matplotlib-users Mailing List for matplotlib

I have a bug that I am seeing with a default ubuntu 9.10 matplotlib 
install, version 0.99.0.  Contourf plots that I output in vector format 
files have little triangular glitches at the contour boundaries if the 
contoured array is larger than about 200x200.  The same files in png 
format are perfect, even at very high dpi values.  Attached is a sample 
script, and the png and eps output it generates on my machine.  I'm 
trying to make eps files for a paper, and this is driving me nuts.  Any 
ideas?

Jordan

Manuel Wittchen skrev:
> Is it possible to print the value of a variable in an annotation?
> Example:
> 
> gradient = 2.0
> intercept = 3.0
> r-value = 0.99
> 
> ax.annotate('f(x) = gradient * x + intercept R^2 = r-value',
> xy=(2.9,-0.75), xytext=(2.9,-0.75))
> 

I feel that a main advantage of matplotlib (over other solutions I have 
used) is that there is a complete programming language available. In 
this case, just use the standard string handling of python.

See e.g. http://docs.python.org/library/stdtypes.html#string-formatting

Untested code:

annotation_string = "f(x) = %f * x + %f R^2 = %f" % (gradient, 
intercept, r-value)

ax.annotate(annotation_string,
xy=(2.9,-0.75), xytext=(2.9,-0.75))




/ johan

Eric Emsellem <eem...@es...> writes:

> regarding my last post, I still have pb generating simple eps files.

Can you be more specific about the "last post" you are referring to? I
searched using Gmane and didn't find anything recent:

http://search.gmane.org/?author=eric+emsellem&group=gmane.comp.python.matplotlib.general&sort=date

> thanks a lot for the quick tip. But no xpdf does not do it (I had
> tried it).

What exact error message do you get in that case?

> ps.usedistiller   : None
> ## I tried all possible distiller... didn't change the pb.

Certainly the error message must have changed between runs, since your
first post showed a Ghostscript-specific message.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Hi,

Is it possible to print the value of a variable in an annotation?
Example:

gradient = 2.0
intercept = 3.0
r-value = 0.99

ax.annotate('f(x) = gradient * x + intercept R^2 = r-value',
xy=(2.9,-0.75), xytext=(2.9,-0.75))

Where gradient, intercept and r-value should be replaced by the value
of the variables in the output.

Regards and a happy new year!
Manuel Wittchen

When I run the script below, the first plot window prints fine, but the
second plot causes the script to crash and prints this error message:
<<
Fatal Python error: PyEval_RestoreThread: NULL tstate
This application has requested the Runtime to terminate in an unusual way.
Please contact the applications support team for more information.
>>

Anybody know what I'm doing wrong?  (WinXP, Matplotlib 0.99.1, Python v2.5)



import matplotlib.pyplot as plt

y=[1,2,3,2,1]
plt.plot(y)
plt.show()

raw_input("hit [enter] to show the next plot: ")

z=[4,5,4,5,4]
plt.plot(z)
plt.show()
-- 
View this message in context: http://old.nabble.com/Problem-with-multiple-plots-tp26976541p26976541.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

great. Thanks! I had a look at the thumbnails but didn't find the one
you point out. (And the doc is confusing)

Thanks!

and yes, very weird behaviour when the two arrays have the same length...

Eric

On 30/12/09 19:53, Jae-Joon Lee wrote:
> x1 = random(1000)
> x2 = random(1000)
> 
> n, bins, patches = hist(np.array([x1, x2]).transpose())
> 
> plt.setp(patches[0], color="r")
> plt.setp(patches[1], color="b")
> 
> also see
> 
> http://matplotlib.sourceforge.net/examples/pylab_examples/hist_colormapped.html

Hi
thanks a lot for the quick tip. But no xpdf does not do it (I had tried it).

Just to be consistent below is an account of my config (may not help
much). I'll tried to write some simple script to reproduce the bug and
post it but I am afraid this won't be very simple on my side.

cheers
Eric
==========================================
# OS is OpenSuse 11.2 with KDE, 64b laptop

matplotlib version 0.99.1.1
verbose.level helpful
interactive is False
units is False
platform is linux2
backend WXAgg version 2.8.10.1
Python 2.6.2 (r262:71600, Oct 24 2009, 03:15:21)
IPython 0.10 -- An enhanced Interactive Python.

