the top,
> but it's certainly a good reference.

I agree, a bit too rich for my taste too.  But our sites tend to be
the opposite extreme, so it's a good data point to keep in mind.

Cheers,

f

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Damon McDougall 
On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever  wrote:
> Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would

This is not true. A lot of articles are unavailable to certain
institutions due to a lack of subscription. A major sticking point.

Am I wrong in thinking that journals copyright the final product?
Thus, it would be up to the author(s) to decide whether or not to
'donate' a figure for a gallery.

> provide context to the use of plots rather that extracting figures and
> putting them separately (dealing with copyright issues and such) on an
> alternative gallery page. The figures you linked look shinny but not much
> practical use in my field.

Point taken on the context argument. I'll take that. To resolve it,
make the figure/html image link to the underlying publication?



-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Floris van Breugel 
On Fri, Oct 5, 2012 at 12:23 PM, Damon McDougall
wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
> wrote:
> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
> would
>
> This is not true. A lot of articles are unavailable to certain
> institutions due to a lack of subscription. A major sticking point.
>


Yes.. this is indeed a problem.. perhaps there could be a list of citations
specifically to open journal articles (many journals make papers public
after some period of time), in addition to ones that are only available
with a subscription. After all, many of those looking to use matplotlib in
a scientific publication are usually at an institution with access. That
way people who don't have access don't have to waste time finding links
that work for them.



>
> Am I wrong in thinking that journals copyright the final product?
> Thus, it would be up to the author(s) to decide whether or not to
> 'donate' a figure for a gallery.
>

Many journals copyright the final product, so an author could only 'donate'
a figure to the gallery if they had written permission from the journal
that published their paper. Lame, I know.

Similarly, if someone wishes to reproduce a figure for news coverage or a
review article, they need permission from the journal, not the author.

- Floris





>
> > provide context to the use of plots rather that extracting figures and
> > putting them separately (dealing with copyright issues and such) on an
> > alternative gallery page. The figures you linked look shinny but not much
> > practical use in my field.
>
> Point taken on the context argument. I'll take that. To resolve it,
> make the figure/html image link to the underlying publication?
>
>
>
> --
> Damon McDougall
> http://www.damon-is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>
>
> --
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Control and Dynamical Systems
(925) 963 8280

Wildlife and Landscape Photographer
Galleries: http://www.ArtInNaturePhotography.com/
Blog: http://www.ArtInNaturePhotography.com/wordpress/
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Nelle Varoquaux 
On 5 October 2012 21:23, Damon McDougall  wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
> wrote:
> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
> would
>
> This is not true. A lot of articles are unavailable to certain
> institutions due to a lack of subscription. A major sticking point.
>
> Am I wrong in thinking that journals copyright the final product?
> Thus, it would be up to the author(s) to decide whether or not to
> 'donate' a figure for a gallery.
>

I think it depends on the journal, and on the agreement. I think in most
journals you/your institute can pay to have your paper publicly available.

I wouldn't be shocked if a requirement to be in the gallery would be to
donate a figure.


>
> > provide context to the use of plots rather that extracting figures and
> > putting them separately (dealing with copyright issues and such) on an
> > alternative gallery page. The figures you linked look shinny but not much
> > practical use in my field.
>

I was just showing an example of a gallery of published figures. It is much
easier to go through a gallery, to quickly see what a library is capable
of, than clicking on links to articles, that may often be of closed access.



>
> Point taken on the context argument. I'll take that. To resolve it,
> make the figure/html image link to the underlying publication?
>
>
>
> --
> Damon McDougall
> http://www.damon-is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Steven Boada 
For example, in astronomy, a lot of people will 'publish' their paper 
to Arxiv before it is accepted into a journal. Arxiv is accessible by 
the general public and a little digging around will reveal that you can 
download the actual Latex source for the paper. This includes all of 
the figures. I have never heard of anyone getting sued by a journal for 
posting their stuff on the arxiv.

Steven

On Fri 05 Oct 2012 02:42:06 PM CDT, Nelle Varoquaux wrote:
>
>
> On 5 October 2012 21:23, Damon McDougall  > wrote:
>
> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever
> mailto:gokhanse...@gmail.com>> wrote:
> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus
> this would
>
> This is not true. A lot of articles are unavailable to certain
> institutions due to a lack of subscription. A major sticking point.
>
> Am I wrong in thinking that journals copyright the final product?
> Thus, it would be up to the author(s) to decide whether or not to
> 'donate' a figure for a gallery.
>
>
> I think it depends on the journal, and on the agreement. I think in
> most journals you/your institute can pay to have your paper publicly
> available.
>
> I wouldn't be shocked if a requirement to be in the gallery would be
> to donate a figure.
>
>
> > provide context to the use of plots rather that extracting
> figures and
> > putting them separately (dealing with copyright issues and such)
> on an
> > alternative gallery page. The figures you linked look shinny but
> not much
> > practical use in my field.
>
>
> I was just showing an example of a gallery of published figures. It is
> much easier to go through a gallery, to quickly see what a library is
> capable of, than clicking on links to articles, that may often be of
> closed access.
>
>
> Point taken on the context argument. I'll take that. To resolve it,
> make the figure/html image link to the underlying publication?
>
>
>
> --
> Damon McDougall
> http://www.damon-is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>
>
>
>
> --
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Gökhan Sever 
On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall
wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
> wrote:
> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
> would
>
> This is not true. A lot of articles are unavailable to certain
> institutions due to a lack of subscription. A major sticking point.
>
>
I was only thinking open-access journals, which open-source users (i.e.
users of python tools) tend to publish their articles in open-journals. Of
course, there are subscription required articles but those are secondary
concerns. Sometimes authors make their articles publicly available even the
article is on a paid journal.



