matplotlib-users Mailing List for matplotlib

On 8/6/2013 3:31 PM, Eric Firing [via matplotlib] wrote:
> Before the *first* import of pyplot, you need to have:
>
> import matplotlib
> matplotlib.use("agg")
>
> or specify any other non-interactive backend. Alternatively, you can
> specify the backend in a matplotlibrc file.
>
> This assumes you don't actually need an interactive backend. If you do
> need it, then I suspect you will need to change the strategy you are
> using in your program, ideally eliminating the input thread. You might
> use a gtk idle event callback to handle the user input, for example.
> The problem here is that python threads and gui toolkits tend not to mix
> well.
>
> I suspect that raw_input is using the PyOS_InputHook, which is also
> being used by gtk, so you are violating the prohibition against
> gui-related activities being in more than one thread.
>
> Eric
Thanks Eric, that did work for me. I don't necessarily need an 
interactive backend for this, but it could be nice to get it to work. I 
just tried switching raw_input to sys.stdin.readline, and that seems to 
work even with the interactive backend.
John
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On 2013年08月06日 10:08 AM, John McFarland wrote:
> I am trying to write some code that uses an input thread to check for user
> input while another thread is running some calculations (see example below).
> What I have noticed is that just including an import of pyplot (regardless
> of whether it is used by the code or not) causes the call to raw_input in
> the input thread to block the main thread. It works fine when I don't
> import pyplot. Importing pyplot is a consequence of other libraries that I
> need to use in the code, so I would like to find a way to make this work.
>
> I have python 2.7.3, matplotlib 1.2.0, and am currently using the GTKAgg
> backend. Any help is much appreciated.
>
> Here is the example code:
>
> import time
> import threading
Before the *first* import of pyplot, you need to have:
import matplotlib
matplotlib.use("agg")
or specify any other non-interactive backend. Alternatively, you can 
specify the backend in a matplotlibrc file.
This assumes you don't actually need an interactive backend. If you do 
need it, then I suspect you will need to change the strategy you are 
using in your program, ideally eliminating the input thread. You might 
use a gtk idle event callback to handle the user input, for example. 
The problem here is that python threads and gui toolkits tend not to mix 
well.
I suspect that raw_input is using the PyOS_InputHook, which is also 
being used by gtk, so you are violating the prohibition against 
gui-related activities being in more than one thread.
Eric
> import matplotlib.pyplot # Works fine if this is commented out
>
> def input_thread():
> raw_input('Press a key:')
> print "Input data received"
>
> thread = threading.Thread(target=input_thread)
> thread.start()
> time.sleep(.01)
> print
>
> # Main thread (e.g. a calculation that can take some time)
> for i in xrange(10):
> print i
> time.sleep(.5)
>
>
>
> --
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>
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I am trying to write some code that uses an input thread to check for user
input while another thread is running some calculations (see example below). 
What I have noticed is that just including an import of pyplot (regardless
of whether it is used by the code or not) causes the call to raw_input in
the input thread to block the main thread. It works fine when I don't
import pyplot. Importing pyplot is a consequence of other libraries that I
need to use in the code, so I would like to find a way to make this work.
I have python 2.7.3, matplotlib 1.2.0, and am currently using the GTKAgg
backend. Any help is much appreciated.
Here is the example code:
import time
import threading
import matplotlib.pyplot # Works fine if this is commented out
def input_thread():
 raw_input('Press a key:')
 print "Input data received"
thread = threading.Thread(target=input_thread)
thread.start()
time.sleep(.01)
print
# Main thread (e.g. a calculation that can take some time)
for i in xrange(10):
 print i
 time.sleep(.5)
--
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Good afternoon.
I have a list of 20000 points with coordinates x,y and category in three
lists.
x_coordinate=[3000,3100,3234,.....]
x_coordinate=[15678,16768,14590,.....]
category=[1,3,5,....]
The categories values are between [1 and 10]
I need to make a 2D animation of this in matplotlib, starting showing the
first element and finalizing showing all elements in the graph, showing the
color points cording to the category.