# And in my matplotlibrc:
usetex False
## tried usetex True too
ps.papersize      : A4
ps.useafm         : False
ps.usedistiller   : None
## I tried all possible distiller... didn't change the pb.
ps.distiller.res  : 120      # dpi
ps.fonttype       : 3
==========================================

On 30/12/09 20:35, Jae-Joon Lee wrote:
> This is a kind of bug that is quite hard to trace unless we can
> reproduce the error.
> 
> As far as I know, there has been a report that matplotlib does not
> work well with GPL Ghostscript 8.63. And I'm not sure if it is
> related.
> 
> http://old.nabble.com/Segmentation-fault-with-EPS-output-on-matplotlib->%3D0.98.5.2-to25257581.html#a25334270
> 
> So, see if using "xpdf" as a distiller works.
>>

-- 
=================================================================
Eric Emsellem                       European Southern Observatory
                                        Karl-Schwarzschild Str. 2
e-mail: eem...@es...              85748 Garching bei Muenchen
tel: +49 (0)89 3200 6914                                  Germany
fax: +49 (0)89 3200 6480
=================================================================

http://matplotlib.sourceforge.net/faq/howto_faq.html#automatically-make-room-for-tick-labels

-JJ

On Wed, Dec 30, 2009 at 6:30 AM, Eero Nevalainen
<eer...@in...> wrote:
> Hi,
>
> I find myself repeatedly manually adjusting subplot params, e.g.
> figure.subplot.left, to remove extra white space on my figures. Is there
> a better, automatic way to do this?
>
> Regards,
>
> Eero
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

This is a kind of bug that is quite hard to trace unless we can
reproduce the error.

As far as I know, there has been a report that matplotlib does not
work well with GPL Ghostscript 8.63. And I'm not sure if it is
related.

http://old.nabble.com/Segmentation-fault-with-EPS-output-on-matplotlib->%3D0.98.5.2-to25257581.html#a25334270

So, see if using "xpdf" as a distiller works.

Regards,

-JJ

On Wed, Dec 30, 2009 at 9:39 AM, Eric Emsellem <eem...@es...> wrote:
> Hi again
>
> regarding my last post, I still have pb generating simple eps files.
> Now I turned on "usetex" to True and I get the message given below. If
> anyone can help me with this, it would be great since I am now stuck
> with this.
>
> Reminder: the pb occurs when I save a figure (savefig) in postscript
> format (.eps), after plotting a number of small thumbnail images (using
> pcolormesh and contour).
>
> cheers
>
> Eric
> =======================================================================
> GPL Ghostscript 8.64: Unrecoverable error, exit code 1
> ---------------------------------------------------------------------------
> RuntimeError                              Traceback (most recent call last)
>
> /home/science/ATLAS3D/python/Analysis/show_maps.py in <module>()
> ----> 1
>      2
>      3
>      4
>      5
>
> /usr/lib64/python2.6/site-packages/matplotlib/pyplot.pyc in
> savefig(*args, **kwargs)
>    354 def savefig(*args, **kwargs):
>
>    355     fig = gcf()
>
> --> 356     return fig.savefig(*args, **kwargs)
>
>    357 if Figure.savefig.__doc__ is not None:
>
>    358     savefig.__doc__ = dedent(Figure.savefig.__doc__)
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/figure.pyc in
> savefig(self, *args, **kwargs)
>   1030                 patch.set_alpha(0.0)
>
>   1031
>
> -> 1032         self.canvas.print_figure(*args, **kwargs)
>
>   1033
>
>   1034         if transparent:
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_wxagg.pyc
> in print_figure(self, filename, *args, **kwargs)
>     98     def print_figure(self, filename, *args, **kwargs):
>
>     99         # Use pure Agg renderer to draw
>
>
> --> 100         FigureCanvasAgg.print_figure(self, filename, *args,
> **kwargs)
>    101         # Restore the current view; this is needed because the
>
>
>    102         # artist contains methods rely on particular attributes
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backend_bases.pyc in
> print_figure(self, filename, dpi, facecolor, edgecolor, orientation,
> format, **kwargs)
>   1474                 orientation=orientation,
>
>
>   1475                 bbox_inches_restore=_bbox_inches_restore,
>
>
> -> 1476                 **kwargs)
>
>
>   1477         finally:
>
>
>   1478             if bbox_inches and restore_bbox:
>
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backend_bases.pyc in
> print_eps(self, *args, **kwargs)
>   1327         from backends.backend_ps import FigureCanvasPS # lazy
> import
>   1328         ps = self.switch_backends(FigureCanvasPS)
>
> -> 1329         return ps.print_eps(*args, **kwargs)
>
>   1330
>
>   1331     def print_pdf(self, *args, **kwargs):
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
> print_eps(self, outfile, *args, **kwargs)
>    853
>
>    854     def print_eps(self, outfile, *args, **kwargs):
>
> --> 855         return self._print_ps(outfile, 'eps', *args, **kwargs)
>
>    856
>
>    857
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
> _print_ps(self, outfile, format, *args, **kwargs)
>    882             self._print_figure_tex(outfile, format, imagedpi,
> facecolor, edgecolor,
>    883                                    orientation, isLandscape,
> papertype,
> --> 884                                    **kwargs)
>
>    885         else:
>
>
>    886             self._print_figure(outfile, format, imagedpi,
> facecolor, edgecolor,
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
> _print_figure_tex(self, outfile, format, dpi, facecolor, edgecolor,
> orientation, isLandscape, papertype, **kwargs)
>
>
>
>   1191         elif rcParams['text.usetex']:
>
>
>   1192             if False: pass # for debugging
>
>
> -> 1193             else: gs_distill(tmpfile, isEPSF, ptype=papertype,
> bbox=bbox)
>
>   1194
>
>
>   1195         if  isinstance(outfile, file):
>
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
> gs_distill(tmpfile, eps, ptype, bbox)
>   1311     fh = file(outfile)
>
>   1312     if exit_status: raise RuntimeError('ghostscript was not able
> to process \
> -> 1313 your image.\nHere is the full report generated by
> ghostscript:\n\n' + fh.read())
>   1314     else: verbose.report(fh.read(), 'debug')
>
>
>   1315     fh.close()
>
>
>
> RuntimeError: ghostscript was not able to process your image.
> Here is the full report generated by ghostscript:
>
> GPL Ghostscript 8.64 (2009-02-03)
> Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
> This software comes with NO WARRANTY: see the file COPYING for details.
> Loading NimbusSanL-Regu font from
> /usr/share/ghostscript/8.64/Resource/Font/NimbusSanL-Regu... 3968216
> 1927802 6785440 4864692 1 done.
> Loading CenturySchL-Roma font from
> /usr/share/ghostscript/8.64/Resource/Font/CenturySchL-Roma... 4008424
> 2092670 6785440 4877110 1 done.
> Error: /limitcheck in --def--
> Operand stack:
>   p1c_37d   --nostringval--
> Execution stack:
>   %interp_exit   .runexec2   --nostringval--   --nostringval--
> --nostringval--   2   %stopped_push   --nostringval--   --nostringval--
>  --nostringval--   false   1   %stopped_push   1878   1   3
> %oparray_pop   1877   1   3   %oparray_pop   1861   1   3   %oparray_pop
>  1755   1   3   %oparray_pop   --nostringval--   %errorexec_pop
> .runexec2   --nostringval--   --nostringval--   --nostringval--   2
> %stopped_push   --nostringval--
> Dictionary stack:
>   --dict:1169/3371(ro)(G)--   --dict:1/20(G)--   --dict:74/200(L)--
> --dict:5/6(ro)(L)--   --dict:176/300(L)--   --dict:44/200(L)--
> --dict:65534/65534(L)--
> Current allocation mode is local
> Last OS error: 2
> Current file position is 14089308
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Wed, Dec 30, 2009 at 12:05 PM, Eric Emsellem <eem...@es...> wrote:
> I have tried with rgba sequences but no luck there. The help of hist
> << color: matplotlib color arg or sequence of rgba tuples >>
>