>
>
> > provide context to the use of plots rather that extracting figures and
> > putting them separately (dealing with copyright issues and such) on an
> > alternative gallery page. The figures you linked look shinny but not much
> > practical use in my field.
>
> Point taken on the context argument. I'll take that. To resolve it,
> make the figure/html image link to the underlying publication?
>
>
Citation listing is easier for me, we can go both ways, a page listing only
citations, another one a more experimental figure/citation if copyright
issues can be resolved easily. In anyways, we will have to gather
citations. Let's start doing that?


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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Francesco Montesano 
2012/10/5 Gökhan Sever 

>
>
> On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall  > wrote:
>
>> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
>> wrote:
>> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
>> would
>>
>> This is not true. A lot of articles are unavailable to certain
>> institutions due to a lack of subscription. A major sticking point.
>>
>>
> I was only thinking open-access journals, which open-source users (i.e.
> users of python tools) tend to publish their articles in open-journals. Of
> course, there are subscription required articles but those are secondary
> concerns. Sometimes authors make their articles publicly available even the
> article is on a paid journal.
>
>
>
>>
>>
>> > provide context to the use of plots rather that extracting figures and
>> > putting them separately (dealing with copyright issues and such) on an
>> > alternative gallery page. The figures you linked look shinny but not
>> much
>> > practical use in my field.
>>
>> Point taken on the context argument. I'll take that. To resolve it,
>> make the figure/html image link to the underlying publication?
>>
>>
> Citation listing is easier for me, we can go both ways, a page listing
> only citations, another one a more experimental figure/citation if
> copyright issues can be resolved easily. In anyways, we will have to gather
> citations. Let's start doing that?
>
>
I think that an official acknowledgment that people can copy and paste (and
adapt) in their paper would be a great idea.

Francesco


>
> --
> Gökhan
>
>
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Gökhan Sever 
On Fri, Oct 5, 2012 at 2:02 PM, Francesco Montesano <
franz.berges...@gmail.com> wrote:
>
>
> I think that an official acknowledgment that people can copy and paste
> (and adapt) in their paper would be a great idea.
>
> Francesco
>
>

Some open-access journals permit this:

See for instance (also an example of a title that has all mpl produced
figures):

Dawe, J. T. and Austin, P. H.: Statistical analysis of an LES shallow
cumulus cloud ensemble using a cloud tracking algorithm, Atmos. Chem.
Phys., 12, 1101-1119, doi:10.5194/acp-12-1101-2012, 2012,
http://www.atmos-chem-phys.net/12/1101/2012/acp-12-1101-2012.html
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Damon McDougall 
On Fri, Oct 5, 2012 at 8:58 PM, Gökhan Sever  wrote:
>
>
> On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall 
> wrote:
>>
>> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
>> wrote:
>> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
>> > would
>>
>> This is not true. A lot of articles are unavailable to certain
>> institutions due to a lack of subscription. A major sticking point.
>>
>
> I was only thinking open-access journals, which open-source users (i.e.
> users of python tools) tend to publish their articles in open-journals. Of
> course, there are subscription required articles but those are secondary
> concerns. Sometimes authors make their articles publicly available even the
> article is on a paid journal.

That's a good idea. Steven Boada's comment re: the arxiv is also a
good one. This looks workable :)

>> > provide context to the use of plots rather that extracting figures and
>> > putting them separately (dealing with copyright issues and such) on an
>> > alternative gallery page. The figures you linked look shinny but not
>> > much
>> > practical use in my field.
>>
>> Point taken on the context argument. I'll take that. To resolve it,
>> make the figure/html image link to the underlying publication?
>>
>
> Citation listing is easier for me, we can go both ways, a page listing only
> citations, another one a more experimental figure/citation if copyright
> issues can be resolved easily. In anyways, we will have to gather citations.
> Let's start doing that?

