matplotlib-users Mailing List for matplotlib (Page 5)

Hi,

It looks like the 
http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/branches/py3k/ 
in dead.
The last commit was 8months ago.

Numpy is ok with python3.1, scipy is ok, nose is ok, ipython is usable.
Ubuntu already provides python-tk for python3.x
It would be nice to port matplotlib to python3.
Is there a plan? another svn/git branch?

Xavier

--- On Wed, 3/16/11, Daniel Welling <dan...@gm...> wrote:
After
 playing with backends quite a bit, I have found that the best one in 
terms of speed, robustness, and features is Qt4Agg - especially on OSX, 
where the MacOSX backend is buggy and many others just don't plain 
work.  



Why do you think that the MacOSX backend is buggy?

--Michiel.







      

Hi all,
So I tried what was advised to me.
python -c 'import pylab; pylab.plot([4]);'
terminate called after throwing an instance of 'std::exception'
terminate called recursively
Abort

which happens here:
     14 agg::trans_affine
     15 py_to_agg_transformation_matrix(PyObject* obj, bool errors = true)
     16 {
     17     PyArrayObject* matrix = NULL;
     18
     19     try
     20     {
     21         if (obj == Py_None)
     22             throw std::exception();

Since I compiled w/o optimization flags I have this now:
#11 0xfffffd7ff46cf0b6 in __cxxabiv1::__cxa_throw (obj=<value
optimized out>, tinfo=<value optimized out>,
    dest=<value optimized out>) at
../../../../../libstdc++-v3/libsupc++/eh_throw.cc:83
#12 0xfffffd7ff4a3c708 in py_to_agg_transformation_matrix
(obj=0x774380, errors=false) at src/agg_py_transforms.cpp:22
#13 0xfffffd7ff4a4132e in _path_module::update_path_extents
(this=0x144e230, args=...) at src/path.cpp:380
#14 0xfffffd7ff4a537ce in
Py::ExtensionModule<_path_module>::invoke_method_varargs
(this=0x144e230, method_def=0x14009b0,
    args=...) at ./CXX/Python2/ExtensionModule.hxx:184
#15 0xfffffd7ff4a389df in Py::method_varargs_call_handler
(_self_and_name_tuple=0x1244170, _args=0x1977fb0)
    at CXX/Python2/cxx_extensions.cxx:1714
#16 0x00000000004a6071 in call_function (f=0x201e980, throwflag=<value
optimized out>)
    at /usr/local/src/lang/Python-2.7.1/Python/ceval.c:4012
#17 PyEval_EvalFrameEx (f=0x201e980, throwflag=<value optimized out>)
    at /usr/local/src/lang/Python-2.7.1/Python/ceval.c:2665
#18 0x00000000004a79c1 in PyEval_EvalCodeEx (co=0x123a130,
globals=<value optimized out>, locals=<value optimized out>,
    args=0x201eb20, argcount=<value optimized out>, kws=0x3,
kwcount=2, defs=0x12467e8, defcount=3, closure=0x0)
    at /usr/local/src/lang/Python-2.7.1/Python/ceval.c:3252

The function has now obj=0x774380 as an argument instead of <value
optimized out>

So what is generating a PyNull object is in src/path.cpp:380
but this file doesn't exist! If I look in _path.cpp though this is
where it fails:
    360         ::get_path_extents(path, trans, &extents_data[0],
&extents_data[1],
    361                            &extents_data[2], &extents_data[3],
&xm, &ym);

I have no idea how to debug this since it seems the problem are in the
CXX extensions (calls to ceval.c)

Any idea how I can narrow down the problem?

Thanks!