Based on my quick look at the code, it seems that the documentation is
incorrect. I believe it should be  "a tuple of rgba values", not
"sequence of rgba tuples", and I don't think it is possible to specify
color"s" using keyword arguments.

x1 = random(1000)
x2 = random(1000)

n, bins, patches = hist(np.array([x1, x2]).transpose())

plt.setp(patches[0], color="r")
plt.setp(patches[1], color="b")

also see

http://matplotlib.sourceforge.net/examples/pylab_examples/hist_colormapped.html

Regards,

-JJ

p.s., Is it just me who think it is confusing that hist([x1,x2])
interprets input differently when len(x1) == len(x2) and when len(x1)
!= len(x2)?

Hi

how do I specify the colour of the bars in an histogram done with more than one 
set of data?

Example:

x1 = random(1000)
x2 = random(1000)

hist([x1,x2], c=['r','b'])

does not work...

I have tried with rgba sequences but no luck there. The help of hist
<< color: matplotlib color arg or sequence of rgba tuples >>

so I guess we can specify the individual colours of each set of bars (one colour 
per dataset) no?

thanks.

Eric

Hi again

regarding my last post, I still have pb generating simple eps files.
Now I turned on "usetex" to True and I get the message given below. If
anyone can help me with this, it would be great since I am now stuck
with this.