I tried modifying the example of animatedScatter, but I can see that the
number of points in the scatter plot is constant from the beginning. is
there any way to make the program, for example show in the first time step
one element one point in the second time step, two points, etc? and also
one important thing is could cop with a big list of points with the minimum
lag of time in the animation?
Many thanks for your help
German

Hey, everyone! 
Just thought I'd post this link to a new piece of code I put together for making a Pareto chart. I originally created it for my own use, but I feel like it's time to share. It can be found at: http://github.com/tisimst/paretochart[1]. It's just a single .py file, so just download it and put it in a directory that python can find (like the "Scripts" directory). 
It is designed to be very flexible as seen in this graphic: 
--------
[1] http://github.com/tisimst/paretochart

Hi Michael et al,
Attached...
A
p.s. I've posted this via the gmane newsgroup, but a version of was sent 
to the ML and is awaiting moderator approval...
On 02/08/2013 15:32, Michael Droettboom wrote:
> Can you provide the output of the build?
>
> On 08/02/2013 06:53 AM, Andrew Jaffe wrote:
>> Hi,
>>
>>
>> On 01/08/2013 19:06, Michael Droettboom wrote:
>>> On behalf of a veritable army of super coders, I'm pleased to announce
>>> the release of matplotlib 1.3.0.
>> Two issues on OSX 10.8.4. I had been previously using the dmg installer.
>> Lacking that, I tried easy-install and pip install, both of which gave
>> me the following problems:
>>
>> - I needed to set CC=clang
>> - When attempting to load matplotlib, I got the following error:
>>
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/font_manager.py
>> in <module>()
>> 51 import matplotlib
>> 52 from matplotlib import afm
>> ---> 53 from matplotlib import ft2font
>> 54 from matplotlib import rcParams, get_cachedir
>> 55 from matplotlib.cbook import is_string_like
>>
>> ImportError:
>> dlopen(/Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so,
>> 2): Symbol not found: _FT_Attach_File
>> Referenced from:
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so
>> Expected in: flat namespace
>> in
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so
>>
>>
>> This is a freetype problem, probably an incompatible version somewhere.
>> Ideas?
>>
>> Andrew
>>
>>

Thanks, for the moment, it seems that removing the 'mpl_toolkits' from
packages makes it work.
Also, with the removal of dateutil from the binary, and installation of
dateutil from source pulling in six via easy_install/pip meant it also was
not found by py2exe. I got around this by using Christoph Gohlke's binary
installer of six. HTH someone else.
Regards,
RuiDC
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On 08/06/2013 08:39 AM, Rita wrote:
> Yes, I mean a self-built package.
>
> When linking I think setupext.py is using /usr/lib and /usr/local/lib 
> first, instead it should use PKG_CONFIG_PATH and then /usr/lib and 
> then /usr/local/lib. Basically, the ordering or linking matters. I 
> hope that helps. This isnt a big deal but just though I put out the 
> solution.
I don't think PKG_CONFIG_PATH is supposed to have anything to do with 
linking directories. PKG_CONFIG_PATH tells pkg-config where to look for 
.pc files, which *in turn*, by querying pkg-config, may contain 
information about link directories. So when you say it should prepend 
PKG_CONFIG_PATH, do you mean it should prepend "what pkg-config 
returns"? I think that probably what it should be doing, and it's a 
bonafide bug that it is not.
Any chance you can share the linker command line that you think is 
wrong, and how it needs to be re-ordered?
Mike
>
>
> On Mon, Aug 5, 2013 at 10:29 AM, Michael Droettboom <md...@st... 
> <mailto:md...@st...>> wrote:
>
> On 08/03/2013 07:50 AM, Rita wrote:
>> Same problem in Linux also. Here is what I did to fix it: Remove
>> the freetype/fontconfig rpm from my local install (yum remove)
>> and then place the proper PKG_CONFIG_PATH to point to my remote
>> freetype/fontconfig.
>
> By remote, you mean self-built, rather than from a package?
>
>
>> The problem is there is a bug with setupext.py. We ought to
>> prepend PKG_CONFIG_PATH in the gcc compile statement. I hope
>> this helps.