On Sun, Mar 13, 2011 at 6:18 PM, Nicolas SCHEFFER
<sch...@gm...> wrote:
> Thanks much for the reply!
> I'll try your advice as soon as I can.
>
> BTW, I don't think this is a Solaris-related problem.
> If you look at the pointers in my original post, the same error can
> happen on other arch (I confess it can be for other reasons though).
>
> -n
>
> On Sun, Mar 13, 2011 at 1:03 PM, Jouni K. Seppänen <jk...@ik...> wrote:
>> Nicolas SCHEFFER <sch...@gm...> writes:
>>
>>> I didn't get much reply on this issue, so I'm just trying to resurrect
>>> the question.
>>
>> Probably not many devs using Solaris, so no-one has been able to
>> reproduce this.
>>
>>>> #12 0xfffffd7ff4a22fd8 in py_to_agg_transformation_matrix
>>>> (obj=0x774380, errors=<value optimized out>) at
>>>> src/agg_py_transforms.cpp:22
>>>> #13 0xfffffd7ff4a32e7c in _path_module::update_path_extents
>>>> (this=<value optimized out>, args=...) at src/path.cpp:380
>>
>> So it's in transforms-related code, but we can't see the locals. First
>> I'd try to recompile without optimizations and (hoping it still crashes)
>> inspect the local variables in these frames in gdb. Or maybe make the
>> functions print out their arguments and any other relevant locals.
>>
>> --
>> Jouni K. Seppänen
>> http://www.iki.fi/jks
>>
>>
>> ------------------------------------------------------------------------------
>> Colocation vs. Managed Hosting
>> A question and answer guide to determining the best fit
>> for your organization - today and in the future.
>> http://p.sf.net/sfu/internap-sfd2d
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>

On 18. mars 2011, at 12.49, Rita wrote:

> If I have 30 PNGs and i would like to make a slideshow or an animated gif what is the best way to do this? Can matplotlib do this?
> 

I have used ffmpeg in the past with some success. It generates mpeg 4 video files, but maybe that's OK for you?

The only requirement is that your files are named on the format file_0000.png file_0001.png ...
See examples below.

Cheers
Paul.

+++++++++++++++++++++++++

ffmpeg -qscale 5 -r 20 -b 9600 -i img%04d.png movie.mp4
ffmpeg -qscale 5 -r 20 -i img%04d.png movie.mp4

# The options are
# 
#     * -qscale 5 … define fixed video quantizer scale (VBR) where 1 is the best and 31 the worst. Since mpeg/jpeg has problems to compress line graphics it’s a good idea to set this variable close to 1. You get a big movie file, but otherwise the movie doesn’t look, well, that good.
#     * -r … framerate
#     * -b … video bitrate
#     * -i input files, %04d says that we have four numbers in the filename where the number is filled with zeros left of it.
#     * movie.mp4 is the filename, the extension says that it is a quicktime movie. You can also create a Macromedia Flash movie by using the .flv extension.
# Info from: http://tinyurl.com/dlwlnk
# Note that the images have to be numbered 1,2,3,... not (for example) 2, 4, 6... or 10, 20, 30...

On 03/18/2011 11:15 AM, Yves Revaz wrote:
> Dear matplotlib users,
>
> The following very simple script generate an explosion of ram memory :
>
> from numpy  import *
> import pylab as pl
>
> while 1:
>     data = random.random((512,512))
>     pl.imshow(data)

Try adding "pl.clf()" or "pl.cla().
Without that, each call to imshow is adding an image without deleting 
the previous one.

Eric


>
>
> How is it possible to loop over imshow, without having this problem ?
>
> Thanks in advance,
>
> yves
>
>
>
>
>
>

Dear matplotlib users,

The following very simple script generate an explosion of ram memory :

from numpy  import *
import pylab as pl

while 1:
   data = random.random((512,512))
   pl.imshow(data)


How is it possible to loop over imshow, without having this problem ?