Sounds good to me. Thanks for all the input.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

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Re: [Matplotlib-users] Eclipse with PyDev on Ubuntu - updating matplotlib version in eclipse ide

2012-10-05 Thread Paul Hobson 
On Wed, Oct 3, 2012 at 6:25 AM, Harshad Surdi  wrote:
> Hi,
> I am using Eclipse IDE for Java Developers with PyDev on Ubuntu 12.04 and I
> am quite new to Ubuntu and Eclipse. Can you guide me as to hos to update
> matplotlib in PyDev in Eclipse?
>
> --
> Best Regards,
> Harshad Surdi

Harshad,

To the best of my knowledge, you just need to update matplotlib in
Ubuntu. If you're looking to upgrade to a development version, the use
the instructions here:
http://matplotlib.org/faq/installing_faq.html#install-from-git

-paul

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[Matplotlib-users] automating-xkcd-diagrams-transforming-serious-to-funny

2012-10-05 Thread Neal Becker 
http://blog.wolfram.com/2012/10/05/automating-xkcd-diagrams-transforming-
serious-to-funny/

I wonder if mpl has anything along these lines?


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Re: [Matplotlib-users] automating-xkcd-diagrams-transforming-serious-to-funny

2012-10-05 Thread Damon McDougall 
On Fri, Oct 5, 2012 at 11:18 PM, Neal Becker  wrote:
> http://blog.wolfram.com/2012/10/05/automating-xkcd-diagrams-transforming-
> serious-to-funny/
>
> I wonder if mpl has anything along these lines?

https://github.com/matplotlib/matplotlib/pull/1329

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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

2012-10-05 Thread Gökhan Sever 
On Fri, Oct 5, 2012 at 2:47 PM, Phil Austin  wrote:
>
> Nice to see our matplotlib acknowledgement generating ripples. We've also
got some
> mayavi animations and links to other matplotlib-plotted papers and posters
> at http://cafc.ubc.ca
>
> best, Phil
>

Nice visuals Phil. Thanks for making your articles easily accessible from
your page. In addition to your papers here are a couple more atmospheric
science related open-access articles that uses matplotlib for figures:


Mallet, V., Quélo, D., Sportisse, B., Ahmed de Biasi, M., Debry, É.,
Korsakissok, I., Wu, L., Roustan, Y., Sartelet, K., Tombette, M., and
Foudhil, H.: Technical Note: The air quality modeling system Polyphemus,
Atmos. Chem. Phys., 7, 5479-5487, doi:10.5194/acp-7-5479-2007, 2007.
http://www.atmos-chem-phys.net/7/5479/2007/acp-7-5479-2007.html


Batenburg, A. M., Walter, S., Pieterse, G., Levin, I., Schmidt, M., Jordan,
A., Hammer, S., Yver, C., and Röckmann, T.: Temporal and spatial
variability of the stable isotopic composition of atmospheric molecular
hydrogen: observations at six EUROHYDROS stations, Atmos. Chem. Phys., 11,
6985-6999, doi:10.5194/acp-11-6985-2011, 2011.
http://www.atmos-chem-phys.net/11/6985/2011/acp-11-6985-2011.html


Jones, C. R., Bretherton, C. S., and Leon, D.: Coupled vs. decoupled
boundary layers in VOCALS-REx, Atmos. Chem. Phys., 11, 7143-7153,
doi:10.5194/acp-11-7143-2011, 2011.
http://www.atmos-chem-phys.net/11/7143/2011/acp-11-7143-2011.html
(All except the first plot is produced by matplotlib)


Ungermann, J., Kalicinsky, C., Olschewski, F., Knieling, P., Hoffmann, L.,
Blank, J., Woiwode, W., Oelhaf, H., Hösen, E., Volk, C. M., Ulanovsky, A.,
Ravegnani, F., Weigel, K., Stroh, F., and Riese, M.: CRISTA-NF measurements
with unprecedented vertical resolution during the RECONCILE aircraft
campaign, Atmos. Meas. Tech., 5, 1173-1191, doi:10.5194/amt-5-1173-2012,
2012.
http://www.atmos-meas-tech.net/5/1173/2012/amt-5-1173-2012.html


Rautenhaus, M., Bauer, G., and Dörnbrack, A.: A web service based tool to
plan atmospheric research flights, Geosci. Model Dev., 5, 55-71,
doi:10.5194/gmd-5-55-2012, 2012.
http://www.geosci-model-dev.net/5/55/2012/gmd-5-55-2012.html
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Re: [Matplotlib-users] XKCD style graphs?

2012-10-05 Thread Jason Grout 
On 10/4/12 2:16 AM, Fernando Perez wrote:
> This would make for an awesome couple of examples for the gallery, the
> mathematica solutions look really pretty cool:
>
> http://mathematica.stackexchange.com/questions/11350/xkcd-style-graphs
>
> The matlab and R version not quite so much, still for reference:
>
> http://stackoverflow.com/questions/12701841/xkcd-style-graphs-in-matlab
> http://stackoverflow.com/questions/12675147/xkcd-style-graphs-in-r

Just FYI, wolfram now has a blog post up about it: 
http://blog.wolfram.com/2012/10/05/automating-xkcd-diagrams-transforming-serious-to-funny/

Thanks,

Jason



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