matplotlib-users Mailing List for matplotlib (Page 3)

They're the same plotting interface, just different names. Pylab pulls in a
few extra functions that aren't specific to plotting, but aid in providing
matlab-alike functionality. To use matplotlib.pyplot instead of pylab for
any of the examples, just replace lines of:
 import pylab
with:
 import matplotlib.pyplot
Ryan
On Sun, Oct 26, 2008 at 11:29 AM, <ch...@se...> wrote:
> On Sun, Oct 26, 2008 at 11:51:48AM -0400, Charlie Moad wrote:
> > The matplotlib.pyplot is favored over the pylab module now.
>
> Thanks! I find your comment very interesting. As I have negligible
> experience
> with Matlab, I'd love to use matplotlib.pyplot.
>
> The problem is all the docs use pylab right? Where find matplotlib.pyplot
> examples?
>
> Chris
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Eric et al,
Very nice. However, I am running the latest Enthought EPD on Mac OS X 
10.4.11 and I get this:
In [6]: clabel(cs,inline=1,fontsize=10,manual=True)
Select label locations manually using first mouse button.
End manual selection with second mouse button.
/Library/Frameworks/Python.framework/Versions/4.0.30002/lib/python2.5/ 
site-packages/matplotlib-0.98.3.0001-py2.5-macosx-10.3-fat.egg/ 
matplotlib/backend_bases.py:1448: DeprecationWarning: Using default 
event loop until function specific to this GUI is implemented
 warnings.warn(str,DeprecationWarning)
It works, adding labels whenever I click with my mouse, but I cannot 
end labeling. I've tried various combinations with the mouse (ctrl 
+click, option+click, command+click) and keyboard (Enter), to no avail.
Has anyone tried this on a Mac and got the labeling to end?
Thanks.
D.
On Oct 25, 2008, at 5:21 PM, Eric Firing wrote:
> David Arnold wrote:
>> All,
>> Does Matplotlib have a form of the clabel command that uses the 
>> switch manual, as in Matlab:
>> [c,h]=contour(x,y,z);
>> clabel(c,h,'manual')
>> Which allows the user to pick the contours to label with the mouse?
>
> Yes, this was added recently by David Kaplan. It is in svn; I 
> don't know whether it has appeared a released version yet.
>
> The relevant part of the docstring, describing the keyword 
> argument, is:
>
> *manual*:
> if *True*, contour labels will be placed manually using
> mouse clicks. Click the first button near a contour to
> add a label, click the second button (or potentially both
> mouse buttons at once) to finish adding labels. The third
> button can be used to remove the last label added, but
> only if labels are not inline. Alternatively, the keyboard
> can be used to select label locations (enter to end label
> placement, delete or backspace act like the third mouse 
> button,
> and any other key will select a label location).
>
> Eric
>
>> David Arnold
>> College of the Redwoods
>> http://msemac.redwoods.edu/~darnold/index.php
>> --------------------------------------------------------------------- 
>> ----
>> This SF.Net email is sponsored by the Moblin Your Move Developer's 
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win 
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in 
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

This might be something wrong with the way fink has built GTK, but the 
following warnings are showing up for me:
/opt/lib/python2.5/site-packages/matplotlib/backends/backend_gtk.py: 
72: GtkWarning: Unable to find default local directory monitor type
 gtk.main()
/opt/lib/python2.5/site-packages/matplotlib/backends/backend_gtk.py: 
1033: GtkWarning: Unable to find default local directory monitor type
 if self.run() != int(gtk.RESPONSE_OK):
-gideon

On Sun, Oct 26, 2008 at 11:51:48AM -0400, Charlie Moad wrote:
> The matplotlib.pyplot is favored over the pylab module now.
Thanks! I find your comment very interesting. As I have negligible experience
with Matlab, I'd love to use matplotlib.pyplot.
The problem is all the docs use pylab right? Where find matplotlib.pyplot
examples?
Chris

Pylab is just a name for a module in matplotlib that is supposed to mimic
matlab. I would say its intent it to ease the transition for matlab users.
 It wouldn't really make sense to refer to matplotlib as pylab. The
matplotlib.pyplot is favored over the pylab module now.
- Charlie
On Sun, Oct 26, 2008 at 1:28 AM, <ch...@se...> wrote:
>
> So is matplotlib the name of the low level plotting engine?
>
> And, pylab is the user-friendly wrapper?
>
> Would it be ok to call the whole system "Pylab" instead of Matplotlib then?
>
>
> Chris
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
ch...@se... ha scritto:
> So is matplotlib the name of the low level plotting engine?
> 
> And, pylab is the user-friendly wrapper?
> 
> Would it be ok to call the whole system "Pylab" instead of Matplotlib then?
Personally I'd say "no" exactly because they are two different things,
as you correctly pointed out.
m.
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.7 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
iD8DBQFJBG/SpnWWEXZ5PA4RAg7nAKCJ1Jo78MApS3FP5t4FFLnMMel8mwCgpCHL
JSqrVwgyzX3JAD7y77Iyxnw=
=D9oR
-----END PGP SIGNATURE-----