Reminder: the pb occurs when I save a figure (savefig) in postscript
format (.eps), after plotting a number of small thumbnail images (using
pcolormesh and contour).

cheers

Eric
=======================================================================
GPL Ghostscript 8.64: Unrecoverable error, exit code 1
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/home/science/ATLAS3D/python/Analysis/show_maps.py in <module>()
----> 1
      2
      3
      4
      5

/usr/lib64/python2.6/site-packages/matplotlib/pyplot.pyc in
savefig(*args, **kwargs)
    354 def savefig(*args, **kwargs):

    355     fig = gcf()

--> 356     return fig.savefig(*args, **kwargs)

    357 if Figure.savefig.__doc__ is not None:

    358     savefig.__doc__ = dedent(Figure.savefig.__doc__)


/usr/lib64/python2.6/site-packages/matplotlib/figure.pyc in
savefig(self, *args, **kwargs)
   1030                 patch.set_alpha(0.0)

   1031

-> 1032         self.canvas.print_figure(*args, **kwargs)

   1033

   1034         if transparent:


/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_wxagg.pyc
in print_figure(self, filename, *args, **kwargs)
     98     def print_figure(self, filename, *args, **kwargs):

     99         # Use pure Agg renderer to draw


--> 100         FigureCanvasAgg.print_figure(self, filename, *args,
**kwargs)
    101         # Restore the current view; this is needed because the


    102         # artist contains methods rely on particular attributes


/usr/lib64/python2.6/site-packages/matplotlib/backend_bases.pyc in
print_figure(self, filename, dpi, facecolor, edgecolor, orientation,
format, **kwargs)
   1474                 orientation=orientation,


   1475                 bbox_inches_restore=_bbox_inches_restore,


-> 1476                 **kwargs)


   1477         finally:


   1478             if bbox_inches and restore_bbox:



/usr/lib64/python2.6/site-packages/matplotlib/backend_bases.pyc in
print_eps(self, *args, **kwargs)
   1327         from backends.backend_ps import FigureCanvasPS # lazy
import
   1328         ps = self.switch_backends(FigureCanvasPS)

-> 1329         return ps.print_eps(*args, **kwargs)

   1330

   1331     def print_pdf(self, *args, **kwargs):


/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
print_eps(self, outfile, *args, **kwargs)
    853

    854     def print_eps(self, outfile, *args, **kwargs):

--> 855         return self._print_ps(outfile, 'eps', *args, **kwargs)

    856

    857


/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
_print_ps(self, outfile, format, *args, **kwargs)
    882             self._print_figure_tex(outfile, format, imagedpi,
facecolor, edgecolor,
    883                                    orientation, isLandscape,
papertype,
--> 884                                    **kwargs)

    885         else:


    886             self._print_figure(outfile, format, imagedpi,
facecolor, edgecolor,


/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
_print_figure_tex(self, outfile, format, dpi, facecolor, edgecolor,
orientation, isLandscape, papertype, **kwargs)



   1191         elif rcParams['text.usetex']:


   1192             if False: pass # for debugging


-> 1193             else: gs_distill(tmpfile, isEPSF, ptype=papertype,
bbox=bbox)

   1194


   1195         if  isinstance(outfile, file):



/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_ps.pyc in
gs_distill(tmpfile, eps, ptype, bbox)
   1311     fh = file(outfile)

   1312     if exit_status: raise RuntimeError('ghostscript was not able
to process \
-> 1313 your image.\nHere is the full report generated by
ghostscript:\n\n' + fh.read())
   1314     else: verbose.report(fh.read(), 'debug')


   1315     fh.close()



RuntimeError: ghostscript was not able to process your image.
Here is the full report generated by ghostscript:

GPL Ghostscript 8.64 (2009-02-03)
Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file COPYING for details.
Loading NimbusSanL-Regu font from
/usr/share/ghostscript/8.64/Resource/Font/NimbusSanL-Regu... 3968216
1927802 6785440 4864692 1 done.
Loading CenturySchL-Roma font from
/usr/share/ghostscript/8.64/Resource/Font/CenturySchL-Roma... 4008424
2092670 6785440 4877110 1 done.
Error: /limitcheck in --def--
Operand stack:
   p1c_37d   --nostringval--
Execution stack:
   %interp_exit   .runexec2   --nostringval--   --nostringval--
--nostringval--   2   %stopped_push   --nostringval--   --nostringval--
  --nostringval--   false   1   %stopped_push   1878   1   3
%oparray_pop   1877   1   3   %oparray_pop   1861   1   3   %oparray_pop
  1755   1   3   %oparray_pop   --nostringval--   %errorexec_pop
.runexec2   --nostringval--   --nostringval--   --nostringval--   2
%stopped_push   --nostringval--
Dictionary stack:
   --dict:1169/3371(ro)(G)--   --dict:1/20(G)--   --dict:74/200(L)--
--dict:5/6(ro)(L)--   --dict:176/300(L)--   --dict:44/200(L)--
--dict:65534/65534(L)--
Current allocation mode is local
Last OS error: 2
Current file position is 14089308

Hi

I am having reccurrent problem generating postscript files using savefig.

