matplotlib-users Mailing List for matplotlib (Page 4)

On Tuesday 26 July 2005 01:11 pm, Mark Bakker wrote:
> I have the same experience that eps files seem to be much larger than
> you expect, or than produced by other programs for similar plots.
> Is it maybe because fonts are embedded in the eps file?
> Anybody know?
It is because the fonts are embedded in the eps file.
-- 
Darren

Hi John,
 Thanks again for the quick responce. Sorry about not doing the 
simple test earlier. I installed the latest version this time
and used the script you suggested (.py file is attached). Here's the output:
C:\proj\compclust\win32\compclustshell>C:\Python23\python.exe 
matplotlibtest.py
--verbose-helpful
matplotlib data path C:\Python23\share\matplotlib
$HOME=C:\Documents and Settings\King
CONFIGDIR=C:\Documents and Settings\King\.matplotlib
loaded rc file C:\Python23\share\matplotlib\matplotlibrc
matplotlib version 0.83.1
verbose.level helpful
interactive is False
platform is win32
numerix Numeric 23.8
font search path ['C:\\Python23\\share\\matplotlib']
Assertion failed: ob_refcnt == 0, file CXX\cxx_extensions.cxx, line 1031
This application has requested the Runtime to terminate it in an unusual 
way.
Please contact the application's support team for more information.
-Brandon King
P.S. Thank you for the information about the documented API changes! =o)
John Hunter wrote:
>>>>>>"Brandon" == Brandon King <ki...@ca...> writes:
>>>>>> 
>>>>>>
>
> Brandon> Hi John, Thanks for the quick reply. In this case we are
> Brandon> using windows, to make a windows build of our code. I
> Brandon> removed site-packages/matplotlib and re-installed it. I
> Brandon> had to install version 0.80, because an API change in
> Brandon> either .81 or .82 broke some of our code and we haven't
> Brandon> had a chance to fix that. I ran our script as you
> Brandon> said... here's the output with the same error:
>
>You can still install 0.83 and test with that (later you can revert to
>the older version if need be). This will provide helpful diagnostic
>information. So once again, please remove site-packages/matplotlib
>and install the latest and test with a minimal script, eg
>
> import pylab
> pylab.plot([1,2,3])
> pylab.show()
>
>with the verbose-helpful flags.
>
>Note also you can see http://matplotlib.sf.net/API_CHANGES for the
>migration path from 0.80 to 0.83. It's likely as simple as a search
>and replace from set to setp, or something like that. The API is
>fairly stable and all changes are documented there.
>
>JDH
>
>
> 
>

>>>>> "Brandon" == Brandon King <ki...@ca...> writes:
 Brandon> Hi John, Thanks for the quick reply. In this case we are
 Brandon> using windows, to make a windows build of our code. I
 Brandon> removed site-packages/matplotlib and re-installed it. I
 Brandon> had to install version 0.80, because an API change in
 Brandon> either .81 or .82 broke some of our code and we haven't
 Brandon> had a chance to fix that. I ran our script as you
 Brandon> said... here's the output with the same error:
You can still install 0.83 and test with that (later you can revert to
the older version if need be). This will provide helpful diagnostic
information. So once again, please remove site-packages/matplotlib
and install the latest and test with a minimal script, eg
 import pylab
 pylab.plot([1,2,3])
 pylab.show()
with the verbose-helpful flags.
Note also you can see http://matplotlib.sf.net/API_CHANGES for the
migration path from 0.80 to 0.83. It's likely as simple as a search
and replace from set to setp, or something like that. The API is
fairly stable and all changes are documented there.
JDH

Hi John,
 Thanks for the quick reply. In this case we are using windows, to 
make a windows build of our code.
I removed site-packages/matplotlib and re-installed it. I had to install 
version 0.80, because an API change
in either .81 or .82 broke some of our code and we haven't had a chance 
to fix that.
 I ran our script as you said... here's the output with the same error:
C:\>C:\Python23\python.exe compclustweb-local.py --verbose-helpful
matplotlib data path C:\Python23\share\matplotlib
loaded rc file C:\Python23\share\matplotlib\.matplotlibrc
matplotlib version 0.80
verbose.level helpful
interactive is False
platform is win32
numerix Numeric 23.8
font search path ['C:\\Python23\\share\\matplotlib']
Assertion failed: ob_refcnt == 0, file CXX\cxx_extensions.cxx, line 1031
This application has requested the Runtime to terminate it in an unusual 
way.
Please contact the application's support team for more information.
Most of our code (all python code) is open source, so if you want to 
look at it you can.
The only problem is that do to the powers that be, some of c code is 
only available in binary forms
(were working on open sourcing that as well). Let me know if your 
interested.
Thank you for your help!
-Brandon King
John Hunter wrote:
>>>>>>"Brandon" == Brandon King <ki...@ca...> writes:
>>>>>> 
>>>>>>
>
> Brandon> Hi All, I ran into the following error:
>
> Brandon> Assertion failed: ob_refcnt == 0, file
> Brandon> CXX\cxx_extensions.cxx, line 1031
>
>I assume you are using win32.
>
>Please remove site-packages/matplotlib and reinstall the latest
>version. Then run your test script with
>
> > python myscript.py --verbose-helpful
>
>and if the error persists, post any output.
>
>Thanks,
>JDH
>
>
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>
> 
>