I'm answering to myself on the mailing list just in case it might help some
in the future.
As, someone pointed out the error is in the assignment operator:
I wrote in the code:
 sum1 =+ (i-mx)*(j-my)
which does not add the values but puts them.
Instead I should have wrote
 sum1 += (i-mx)*(j-my)
a little difference that does a lot... :-)
here is the correct function:
def slope(x,y):
 sum1 = 0
 sum2 = 0
 mx = mean(x)
 my = mean(y)
 for i,j in zip(x,y):
 sum1 += (i-mx)*(j-my)
 print sum1
 sum2 += (i-mx)**2
 slope = sum1/sum2
 return slope
-- 
 .''`.
: :' : We are debian.org. Lower your prices,
`. `' surrender your code.
 `- We will add your hardware and software
 distinctiveness to our own.
 Resistance is futile.
----
 Imagine there's no countries
 It isn't hard to do
 Nothing to kill or die for
 And no religion too
 Imagine all the people
 Living life in peace
----
 You all must read 'The God Delusion'
 http://en.wikipedia.org/wiki/The_God_Delusion
---
when one person suffers from a delusion it is called insanity. When many
people suffer from a delusion it is called religion."
Robert Pirsig, Zen and the Art of Motorcycle Maintenance

So is matplotlib the name of the low level plotting engine?
And, pylab is the user-friendly wrapper?
Would it be ok to call the whole system "Pylab" instead of Matplotlib then?
Chris

I measured the displayed Matplotlib PDF on the screen and noticed it
has a 4/3 (1.333...) aspect ratio by default.
Is it EXACTLY 4/3? Even if I do:
pylab.figure().subplots_adjust(left = EXTRA_ROOM,
 bottom = EXTRA_ROOM)
???
(Why doesn't the subplots_adjust command seem to mess up the default aspect
ratio?? )
Chris

On 10/25/2008 6:07 PM I. Soumpasis wrote:
> The programs are GPL licensed. More info on the section of copyrights
 > http://wiki.deductivethinking.com/wiki/Deductive_Thinking:Copyrights.
> I hope it is ok,
Well, that depends what you mean by "ok".
Obviously, the author picks the license s/he prefers.
But a GPL license means that some people will avoid
your code, so you make wish to make sure you thought
the licensing issue for this code carefully.
As a point of comparison,
note that all your package dependencies have
a new BSD license.
Alan Isaac

David Arnold wrote:
> All,
> 
> Does Matplotlib have a form of the clabel command that uses the 
> switch manual, as in Matlab:
> 
> [c,h]=contour(x,y,z);
> clabel(c,h,'manual')
> 
> Which allows the user to pick the contours to label with the mouse?
Yes, this was added recently by David Kaplan. It is in svn; I don't 
know whether it has appeared a released version yet.
The relevant part of the docstring, describing the keyword argument, is:
 *manual*:
 if *True*, contour labels will be placed manually using
 mouse clicks. Click the first button near a contour to
 add a label, click the second button (or potentially both
 mouse buttons at once) to finish adding labels. The third
 button can be used to remove the last label added, but
 only if labels are not inline. Alternatively, the keyboard
 can be used to select label locations (enter to end label
 placement, delete or backspace act like the third mouse button,
 and any other key will select a label location).
Eric
> 
> David Arnold
> College of the Redwoods
> http://msemac.redwoods.edu/~darnold/index.php
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

All,
Does Matplotlib have a form of the clabel command that uses the 
switch manual, as in Matlab:
[c,h]=contour(x,y,z);
clabel(c,h,'manual')
Which allows the user to pick the contours to label with the mouse?
David Arnold
College of the Redwoods
http://msemac.redwoods.edu/~darnold/index.php