Thanks in advance,

yves






-- 
                                                  (o o)
--------------------------------------------oOO--(_)--OOo-------
   Yves Revaz
   Laboratory of Astrophysics EPFL
   Observatoire de Sauverny     Tel : ++ 41 22 379 24 28
   51. Ch. des Maillettes       Fax : ++ 41 22 379 22 05
   1290 Sauverny             e-mail : Yve...@ep...
   SWITZERLAND                  Web : http://www.lunix.ch/revaz/
----------------------------------------------------------------

On 03/18/2011 03:56 AM, Michael Droettboom wrote:
> There is an example showing how to create an MPEG-4 movie here:
>
> http://matplotlib.sourceforge.net/examples/animation/movie_demo.html
>
> Creating an animated gif would just be a matter of using the correct third-party tool that can combine a set of image frames.

For example, gifsicle or ImageMagick.

Eric

>
> Mike
>
> ________________________________________
> From: Rita [rmo...@gm...]
> Sent: Friday, March 18, 2011 7:49 AM
> To: mat...@li...
> Subject: [Matplotlib-users] png to slideshow (gif)
>
> If I have 30 PNGs and i would like to make a slideshow or an animated gif what is the best way to do this? Can matplotlib do this?
>
>
>
> --
> --- Get your facts first, then you can distort them as you please.--
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

There is an example showing how to create an MPEG-4 movie here:

http://matplotlib.sourceforge.net/examples/animation/movie_demo.html

Creating an animated gif would just be a matter of using the correct third-party tool that can combine a set of image frames.

Mike

________________________________________
From: Rita [rmo...@gm...]
Sent: Friday, March 18, 2011 7:49 AM
To: mat...@li...
Subject: [Matplotlib-users] png to slideshow (gif)

If I have 30 PNGs and i would like to make a slideshow or an animated gif what is the best way to do this? Can matplotlib do this?



--
--- Get your facts first, then you can distort them as you please.--

Hi everyone. I was trying to produce an irregular heat map broken down by day/weeks, as excellently shown here:

http://revolution-computing.typepad.com/.a/6a010534b1db25970b0120a63e9936970b-500wi

(source: http://stackoverflow.com/questions/2076370/most-underused-data-visualization)

How would you proceed to achieve such a result with matplotlib?

My initial idea was to use different images (one per year), by generating the pixels by manually binning my data. Then use imgshow with a different subplot for each year.
Then place ytics/xtics and the colorbar manually.

I'm wondering if there's a better way though. In this case ggplot2 is so succinct that makes me cringe.

Thanks.

If I have 30 PNGs and i would like to make a slideshow or an animated gif
what is the best way to do this? Can matplotlib do this?



-- 
--- Get your facts first, then you can distort them as you please.--

My legend is going to have a series of entries that look like:

u=2,p=3
u=1,p=4
...


I want to add some (short) text that explains what u and p are.

I'm thinking to get the coordinates of the legend box so I can then annotate?

How would I get the coordinates of the legend box?  Or is there some 
better/easier way to do what I want?

Paul Ivanov skrev 2011-03-17 20:58:
> Jörgen Stenarson, on 2011-03-16 18:04,  wrote:
>>  Hi,
>>
>>  I'm interested in making plots that are plotted on a polar grid or a
>>  smith chart grid but where the data coordinates still are normal
>>  rectangular. It is not clear for me if this is possible with the
>>  standard gridding machinery or if some other approach is necessary.
>>
>>  Another question is how would I get the data to clip inside the maximum
>>  circle of the polar or smithchart?
>
> Hi Jörgen,
>
> there's probably a way of doing this, and not knowing your other
> constraints maybe this isn't an option, but the path of least
> resistance would be to make a polar subplot and transform your
> rectangular data to polar coordinates for the purposes of
> plotting (rather than transforming the grid to polar). This way
> you'll get your clipping "for free."
>
Hi Paul,

I'll test that approach for the polar plots, but it won't work for the 
Smith chart where I need another grid.