>
> Can you elaborate? The setupext.py just calls whatever pkg-config
> is first on the PATH, which should then in turn obey
> PKG_CONFIG_PATH. If the user needs a custom PKG_CONFIG_PATH, it
> is generally the resposibility of the user to set it correctly --
> and matplotlib's build system should (and does) use it. Or maybe
> I'm just misunderstanding what you're suggesting.
>
> Cheers,
> Mike
>
>
>>
>>
>>
>>
>>
>> On Fri, Aug 2, 2013 at 6:53 AM, Andrew Jaffe <a.h...@gm...
>> <mailto:a.h...@gm...>> wrote:
>>
>> Hi,
>>
>>
>> On 01/08/2013 19:06, Michael Droettboom wrote:
>> > On behalf of a veritable army of super coders, I'm pleased
>> to announce
>> > the release of matplotlib 1.3.0.
>>
>> Two issues on OSX 10.8.4. I had been previously using the dmg
>> installer.
>> Lacking that, I tried easy-install and pip install, both of
>> which gave
>> me the following problems:
>>
>> - I needed to set CC=clang
>> - When attempting to load matplotlib, I got the following
>> error:
>>
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/font_manager.py
>> in <module>()
>> 51 import matplotlib
>> 52 from matplotlib import afm
>> ---> 53 from matplotlib import ft2font
>> 54 from matplotlib import rcParams, get_cachedir
>> 55 from matplotlib.cbook import is_string_like
>>
>> ImportError:
>> dlopen(/Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so,
>> 2): Symbol not found: _FT_Attach_File
>> Referenced from:
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so
>> Expected in: flat namespace
>> in
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so
>>
>>
>> This is a freetype problem, probably an incompatible version
>> somewhere.
>> Ideas?
>>
>> Andrew
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Get your SQL database under version control now!
>> Version control is standard for application code, but
>> databases havent
>> caught up. So what steps can you take to put your SQL
>> databases under
>> version control? Why should you start doing it? Read more to
>> find out.
>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> <mailto:Mat...@li...>
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>>
>>
>> -- 
>> --- Get your facts first, then you can distort them as you please.--
>>
>>
>> ------------------------------------------------------------------------------
>> Get your SQL database under version control now!
>> Version control is standard for application code, but databases havent
>> caught up. So what steps can you take to put your SQL databases under
>> version control? Why should you start doing it? Read more to find out.
>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>>
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li... <mailto:Mat...@li...>
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> <mailto:Mat...@li...>
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
>
> -- 
> --- Get your facts first, then you can distort them as you please.--

I have little to no experience with py2exe, so I don't know how much I 
can help there.
However, between 1.2.1 and 1.3.0, mpl_toolkits was changed to a 
"namespace" package, which allowed basemap to install into it despite it 
coming from matplotlib (and being installed with setuptools). I don't 
know if that has any bearing on py2exe.
Mike
On 08/06/2013 07:19 AM, ruidc wrote:
> we have some code that was working fine with matplotlib 1.2.1 using:
>
> from mpl_toolkits.axes_grid import make_axes_locatable, axes_size
>
> now trying to freeze with py2exe (both 0.6.9 and Christoph Gohlke's
> 0.6.10dev)
> results in ImportError: No module named mpl_toolkits
>
> when preparing the actual executable.
> running "from mpl_toolkits.axes_grid import make_axes_locatable, axes_size"
> itself in python works fine.
>
> I've built a machine afresh and am getting this. Also, it seems to build
> fine on win amd64 - but as that is my main development machine, there may be
> some polution there
>
> options={'py2exe': {'packages' : ['matplotlib', 'mpl_toolkits', ...
>
> I've tried various different permutations of the above in includes with no
> success.
> Can anybody suggest why this is failing in 1.3.0 when it is working in 1.2.1
> ?
>
> Regards,
> RuiDC
>
>
>
> --
> View this message in context: http://matplotlib.1069221.n5.nabble.com/1-3-0-and-py2exe-regression-tp41723.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Yes, I mean a self-built package.