>>>>> "Brandon" == Brandon King <ki...@ca...> writes:
 Brandon> Hi All, I ran into the following error:
 Brandon> Assertion failed: ob_refcnt == 0, file
 Brandon> CXX\cxx_extensions.cxx, line 1031
I assume you are using win32.
Please remove site-packages/matplotlib and reinstall the latest
version. Then run your test script with
 > python myscript.py --verbose-helpful
and if the error persists, post any output.
Thanks,
JDH

Hi All,
 I ran into the following error:
Assertion failed: ob_refcnt == 0, file CXX\cxx_extensions.cxx, line 1031
I searched google and found the e-mail post from 2004年06月23日 which I've included
at the bottom of this e-mail. I was wondering if anyone has figured out the 
problem? I'm guessing this is still likely to be a bug related to matplotlib, 
but I don't know for sure.
What I do know is that why I try to import matplotlib directly into python,
I don't get the error (see code below).
 > >>> import matplotlib
 > >>> matplotlib.use("TkAgg")
 > >>> from matplotlib.pylab import *
But when we run our program which uses matplotlib, we get that error. I'll try to debug
our program and figure out where it seems to be crashing. If it's in matplotlib code, 
I'll dig in deeper to try to figure out where. I'll post again when I have more information.
I mainly wanted to give everyone a heads up and also see if anyone can give me some pointers.
-Brandon King
On Wed, 2004年06月23日 at 12:42, Gregory Lielens wrote:
 > Hello All,
 > I just tried to install matplotlib on a WinXP computer, after a
 > successfull install on Linux.
 > The problem I encounter is the following (transcript of an
 > interractive session): 
 > 
 > ---
 > C:\Python23>python
 > Python 2.3.4 (#53, May 25 2004, 21:17:02) [MSC v.1200 32 bit (Intel)]
 > on win32
 > Type "help", "copyright", "credits" or "license" for more information.
 > >>> import matplotlib
 > >>> matplotlib.use("TkAgg")
 > >>> from matplotlib.matlab import *
 > Assertion failed: ob_refcnt == 0, file CXX/cxx_extensions.cxx, line
 > 1031
 > 
 > This application has requested the Runtime to terminate it in an
 > unusual way.
 > Please contact the application"s support team for more information.
 > 
 > C:\Python23>
 > 
 > ---
 > 
 > This work on Linux, and I can not find any hint in the doc to a
 > backend/python interpreter incompatibility explaining this error.
 > 
 > I use numarray version 0.9 (win installer), python 2.3.4 (as shown in
 > the session transcript), and matplotlib 0.54.2, last windows installer
 > (the 2004年06月08日 21:54:42 build which I think correct some problems
 > with numarray)
 > 
 > Now I am wondering if I do something I shouldn"t, if my system or
 > installation is responsible, or if it is a bug in this particular
 > matplotlib distribution...Any idea? 

I have the same experience that eps files seem to be much larger than
you expect, or than produced by other programs for similar plots.
Is it maybe because fonts are embedded in the eps file?
Anybody know?
Thanks, Mark

>>>>> "Christopher" == Christopher Hart <chr...@gm...> writes:
 Christopher> Effectively, I have a situation where I have multiple
 Christopher> "traces" that I would like to display. Each trace
 Christopher> requires a separate subplot with a different Y-axis,
 Christopher> but all subplots should share the exact same X-axis.
 Christopher> I'd like to be able to interactively explore these
 Christopher> plots without fear of the subplots becoming
 Christopher> out-of-sync.
Use the sharex or sharey attribute of the Axes
 ax1 = subplot(211)
 ax1.plot(something)
 ax2 = subplot(212, sharex=ax1)
 ax2.plot(something, else)
See examples/shared_axis_demo.py for a complete example. Now when you
pan or zoom on either subplot, the two x axes remain in sync.
Neat stuff! Thanks to Baptiste Carvello for providing this feature.
JDH