Hello,
I'm having troubles understand something about regression coefficients.
If I have two vectors:
x = [1.38, 1.98, 3.18, 3.56, 4.9, 6.21, 6.44, 7.47, 8.36, 8.81]
y = [8.19, 17.77, 20.12, 14.55, 20.17 ,31.22 ,28.94, 34.79, 40.26, 38.99]
and I would like to find out the regression coefficient I can use polyfit:
b1, b = polyfit(x,y,1)
my first question is can I get from polyfit the corrlation coeficient (I
know about corrcoef, just looking for more opotions).
The second question is about a fuction I wrote: according to
http://en.wikipedia.org/wiki/Regression_analysis#Linear_regression
it's pretty easy to write a little python funcion to calculate the
regression coefficients. Here is mine:
def b1(x,y):
 sum1 = 0
 sum2 = 0
 mx = mean(x)
 my = mean(y)
 for i,j in zip(x,y):
 sum1 =+ (i-mx)*(j-my)
 print sum1
 sum2 =+ (i-mx)**2
 b1 = sum1/sum2
 return b1
both methods yeild two different b1 values. Can anyone please tell me what
wrong with my function ?
Thanks, Oz.
-- 
 .''`.
: :' : We are debian.org. Lower your prices,
`. `' surrender your code.
 `- We will add your hardware and software
 distinctiveness to our own.
 Resistance is futile.
----
 Imagine there's no countries
 It isn't hard to do
 Nothing to kill or die for
 And no religion too
 Imagine all the people
 Living life in peace
----
 You all must read 'The God Delusion'
 http://en.wikipedia.org/wiki/The_God_Delusion
---
when one person suffers from a delusion it is called insanity. When many
people suffer from a delusion it is called religion."
Robert Pirsig, Zen and the Art of Motorcycle Maintenance

2008年10月25日 Alan G Isaac <ai...@am...>
> On 10/25/2008 4:14 PM I. Soumpasis apparently wrote:
> > http://blog.deductivethinking.com/?p=29
>
> This is cool.
> But I do not see a license.
> May I hope this is released under the new BSD license,
> like the packages it depends on?
>
> The programs are GPL licensed. More info on the section of copyrights
http://wiki.deductivethinking.com/wiki/Deductive_Thinking:Copyrights.
I hope it is ok,
Ilias

On 10/25/2008 4:14 PM I. Soumpasis apparently wrote:
> http://blog.deductivethinking.com/?p=29
This is cool.
But I do not see a license.
May I hope this is released under the new BSD license,
like the packages it depends on?
Thanks,
Alan Isaac

Dear lists,
DeductiveThinking.com now provides the Python programs for the book of M.
Keeling & P. Rohani "Modeling Infectious Diseases in Humans and Animals",
Princeton University Press, 2008. The book has on-line material which
includes programs for different models in various programming languages and
mathematical tools such as, "C++, FORTRAN and Matlab, while some are also
coded in the web-based Java programming language to allow readers to quickly
experiment with these types of models", as it is stated at the website. The
Python version of the programs were written long ago and submitted to the
book's on line material website (available soon). The Python programs with
the basic equations modelled and the results in figures were now uploaded on
a special wiki page of DeductiveThinking.com.
Since, the programs are heavily using numpy, scipy and matplotlib libraries,
I send this announcement to all the three lists and the main python-list;
sorry for double-posting. The announcement with the related links is
uploaded here http://blog.deductivethinking.com/?p=29. The programs are at
http://wiki.deductivethinking.com/wiki/Python_Programs_for_Modelling_Infectious_Diseases_book.
For those who are interested on modelling and epidemiology, they can take a
look at the main site (http://deductivethinking.com) or the main page of the
wiki (http://wiki.deductivethinking.com) and follow the epidemiology links.
The website is in its beginning, so limited information is uploaded up to
now.
Thanks for your time and I hope it will be useful for some people,
Best Regards,
Ilias Soumpasis

Florian Koelling wrote:
> Hi Folks!
> 
> I want to create a bar chart having 85 different Objects, each Object 
> owning a certain name of four letters -- I followed the examples on 
> the matplotlib examples page - so far so good.
> 
> I have some problems with the y_labeling because every objects name is 
> overlaid by it' s neighbour and so a proper assignment is not 
> possible. I tried to change the bar size, but that did not have any 
> effect on the y_label.
I think you are talking about labels for the bars, not tick labels or 
the y-axis label, correct?
> 
> Is it possible to display the object names vertical 1
> y
> k
> 7
> 
> instead of horizontal (1yk7) to obtain a better readable figure?
> or maybe some of you have a better idea?
Yes, text objects can be rotated. In the barchart_demo.py example, you 
can add to the text command the keyword argument rotation='vertical' 
(or give a number for angle in degrees).
Eric

Hi Folks!
I want to create a bar chart having 85 different Objects, each Object 
owning a certain name of four letters -- I followed the examples on 
the matplotlib examples page - so far so good.
I have some problems with the y_labeling because every objects name is 
overlaid by it' s neighbour and so a proper assignment is not 
possible. I tried to change the bar size, but that did not have any 
effect on the y_label.
Is it possible to display the object names vertical 1
 y
 k
 7
instead of horizontal (1yk7) to obtain a better readable figure?
or maybe some of you have a better idea?