I am basically generating a figure with lots of small thumbnail images
(loaded with mpl pcolormesh and contour) and some overimposed text.

When I do:
savefig("myfig.eps")

it takes quite a while, and makes rather big figures (> 20 Mb). But then
I cannot load that eps file anymore with any of the software I have
tried (okular, display, gimp...). The file seems corrupted and when I
e.g. try with display it tells me:


   Error: /limitcheck in --def--
   Operand stack:
      p1c_37d   --nostringval--
   Execution stack:
      %interp_exit   .runexec2   --nostringval--   --nostringval--
 --nostringval--   2   %stopped_push   --nostringval--   --nostringval--
  --nostringval--   false   1   %stopped_push   1878   1   3
%oparray_pop   1877   1   3   %oparray_pop   --nostringval--   1861   1
  3   %oparray_pop   1755   1   3   %oparray_pop   --nostringval--
%errorexec_pop   .runexec2   --nostringval--   --nostringval--
--nostringval--   2   %stopped_push   --nostringval--
   Dictionary stack:
     --dict:1172/3371(ro)(G)--   --dict:0/20(G)--
--dict:75/200(L)--   --dict:65534/65534(L)--
   Current allocation mode is local
   Last OS error: 2
   Current file position is 14073283
   GPL Ghostscript 8.64: Unrecoverable error, exit code 1


Any help with this please!?

THANKS!

Eric
#########################################################
# Some info on my config here
#########################################################
# OS is OpenSuse 11.2 with KDE, 64b laptop

matplotlib version 0.99.1.1
verbose.level helpful
interactive is False
units is False
platform is linux2
backend WXAgg version 2.8.10.1
Python 2.6.2 (r262:71600, Oct 24 2009, 03:15:21)
IPython 0.10 -- An enhanced Interactive Python.

# And in my matplotlibrc:
usetex False
ps.papersize      : A4
ps.useafm         : False
ps.usedistiller   : None
ps.distiller.res  : 120      # dpi
ps.fonttype       : 3

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Eric Firing wrote:
> Dominik Szczerba wrote:
> OK I started hacking and added a color_cycle property to matplotlibrc.
> Would you be so kind to add this fix to the official version? Thanks!
> Dominik
> 
>> Your basic idea--that the colorcycle should be settable in 
>> rcParams--makes good sense, but the implementation needs some changes, 
>> maybe including a bit of redesign of the color cycle handling.  I will 
>> look into it.  A little discussion on the devel list may be required.  I 
>> think we will want to completely decouple lines.color from a new 
>> lines.colorcycle, but maybe there is some good reason, other than 
>> history, for why they are coupled.

Hi Eric,
That's great. I would be happy if a final conclusion from the devel list
could be forwarded here as well.
Thanks,
Dominik

> 
>> Eric
> 
> $ diff -w axes.py axes.py.org
> 135,137c135
> <     # DSZ take defaultColors from rcParams
> <     # defaultColors = ['b','g','r','c','m','y','k']
> <     defaultColors = rcParams['axes.color_cycle']
> ---
>>>>     defaultColors = ['b','g','r','c','m','y','k']
> 
> $ diff -w rcsetup.py rcsetup.py.org
> 442,443d441
> <     # DSZ add color_cycle property
> <     'axes.color_cycle' : [['b','g','r','c','m','y','k'],
> validate_stringlist],
> 
> 
> 
> Add to custom matplotlibrc as e.g.:
> 
> axes.color_cycle    : w, w, w, w, w, w, w
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dominik Szczerba wrote:
>>>> I want to specify my own color cycle in matplotlibrc. I know I can do in
>>>> the actual script:
>>>>
>>>> matplotlib.axes.set_default_color_cycle(['w', 'w', 'w', 'w', 'w', 'w', 'w'])
>>>>
>>>> but it renders my scripts not portable (if somebody does not have black
>>>> bg in matplotlibrc as I do then he will not see the plot).
>>>>
>>>> (How) Can I specify my color cycle in matplotlibrc - or another portable
>>>> fashion? Or at least disable it so the lines.color is used for all colors?
>>>>
>>>> Dominik
> -
> ------------------------------------------------------------------------------
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>>
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Hi,

I find myself repeatedly manually adjusting subplot params, e.g.
figure.subplot.left, to remove extra white space on my figures. Is there
a better, automatic way to do this?