/Jörgen

Evan Mason, on 2011-03-16 15:27,  wrote:
> Hi, I get unexpected behaviour using the script below.  xticks only appear in
> the 4th subplot.  If the lines marked ### are moved out of the loop (and edited
> so that they are constants), then xticks do appear on each subplot.  Is this a
> bug or am I missing something?
> 
> I am using matplotlib 1.1.0svn.

Hi Evan,

What you're seeing is the result of each instance of locator
belonging to one and only one axis (namely months.axis), and
every time you call ax.xaxis_major_locator, you're moving it to
the newest subplot.

Just move the 'months = ...' line inside the for-loop, and you'll
be all set.

best,
-- 
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Stef Mientki, on 2011-03-16 19:45,  wrote:
> hello,
> 
> The text in matplotlib pictures is very fuzzy (certainly if you compare that to fixed texts).
> The picture below is from an html page, the html page is generated from a python script,
> which also produces the matplotlib pictures, which are stored in a png-file and linked in the html page.
> 
> Are there ways to improve the font quality of the texts in the MatPlotLib image ?

Hi Stef,

Have you tried increasing the resolution of the images before you
save them, via plt.savefig("something.png",dpi=160) or by setting
the savefig.dpi rcParam to affect all plots. You might also play
with using different fontsize parameters when calling .text(...)
 
best,
-- 
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Jörgen Stenarson, on 2011-03-16 18:04,  wrote:
> Hi,
> 
> I'm interested in making plots that are plotted on a polar grid or a 
> smith chart grid but where the data coordinates still are normal 
> rectangular. It is not clear for me if this is possible with the 
> standard gridding machinery or if some other approach is necessary.
> 
> Another question is how would I get the data to clip inside the maximum 
> circle of the polar or smithchart?

Hi Jörgen,

there's probably a way of doing this, and not knowing your other
constraints maybe this isn't an option, but the path of least
resistance would be to make a polar subplot and transform your
rectangular data to polar coordinates for the purposes of
plotting (rather than transforming the grid to polar). This way
you'll get your clipping "for free."

best,
-- 
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Francesco Montesano, on 2011-03-17 12:05,  wrote:
> Dear all,
> 
> I have a rather complex code that takes a list of file names and of
> legend tags from command line and compute contour plots
> 
> ./contour_plots.py [options] filename1 ... filename2 tag1 ... tagn
> 
> The codes make filled contours at required levels, then line contours.
> >From the latter I extract one line from each file and create a legend
> 
> spl.legend(lines, [tag1...tagn], other options)
> 
> All it works fine. The only problem is that sometimes I have tags that
> are long and I would like to be able to break between multiple lines.
> In examples/legend_demo3.py is shown that 'ax1.plot([1],
> label="multi\nline")' the \n is interpreted (correctly) as new line.
> 
> Normaly I have something like
> ./contour_plots.py [options] filename1 \(long\)tag\$_\{very long\}\$
> that gives me a legend with the correct formatting. If I try to add a
> '\n' after 'tag', I get out the tag as before plus a 'n' after 'tag'.
> I've tried to enclose the whole string or just \n in "" or r"" but
> nothing good happens (either I get 'n' or 'rn').
> Is there a way to do what I want to do?

Hi Francesco,

If you are using bash, you can insert newlines using the
Enter/Return key if you start an argument with a quote like this:

$ cat commandline.py
#!/usr/bin/env python
import sys
print "Program output:", sys.argv
print sys.argv[-1]

$ ./commandline.py "something
with
newlines"

Program output: ['./commandline.py', 'something\nwith\nnewlines']
something
with
newlines

best,
-- 
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: 
findfont: Font family ['STIXSizeOneSym'] not found. Falling back to Bitstream 
Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))
/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: 
findfont: Font family ['STIXSizeThreeSym'] not found. Falling back to Bitstream 
Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))
/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: 
findfont: Font family ['STIXSizeFourSym'] not found. Falling back to Bitstream 
Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))
/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: 
findfont: Font family ['STIXSizeFiveSym'] not found. Falling back to Bitstream 
Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))
/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: 
findfont: Font family ['STIXSizeTwoSym'] not found. Falling back to Bitstream 
Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))
/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: 
findfont: Font family ['STIXNonUnicode'] not found. Falling back to Bitstream 
Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))