Michael Droettboom wrote:
> I think what's going on there is a syntax error in the clabel docstring
> that is truncating it. I fixed this in SVN. I think there's a cron job
> running, so this should update in due time.
> 
> In general, the documentation is built directly from the docstrings in
> SVN so they should correspond, but let us know if you find anything else
> like this.
> 
Thanks. I think I would have found this, but unfortunately I couldn't
get the docs to build. Right now, the stix_fonts_demo.py is failing on
my box:
(0, '$\\mathcircled{123} \\mathrm{\\mathcircled{123}}
\\mathbf{\\mathcircled{123}}$')
(1, '$\\mathsf{Sans \\Omega} \\mathrm{\\mathsf{Sans \\Omega}}
\\mathbf{\\mathsf{Sans \\Omega}}$')
(2, '$\\mathtt{Monospace}$')
(3, '$\\mathcal{CALLIGRAPHIC}$')
(4, '$\\mathbb{Blackboard \\pi}$')
(5, '$\\mathrm{\\mathbb{Blackboard \\pi}}$')
(6, '$\\mathbf{\\mathbb{Blackboard \\pi}}$')
(7, '$\\mathfrak{Fraktur} \\mathbf{\\mathfrak{Fraktur}}$')
(8, '$\\mathscr{Script}$')
(9, 'Direct Unicode: $\\u23ce \\mathrm{\\ue0f2 \\U0001d538}$')
python: CXX/cxx_extensions.cxx:1128: virtual
Py::PythonExtensionBase::~PythonExtensionBase(): Assertion `ob_refcnt ==
0' failed.
[1] 1709 abort (core dumped) python
Here's the backtrace (though without debugging symbols):
#0 0x00007fa5c042c3c5 in raise () from /lib/libc.so.6
#1 0x00007fa5c042d73e in abort () from /lib/libc.so.6
#2 0x00007fa5c0425b1f in __assert_fail () from /lib/libc.so.6
#3 0x00007fa5b8f37e3e in Py::PythonExtensionBase::~PythonExtensionBase ()
 from
/home/rmay/.local/lib64/python2.5/site-packages/matplotlib/ft2font.so
#4 0x00007fa5b8f30f43 in Py::PythonExtension<FT2Font>::~PythonExtension ()
 from
/home/rmay/.local/lib64/python2.5/site-packages/matplotlib/ft2font.so
#5 0x00007fa5b8f20a35 in FT2Font::FT2Font ()
 from
/home/rmay/.local/lib64/python2.5/site-packages/matplotlib/ft2font.so
#6 0x00007fa5b8f20bd1 in ft2font_module::new_ft2font ()
 from
/home/rmay/.local/lib64/python2.5/site-packages/matplotlib/ft2font.so
#7 0x00007fa5b8f2dc5b in
Py::ExtensionModule<ft2font_module>::invoke_method_varargs ()
 from
/home/rmay/.local/lib64/python2.5/site-packages/matplotlib/ft2font.so
#8 0x00007fa5b8f34b62 in method_varargs_call_handler ()
 from
/home/rmay/.local/lib64/python2.5/site-packages/matplotlib/ft2font.so
I'm not sure if you care about the failed assertion. It could be a
reference leak, maybe not. Obviously, being an assertion, it only does
this when debugging is enabled (though I can't seem to see where my
system package on Gentoo turns this off).
Ryan
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

The problem was exposed by running python -c "import pylab" from the
command shell.
 
A message box indicated that msvcp71.dll was missing.
 
I copied this file to my python25 folder and it fixed the problem. Note
- it didn't help to copy the missing file to the windows\system32 folder
or even to regsvr32 it.
 