Regards,

Eero

Hello,

Numpy is capable of simple fitting of polynomials, see for a  
definition and an example:
http://docs.scipy.org/doc/numpy/reference/generated/numpy.polyfit.html

Alternatively, there is an entry in the SciPy Cookbook: http:// 
www.scipy.org/Cookbook/FittingData

Regards,

Pierre

Le 30 déc. 09 à 12:07, Manuel Wittchen a écrit :

> Hi,
>
> I want to do a linear regression with my Data but couldn't find a
> ready-to-use matplotlib- or numpy-function. If there is no function
> for linear regression in matplotlib/numpy, could somebody explain to
> me how to code lin. reg. as a function?
>
> Regards,
>
> Manuel Wittchen

Hi,

I want to do a linear regression with my Data but couldn't find a
ready-to-use matplotlib- or numpy-function. If there is no function
for linear regression in matplotlib/numpy, could somebody explain to
me how to code lin. reg. as a function?

Regards,

Manuel Wittchen

One nice thing about gnuplot is the option its GUI provides to toggle 
between using coloured lines and using black lines with various dashed 
patterns. I think it would be nice in matplotlib to also be able to have 
a default series of dashed patterns that could automatically be cycled 
through.

Gary R

Eric Firing wrote:
> Dominik Szczerba wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> OK I started hacking and added a color_cycle property to matplotlibrc.
>> Would you be so kind to add this fix to the official version? Thanks!
>> Dominik
> 
> Your basic idea--that the colorcycle should be settable in 
> rcParams--makes good sense, but the implementation needs some changes, 
> maybe including a bit of redesign of the color cycle handling.  I will 
> look into it.  A little discussion on the devel list may be required.  I 
> think we will want to completely decouple lines.color from a new 
> lines.colorcycle, but maybe there is some good reason, other than 
> history, for why they are coupled.

Dominik Szczerba wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> OK I started hacking and added a color_cycle property to matplotlibrc.
> Would you be so kind to add this fix to the official version? Thanks!
> Dominik

Your basic idea--that the colorcycle should be settable in 
rcParams--makes good sense, but the implementation needs some changes, 
maybe including a bit of redesign of the color cycle handling.  I will 
look into it.  A little discussion on the devel list may be required.  I 
think we will want to completely decouple lines.color from a new 
lines.colorcycle, but maybe there is some good reason, other than 
history, for why they are coupled.

Eric

> 
> $ diff -w axes.py axes.py.org
> 135,137c135
> <     # DSZ take defaultColors from rcParams
> <     # defaultColors = ['b','g','r','c','m','y','k']
> <     defaultColors = rcParams['axes.color_cycle']
> - ---
>>     defaultColors = ['b','g','r','c','m','y','k']
> 
> 
> $ diff -w rcsetup.py rcsetup.py.org
> 442,443d441
> <     # DSZ add color_cycle property
> <     'axes.color_cycle' : [['b','g','r','c','m','y','k'],
> validate_stringlist],
> 
> 
> 
> Add to custom matplotlibrc as e.g.:
> 
> axes.color_cycle    : w, w, w, w, w, w, w
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dominik Szczerba wrote:
>> I want to specify my own color cycle in matplotlibrc. I know I can do in
>> the actual script:
>>
>> matplotlib.axes.set_default_color_cycle(['w', 'w', 'w', 'w', 'w', 'w', 'w'])
>>
>> but it renders my scripts not portable (if somebody does not have black
>> bg in matplotlibrc as I do then he will not see the plot).
>>
>> (How) Can I specify my color cycle in matplotlibrc - or another portable
>> fashion? Or at least disable it so the lines.color is used for all colors?
>>
>> Dominik
> 
> -
> ------------------------------------------------------------------------------
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> 
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> 
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Tony S Yu wrote:
>>
>> Tony S Yu wrote:
>>> On Dec 29, 2009, at 3:35 AM, Dominik Szczerba wrote:
>>>> Tony S Yu wrote:
>>>>> Hey Dominik,
>>>>>
>>>>> I'd also like to see the default color_cycle be customizeable. But, if
>>>>> I'm not mistaken, this approach doesn't quite do what you want (at
>>>>> least
>>>>> it doesn't on a recent version of mpl). The problem is that the color
>>>>> given by lines.color (rcParam) sort of overrides the first color in the
>>>>> specified color cycle (see
>>>>> ``_process_plot_var_args._clear_color_cycle`` in  axes.py).
>>>>>
>>>>> It seems important for lines.color and the first color in the color
>>>>> cycle to match since this matching is also enforced in
>>>>> ``axes.set_default_color_cycle``, except in reverse (the first color in
>>>>> the color cycle overrides line.color). If both lines.color and
>>>>> axes.color_cycle (or maybe lines.color_cycle) are rcParams, there would
>>>>> be issues with how to match the two (e.g. which takes precedence if
>>>>> they
>>>>> differ).
>>>>>
>>>>> As I said earlier, I'd like to see this change made, but I think it may
>>>>> change the current behavior. Maybe a mpl developer could weigh in?
>>>>>
>>>>> -Tony
>>>> Hi Tony,
>>>> You are correct, line color overrides the first cycle color. That does
>>>> not appear a very happy choice to me but this way or another you can
>>>> still specify BOTH lines.color and the cycle in the param file to get
>>>> whatever you want, no?
>>>>
>>>> Dominik
>>>
>>> Yup, that should do exactly what you want. But, since it's a bit of a
>>> hack (you should only need to make 1 change to matplotlibrc), I doubt
>>> this patch would be appropriate for the main distribution.
>>>
>>> Ideally, we'd need to figure out if the matplotlibrc changes 1) only
>>> lines.color and make this the first color in color_cycle, 2) only
>>> lines.color_cycle and make the first color override lines.color, or
>>> 3) both lines.color and lines.color_cycle (behavior unknown if colors
>>> don't match). Unfortunately, I don't see an easy way to tell if
>>> rcParams have been changed from their default values.
>>
>> Hi Tony,
>> My patches (there were two!) remove the badly hardcoded definition of
>> defaultColors in axes.py and instead define default axes.color_cycle in
>> rcsetup.py (defaulting it to the already established color array
>> ['b','g','r','c','m','y','k']). Now, in axes.py, defaultColors are taken
>> from rcParams, and not a hardcoded array, so unless you modify your own
>> rc file, you will get the old behavior. It is if and only if you define
>> your color_cycle in your own rc file that will do anything new. I do not
>> see how this introduces any incompatibilities.
>> Dominik
> 
> Sorry for the confusion. I wasn't saying your patches introduce
> incompatibilities, but I did say that their behavior is not ideal. For
> example, your matplotlibrc requires *both* "lines.color_cycle : w, w, w,
> w, w, w" (actually I think you only need one "w,") *and* "lines.color :
> w". Ideally (at least IMO), I should only need to set the color cycle,
> and it was surprising to me (surprises = bad) that I'd have to also set
> "lines.color"