But I have stix fonts installed
stix-pua-fonts-1.0.0-1.fc14.noarch
stix-variants-fonts-1.0.0-1.fc14.noarch
stix-fonts-doc-1.0.0-1.fc14.noarch
stix-sizes-fonts-1.0.0-1.fc14.noarch
stix-fonts-1.0.0-1.fc14.noarch
stix-integrals-fonts-1.0.0-1.fc14.noarch

What could be wrong?

Dear all,

I have a rather complex code that takes a list of file names and of
legend tags from command line and compute contour plots

./contour_plots.py [options] filename1 ... filename2 tag1 ... tagn

The codes make filled contours at required levels, then line contours.
>From the latter I extract one line from each file and create a legend

spl.legend(lines, [tag1...tagn], other options)

All it works fine. The only problem is that sometimes I have tags that
are long and I would like to be able to break between multiple lines.
In examples/legend_demo3.py is shown that 'ax1.plot([1],
label="multi\nline")' the \n is interpreted (correctly) as new line.

Normaly I have something like
./contour_plots.py [options] filename1 \(long\)tag\$_\{very long\}\$
that gives me a legend with the correct formatting. If I try to add a
'\n' after 'tag', I get out the tag as before plus a 'n' after 'tag'.
I've tried to enclose the whole string or just \n in "" or r"" but
nothing good happens (either I get 'n' or 'rn').
Is there a way to do what I want to do?

Thanks in advance
Francesco

On 13 Jan 2011, at 5:50 AM, Michael Droettboom wrote:

> Can you provide a simple LaTeX document that illustrates the problem  
> with psfrag?  This is still compliant Postscript, AFAICT.

It is not a postscript compliance issue, but rather a requirement of  
the psfrag package which relys on searching for complete strings of  
the form "(...) show" for replacement.

Here is a simple example.  Prior to this change, matplotlib would  
output the entire string "(0) show", "(1) show" and "(Np) show".  The  
psfrag package replaces these with typeset versions of "zero", "one"  
and "$N_+$ in whatever font, size, etc. is active in the LaTeX file  
(providing an exact match with the surrounding text).

The new version of matplotlib has instead the individual characters  
followed by glyphshow: "/zero glyphshow" etc. and psfrag can no-longer  
locate the appropriate strings and replace them.  Please provide a way  
for users to revert to the old behaviour of outputing the complete  
string rather than one glyph at a time as some of us use psfrag  
extensively for publication-quality figures.

% import matplotlib.pyplot as plt
% plt.plot([0,1],[0,1])
% plt.xticks([0,1], ['0', '1'])
% plt.xlabel(r'Np')
% savefig('bad.eps')
\documentclass{article}
\usepackage{graphicx}
\usepackage{psfrag}
\begin{document}
\psfrag{0}{zero}
\psfrag{1}{one}
\psfrag{Np}{$N_+$}
\includegraphics[width=\textwidth]{bad.eps}
\end{document}

> On 01/11/2011 10:43 AM, Benjamin Root wrote:
>>
>>
>>
>> On Tue, Jan 11, 2011 at 8:45 AM, Lebostein <Leb...@gm...> wrote:
>>
>> I have compared the new and old output. For example the "0.0" in a  
>> diagram:
>>
>> old eps (1.0.0):
>>
>> 35.223 19.934 m
>> 0 0.141 rmoveto
>> (0.0) show
>> [1 2] 0 setdash
>> 0.502 setgray
>>
>> new eps (1.0.1):
>>
>> 35.222810 19.933563 translate
>> 0.000000 rotate
>> 0.000000 0.140625 m /zero glyphshow
>> 6.362305 0.140625 m /period glyphshow
>> 9.541016 0.140625 m /zero glyphshow
>> grestore
>> [1 2] 0 setdash
>> 0.502 setgray

 hello,

The text in matplotlib pictures is very fuzzy (certainly if you compare that to fixed texts).
The picture below is from an html page, the html page is generated from a python script,
which also produces the matplotlib pictures, which are stored in a png-file and linked in the html page.