When linking I think setupext.py is using /usr/lib and /usr/local/lib
first, instead it should use PKG_CONFIG_PATH and then /usr/lib and then
/usr/local/lib. Basically, the ordering or linking matters. I hope that
helps. This isnt a big deal but just though I put out the solution.
On Mon, Aug 5, 2013 at 10:29 AM, Michael Droettboom <md...@st...> wrote:
> On 08/03/2013 07:50 AM, Rita wrote:
>
> Same problem in Linux also. Here is what I did to fix it: Remove the
> freetype/fontconfig rpm from my local install (yum remove) and then place
> the proper PKG_CONFIG_PATH to point to my remote freetype/fontconfig.
>
>
> By remote, you mean self-built, rather than from a package?
>
>
> The problem is there is a bug with setupext.py. We ought to prepend
> PKG_CONFIG_PATH in the gcc compile statement. I hope this helps.
>
>
> Can you elaborate? The setupext.py just calls whatever pkg-config is
> first on the PATH, which should then in turn obey PKG_CONFIG_PATH. If the
> user needs a custom PKG_CONFIG_PATH, it is generally the resposibility of
> the user to set it correctly -- and matplotlib's build system should (and
> does) use it. Or maybe I'm just misunderstanding what you're suggesting.
>
> Cheers,
> Mike
>
>
>
>
>
>
>
> On Fri, Aug 2, 2013 at 6:53 AM, Andrew Jaffe <a.h...@gm...> wrote:
>
>> Hi,
>>
>>
>> On 01/08/2013 19:06, Michael Droettboom wrote:
>> > On behalf of a veritable army of super coders, I'm pleased to announce
>> > the release of matplotlib 1.3.0.
>>
>> Two issues on OSX 10.8.4. I had been previously using the dmg installer.
>> Lacking that, I tried easy-install and pip install, both of which gave
>> me the following problems:
>>
>> - I needed to set CC=clang
>> - When attempting to load matplotlib, I got the following error:
>>
>>
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/font_manager.py
>> in <module>()
>> 51 import matplotlib
>> 52 from matplotlib import afm
>> ---> 53 from matplotlib import ft2font
>> 54 from matplotlib import rcParams, get_cachedir
>> 55 from matplotlib.cbook import is_string_like
>>
>> ImportError:
>>
>> dlopen(/Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so,
>> 2): Symbol not found: _FT_Attach_File
>> Referenced from:
>>
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so
>> Expected in: flat namespace
>> in
>>
>> /Volumes/Data/Users/jaffe/Library/Python/2.7/lib/python/site-packages/matplotlib/ft2font.so
>>
>>
>> This is a freetype problem, probably an incompatible version somewhere.
>> Ideas?
>>
>> Andrew
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Get your SQL database under version control now!
>> Version control is standard for application code, but databases havent
>> caught up. So what steps can you take to put your SQL databases under
>> version control? Why should you start doing it? Read more to find out.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
>
> --
> --- Get your facts first, then you can distort them as you please.--
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Matplotlib-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
-- 
--- Get your facts first, then you can distort them as you please.--

we have some code that was working fine with matplotlib 1.2.1 using:
from mpl_toolkits.axes_grid import make_axes_locatable, axes_size
now trying to freeze with py2exe (both 0.6.9 and Christoph Gohlke's
0.6.10dev)
results in ImportError: No module named mpl_toolkits
when preparing the actual executable.
running "from mpl_toolkits.axes_grid import make_axes_locatable, axes_size"
itself in python works fine.
I've built a machine afresh and am getting this. Also, it seems to build
fine on win amd64 - but as that is my main development machine, there may be
some polution there
options={'py2exe': {'packages' : ['matplotlib', 'mpl_toolkits', ...
I've tried various different permutations of the above in includes with no
success.
Can anybody suggest why this is failing in 1.3.0 when it is working in 1.2.1
?
Regards,
RuiDC
--
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Hi,
I am using mat 1.20 and basemap 1.0.5, I tried your code and don't have the
same issue.