Andre de Fortier Smit
 
 

I think what's going on there is a syntax error in the clabel docstring 
that is truncating it. I fixed this in SVN. I think there's a cron job 
running, so this should update in due time.
In general, the documentation is built directly from the docstrings in 
SVN so they should correspond, but let us know if you find anything else 
like this.
Mike
Ryan May wrote:
> John Hunter wrote:
> 
>> On Thu, Oct 23, 2008 at 10:51 AM, Ryan May <rm...@gm...> wrote:
>>
>> 
>>> I've done it for barbs and I'll see if I notice anything else as time
>>> allows. Obviously I'm biased towards certain functionality. :) I'm
>>> guessing you guys have to do regenerate the docs and push them somewhere
>>> before any of this becomes live.
>>>
>>> 
>> Yes, but it's pretty easy. To build and update from the docs dir, I just do
>>
>> 
>>> python make.py html sf
>>> 
>> I've pushed your changes out -- thanks!
>> 
>
> Related to the barbs non-updating issue, I just noticed that the
> pyplot.clabel docs online are woefully out of date while the docstring
> is actually quite nice. I just had someone come by asking a question
> about clabel that would have been in the docs had the online ones been
> up to date. Do we have some kind of problem with getting these docs to
> update when we build them? Is there something I can help with here?
>
> Ryan
>
> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

FYI
 
pylab fails to import on Windows Server 2008. I'm using the latest
installs of numpy, scipy and matplotlib.
 
>>> from pylab import *
Traceback (most recent call last):
 File "<interactive input>", line 1, in <module>
 File "C:\Python25\Lib\site-packages\pylab.py", line 1, in <module>
 from matplotlib.pylab import *
 File "C:\Python25\Lib\site-packages\matplotlib\pylab.py", line 206, in
<module>
 from matplotlib import mpl # pulls in most modules
 File "C:\Python25\Lib\site-packages\matplotlib\mpl.py", line 1, in
<module>
 from matplotlib import artist
 File "C:\Python25\Lib\site-packages\matplotlib\artist.py", line 4, in
<module>
 from transforms import Bbox, IdentityTransform, TransformedBbox,
TransformedPath
 File "C:\Python25\lib\site-packages\matplotlib\transforms.py", line
34, in <module>
 from matplotlib._path import affine_transform
ImportError: DLL load failed: The specified module could not be found.
 
 
Andre de Fortier Smit
 

John Hunter wrote:
> On Thu, Oct 23, 2008 at 10:51 AM, Ryan May <rm...@gm...> wrote:
> 
>> I've done it for barbs and I'll see if I notice anything else as time
>> allows. Obviously I'm biased towards certain functionality. :) I'm
>> guessing you guys have to do regenerate the docs and push them somewhere
>> before any of this becomes live.
>>
> 
> Yes, but it's pretty easy. To build and update from the docs dir, I just do
> 
>> python make.py html sf
> 
> I've pushed your changes out -- thanks!
Related to the barbs non-updating issue, I just noticed that the
pyplot.clabel docs online are woefully out of date while the docstring
is actually quite nice. I just had someone come by asking a question
about clabel that would have been in the docs had the online ones been
up to date. Do we have some kind of problem with getting these docs to
update when we build them? Is there something I can help with here?
Ryan
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

imshow doesn't handle logarithmic data. You'll want to use pcolor or 
pcolormesh instead.
As for the graininess, unfortunately, pcolor and pcolormesh don't 
support any kind of interpolation. (imshow does, but it can only draw 
uniform data).
Mike
John [H2O] wrote:
> Hello,
>
> I'm trying to get imshow to plot logarithmic data. I'm having some problems
> with the colorbar or data??
>
> Note, I plot the max_dat value on the bottom of the figure, but it does not
> seem to correspond with the values in the plot??? Any ideas? Also, does
> anyone have some recommendations on how to better smooth the values, i.e.
> make the plume less 'grainy'? Thanks!
>
> My code is here:
> http://numpy.pastebin.com/m4ae6331a
>
> Example output is here:
> http://picasaweb.google.com/washakie/Temp#5260746894103850338
>
> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hello,
I'm trying to get imshow to plot logarithmic data. I'm having some problems
with the colorbar or data??
Note, I plot the max_dat value on the bottom of the figure, but it does not
seem to correspond with the values in the plot??? Any ideas? Also, does
anyone have some recommendations on how to better smooth the values, i.e.
make the plume less 'grainy'? Thanks!
My code is here:
http://numpy.pastebin.com/m4ae6331a
Example output is here:
http://picasaweb.google.com/washakie/Temp#5260746894103850338
-- 
View this message in context: http://www.nabble.com/Problems-with-imshow-logarithmic-plot-tp20152686p20152686.html
Sent from the matplotlib - users mailing list archive at Nabble.com.