Are there ways to improve the font quality of the texts in the MatPlotLib image ?

thanks,
Stef Mientki

hello,

The text in matplotlib pictures is very fuzzy (certainly if you compare that to fixed texts).
The picture below is from an html page, the html page is generated from a python script,
which also produces the matplotlib pictures, which are stored in a png-file and linked in the html page.

Are there ways to improve the font quality of the texts in the MatPlotLib image ?

thanks,
Stef Mientki

Greetings, MPL'ers.

After playing with backends quite a bit, I have found that the best one in
terms of speed, robustness, and features is Qt4Agg - especially on OSX,
where the MacOSX backend is buggy and many others just don't plain work.

To my great disappointment, I have found that this backend doesn't work on
some machines anymore.  As soon as a plot is created, ipython stops
responding, python CPU usage goes to 100%+, and I have to kill ipython or
shut the terminal.  I am not the only person to experience this; a co-worker
has the same problem.  It didn't use to be like this; it has started
happening after an update a few months ago (I'm not sure what update, I use
macports so I update in batches.)

To complicate matters, on a mac laptop (which is updated on a similar
schedule as my desktop machine), I do not have this problem.  Everything
works flawlessly.

Has anyone else had this problem, and does anyone know of a solution?
Thanks for your help.

Details:
All software through MacPorts.
OSX 10.6.5
Ipython 0.10.1
python 2.6.6
MPL 1.0.1_2
pyqt4 4.8.3_1
Qt4-mac 4.7.1_1/4.7.2_0

Hi,

I'm interested in making plots that are plotted on a polar grid or a 
smith chart grid but where the data coordinates still are normal 
rectangular. It is not clear for me if this is possible with the 
standard gridding machinery or if some other approach is necessary.

Another question is how would I get the data to clip inside the maximum 
circle of the polar or smithchart?

/Jörgen

Hi, I get unexpected behaviour using the script below.  xticks only appear in
the 4th subplot.  If the lines marked ### are moved out of the loop (and edited
so that they are constants), then xticks do appear on each subplot.  Is this a
bug or am I missing something?

I am using matplotlib 1.1.0svn.

Many thanks, Evan


import numpy as np
import datetime as dt
import matplotlib.dates as dates
import matplotlib.pyplot as plt

months    = dates.MonthLocator(range(1,13), bymonthday=1, interval=1)
monthsFmt = dates.DateFormatter("%b %Y")
deltad   = 2
delta    = dt.timedelta(days=deltad)


plt.close('all')
fig1 = plt.figure(1)
for i in range(4):
    date_str = dt.date(i+2,11,1) ###
    date_end = dt.date(i+3,3,1) ###
    date_range = dates.drange(date_str,date_end,delta) ###
    ax = fig1.add_subplot(2,2,i+1)
    ax.plot_date(date_range,np.sin(date_range))
    ax.xaxis.set_major_locator(months)
    ax.xaxis.set_major_formatter(monthsFmt)

plt.show()

Hello,
   I have written a program which plots some data and then performs certain actions when the "down arrow" key is pressed.  The problem is that the "down arrow" key is also used to move the focus to the pylab tool bar at the bottom of the window.  It seems to move the focus to the tool bar before it gets to my key press call back function which handles all key strokes, which implies that I cannot do anything to stop it from performing the default behavior from my key press function.  I was curious if anyone knew of a way to disable the default short cuts in pylab so that the down arrow will not switch focus to the new window.  If someone knows of a way to override the default behavior, that would also suffice.

My backend is GTKAgg.

Regards,
Neko