True, in this context my solution is not ideal indeed, but the current
solution is dramatic: it forces one to use black on white color scheme,
else the colors are very poorly visible. Setting them in the user script
ruins the portability.

Most people will probably not care, therefore I believe my solution is
optimal. I have to work with black background, and I am sure those like
me will bother to add two extra lines to the rc file.

Dominik

> 
> The incompatibilities I spoke of would only be true if you went with my
> suggestion to deprecate "lines.color".
> 
> -T
> 

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> 
> Tony S Yu wrote:
>> On Dec 29, 2009, at 3:35 AM, Dominik Szczerba wrote:
>>> Tony S Yu wrote:
>>>> Hey Dominik,
>>>> 
>>>> I'd also like to see the default color_cycle be customizeable. But, if
>>>> I'm not mistaken, this approach doesn't quite do what you want (at least
>>>> it doesn't on a recent version of mpl). The problem is that the color
>>>> given by lines.color (rcParam) sort of overrides the first color in the
>>>> specified color cycle (see
>>>> ``_process_plot_var_args._clear_color_cycle`` in  axes.py). 
>>>> 
>>>> It seems important for lines.color and the first color in the color
>>>> cycle to match since this matching is also enforced in
>>>> ``axes.set_default_color_cycle``, except in reverse (the first color in
>>>> the color cycle overrides line.color). If both lines.color and
>>>> axes.color_cycle (or maybe lines.color_cycle) are rcParams, there would
>>>> be issues with how to match the two (e.g. which takes precedence if they
>>>> differ).
>>>> 
>>>> As I said earlier, I'd like to see this change made, but I think it may
>>>> change the current behavior. Maybe a mpl developer could weigh in?
>>>> 
>>>> -Tony
>>> Hi Tony,
>>> You are correct, line color overrides the first cycle color. That does
>>> not appear a very happy choice to me but this way or another you can
>>> still specify BOTH lines.color and the cycle in the param file to get
>>> whatever you want, no?
>>> 
>>> Dominik
>> 
>> Yup, that should do exactly what you want. But, since it's a bit of a hack (you should only need to make 1 change to matplotlibrc), I doubt this patch would be appropriate for the main distribution. 
>> 
>> Ideally, we'd need to figure out if the matplotlibrc changes 1) only lines.color and make this the first color in color_cycle, 2) only lines.color_cycle and make the first color override lines.color, or 3) both lines.color and lines.color_cycle (behavior unknown if colors don't match). Unfortunately, I don't see an easy way to tell if rcParams have been changed from their default values. 
> 
> Hi Tony,
> My patches (there were two!) remove the badly hardcoded definition of
> defaultColors in axes.py and instead define default axes.color_cycle in
> rcsetup.py (defaulting it to the already established color array
> ['b','g','r','c','m','y','k']). Now, in axes.py, defaultColors are taken
> from rcParams, and not a hardcoded array, so unless you modify your own
> rc file, you will get the old behavior. It is if and only if you define
> your color_cycle in your own rc file that will do anything new. I do not
> see how this introduces any incompatibilities.
> Dominik