Chao
On Tue, Aug 6, 2013 at 9:33 AM, vwf [via matplotlib] <
ml-...@n5...> wrote:
>
> Hello,
>
> This weekend I started using matplotlib and I think it is great.
> Beautiful graphs with very little effort.
>
> My data is geographical so I would like to draw on a map, North-Sea (UK
> - Netherlands). For this I installed the basemap on my Debian system
> (Stable/Wheezy). This has a strange problem. If I zoom out, all is
> there. If I start zooming in coastlines disappears. Is this my
> mistake, a problem in the packages in Debian, or something else?
>
> Thanks
>
> The resulting image on my system:
> http://img21.imageshack.us/img21/385/xoe7.png
>
> My system:
> Python 2.7.3 (default, Jan 2 2013, 16:53:07)
> [GCC 4.7.2] on linux2
> >>> import matplotlib
> >>> matplotlib.__version__
> '1.1.1rc2'
>
> My code:
>
> import numpy as np
> import matplotlib.pyplot as plt
> from mpl_toolkits.basemap import Basemap
>
> import matplotlib as mpl
> mpl.rcParams['font.size'] = 8.
> mpl.rcParams['font.family'] = 'Arial'
> mpl.rcParams['axes.labelsize'] = 5.
> mpl.rcParams['xtick.labelsize'] = 5.
> mpl.rcParams['ytick.labelsize'] = 5.
>
> #W-Europe
> x1 = -16.
> x2 = 30.
> y1 = 36.
> y2 = 62.
>
> m = Basemap(resolution='i',projection='merc',
> llcrnrlat=y1,urcrnrlat=y2,llcrnrlon=x1,urcrnrlon=x2,lat_ts=(x1+x2)/2)
> m.drawcountries(linewidth=0.5)
> m.drawcoastlines(linewidth=0.5)
> m.drawparallels(np.arange(y1,y2,2.),labels=[1,0,0,0],color='black',dashes=[1,0],labelstyle='+/-',linewidth=0.2)
>
> m.drawmeridians(np.arange(x1,x2,2.),labels=[0,0,0,1],color='black',dashes=[1,0],labelstyle='+/-',linewidth=0.2)
>
>
> plt.savefig('eur_101.png',dpi=100)
> plt.show()
>
>
> ------------------------------------------------------------------------------
>
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
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Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
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Hello,
This weekend I started using matplotlib and I think it is great.
Beautiful graphs with very little effort.
My data is geographical so I would like to draw on a map, North-Sea (UK
- Netherlands). For this I installed the basemap on my Debian system
(Stable/Wheezy). This has a strange problem. If I zoom out, all is
there. If I start zooming in coastlines disappears. Is this my
mistake, a problem in the packages in Debian, or something else?
Thanks
The resulting image on my system:
http://img21.imageshack.us/img21/385/xoe7.png
My system:
Python 2.7.3 (default, Jan 2 2013, 16:53:07) 
[GCC 4.7.2] on linux2
>>> import matplotlib
>>> matplotlib.__version__
'1.1.1rc2'
My code:
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap
import matplotlib as mpl
mpl.rcParams['font.size'] = 8.
mpl.rcParams['font.family'] = 'Arial'
mpl.rcParams['axes.labelsize'] = 5.
mpl.rcParams['xtick.labelsize'] = 5.
mpl.rcParams['ytick.labelsize'] = 5.
 
#W-Europe
x1 = -16.
x2 = 30.
y1 = 36.
y2 = 62.
 
m = Basemap(resolution='i',projection='merc', llcrnrlat=y1,urcrnrlat=y2,llcrnrlon=x1,urcrnrlon=x2,lat_ts=(x1+x2)/2)
m.drawcountries(linewidth=0.5)
m.drawcoastlines(linewidth=0.5)
m.drawparallels(np.arange(y1,y2,2.),labels=[1,0,0,0],color='black',dashes=[1,0],labelstyle='+/-',linewidth=0.2)
m.drawmeridians(np.arange(x1,x2,2.),labels=[0,0,0,1],color='black',dashes=[1,0],labelstyle='+/-',linewidth=0.2)
plt.savefig('eur_101.png',dpi=100)
plt.show()