Sorry for the confusion. I wasn't saying your patches introduce incompatibilities, but I did say that their behavior is not ideal. For example, your matplotlibrc requires *both* "lines.color_cycle : w, w, w, w, w, w" (actually I think you only need one "w,") *and* "lines.color : w". Ideally (at least IMO), I should only need to set the color cycle, and it was surprising to me (surprises = bad) that I'd have to also set "lines.color"

The incompatibilities I spoke of would only be true if you went with my suggestion to deprecate "lines.color".

-T

TheLonelyStar wrote:
> 
> 
> 
> Jeff Whitaker wrote:
>> 
>> TheLonelyStar wrote:
>>> Hi,
>>>
>>> I am trying to get the exaple from here:
>>> http://matplotlib.sourceforge.net/examples/animation/animate_decay_tk_blit.html
>>>
>>> I copied it into a file and tried to execute it.
>>> I get:
>>>
>>> File "test.py", line 56, in <module>
>>>     manager.window.after(100, run)
>>> AttributeError: 'gtk.Window' object has no attribute 'after'
>>>
>>> What is wrong? How can I correct that?
>>>
>>> Thanks!
>>> Nathan
>>>   
>> 
>> Nathan:  You're using the GTKAgg backend (the default), whereas the 
>> script expects the TkAgg backend.  Either edit your matplotlibrc file to 
>> set TkAgg as your default backend, or run the script like this:
>> 
>> python animate_decay_tk_blit.py -dTkAgg
>> 
>> -Jeff
>> 
>> -- 
>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>> Meteorologist               FAX    : (303)497-6449
>> NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>> 
>> 
>> ------------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Verizon Developer Community
>> Take advantage of Verizon's best-in-class app development support
>> A streamlined, 14 day to market process makes app distribution fast and
>> easy
>> Join now and get one step closer to millions of Verizon customers
>> http://p.sf.net/sfu/verizon-dev2dev 
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> 
>> 
> 
> Hey,
> 
> Thanks, that works. Is it also possible to get it to work with the GTKAgg
> backend?
> 
> Thanks!
> Nathan
> 

I found the examples for the other backends. Sorry for not looking better
before
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On Sat, Dec 26, 2009 at 12:52 PM, Till Stensitzki <mai...@gm...> wrote:
> If you want to use it in the example section or anything else, you are
> welcome.

We also have an existing blitting example at
http://matplotlib.sourceforge.net/examples/animation/animation_blit_qt4.html
. I would prefer not to add blitting to the emedding_in_qt4 example,
so we can keep it as short and simple as possible.

Darren

On Mon, Dec 28, 2009 at 10:24 AM, TheLonelyStar <na...@lo...> wrote:
>
> Hi,
>
> I have a Qt application, where I want to display a matplotlib figure which
> is updated from time to time (not mebeded, in its own window).
>
> Now, I do:
> import pylab
>
> pylab.ion()
> pylab.figure()
>
> within a function of the Qt application. And then I get a segfault.
>
> What is the proper way to do this?

You don't want to use the pylab interface to integrate a figure into a
qt application. Instead, see the example at
http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_qt4.html
, it will show you how to create a plot in a separate window and
update it periodically.

Darren

Jeff Whitaker wrote:
> 
> TheLonelyStar wrote:
>> Hi,
>>
>> I am trying to get the exaple from here:
>> http://matplotlib.sourceforge.net/examples/animation/animate_decay_tk_blit.html
>>
>> I copied it into a file and tried to execute it.
>> I get:
>>
>> File "test.py", line 56, in <module>
>>     manager.window.after(100, run)
>> AttributeError: 'gtk.Window' object has no attribute 'after'
>>
>> What is wrong? How can I correct that?
>>
>> Thanks!
>> Nathan
>>   
> 
> Nathan:  You're using the GTKAgg backend (the default), whereas the 
> script expects the TkAgg backend.  Either edit your matplotlibrc file to 
> set TkAgg as your default backend, or run the script like this:
> 
> python animate_decay_tk_blit.py -dTkAgg
> 
> -Jeff
> 
> -- 
> Jeffrey S. Whitaker         Phone  : (303)497-6313
> Meteorologist               FAX    : (303)497-6449
> NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
> 325 Broadway                Office : Skaggs Research Cntr 1D-113
> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
> 
> 
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
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> 
> 

Hey,

Thanks, that works. Is it also possible to get it to work with the GTKAgg
backend?

Thanks!
Nathan
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