Hi,
I was wondering if there is an "easy" way of linking the x-axis (or
y-axis for that matter) of two subplots. Using the "classic" toolbar
you can select to have pan and zoom events effect all or a specific
subset of axis. Can you do the same using the "toolbar2" mode? Is
there a function to also provide this functionality programmatically,
so if I zoom or pan one subplot, the other subplots follow suite.
Effectively, I have a situation where I have multiple "traces" that I
would like to display. Each trace requires a separate subplot with a
different Y-axis, but all subplots should share the exact same X-axis.
 I'd like to be able to interactively explore these plots without
fear of the subplots becoming out-of-sync.
Thanks,
Chris

N. Volbers wrote:
> 
>> Hmmm now that you mention antialiasing ... I turned it off in my 
>> .matplotlibrc but my plots (GTKAgg on Linux) are still antialiased. I 
>> had the same problem on Win (TkAgg) but didn't bother too much. I 
>> remember that there was a discussion before about this. I'm using mpl 
>> 0.81. Would upgrading fix this issue?
> 
> 
> 
> I tested the python script on my mpl, version 0.83.1 with no custom 
> matplotlibrc. To my surprise, I got the result you were talking about. 
> Then I opened the resulting eps with gv on linux. There is an option 
> "antialias", which when you turn it on, will cause this color mixing.
> 
> To demonstrate this, I wrote a little gnuplot script that produces a 
> similar output. If you look at the attached file with gv and toggle 
> antialiasing, you will notice the same effect as with mpl.
Yes I can varify that (on Win) with gsview (where turning off AA is done 
by setting Media > Display Settings > 'Text Alpha' and 'Graphics Alpha' 
to 1 bit). OK so it really seems to be no mpl issue. Just like Jhon 
mentioned :)
But one problem remains: I'm not able to turn off AA in .matplotlibrc
If anyone could point me in the right direction (upgrading, other 
backend?) ....
> 
> On a side note, when comparing these two graphs I noticed that the 
> gnuplot generated eps is only 15 K while the mpl generated eps has a 
> size of 300 K. Why is this so?
> 
I guess the dpi setting. But playing around with different dpi settings
	figure(dpi=<number>); plot(...); savefig(...)
or
	plot(...); savefig(...,dpi=<number>)
_always_ produces a .eps of 365 kb.
> Regards,
> 
> Niklas.
> 
cheers,
steve
-- 
Women are like cell phones. They like to be held and talked to, but push 
the wrong button, and you'll be disconnected.

> Hmmm now that you mention antialiasing ... I turned it off in my 
> .matplotlibrc but my plots (GTKAgg on Linux) are still antialiased. I 
> had the same problem on Win (TkAgg) but didn't bother too much. I 
> remember that there was a discussion before about this. I'm using mpl 
> 0.81. Would upgrading fix this issue?
I tested the python script on my mpl, version 0.83.1 with no custom 
matplotlibrc. To my surprise, I got the result you were talking about. 
Then I opened the resulting eps with gv on linux. There is an option 
"antialias", which when you turn it on, will cause this color mixing.
To demonstrate this, I wrote a little gnuplot script that produces a 
similar output. If you look at the attached file with gv and toggle 
antialiasing, you will notice the same effect as with mpl.
On a side note, when comparing these two graphs I noticed that the 
gnuplot generated eps is only 15 K while the mpl generated eps has a 
size of 300 K. Why is this so?
Regards,
Niklas.

>>>>> "Malte" == Malte Marquarding <Mal...@cs...> writes:
 Malte> Ditto here. Seems to have been introduced somewhere from
 Malte> version > 0.80.
 Malte> version 0.8 works for me. version 0.82 doesn't.
This was a bug introduce in 0.82, and it was fixed in 0.83.
Thanks,
JDH

Ditto here.
Seems to have been introduced somewhere from version > 0.80.
version 0.8 works for me. version 0.82 doesn't.
Cheers,
Malte.

Hi Philippe,
phi...@ho... wrote:
> fig = Figure()
> canvas = FigureCanvas(fig)
> ax = fig.add_subplot(111)
Here's the problem. The first two numbers of the argument specify the number of 
rows/cols and all calls of add_subplot of a figure must be euqal in these 
values. So the two plots should be created like this:
p1 = fig.add_subplot(211)
p2 = fig.add_subplot(212)
Regards, Christian

In case you didn't notice the licence change of the Bakoma Fonts:
The fonts are now freely distributable even for commercial usage 
since 15-Jun-2005
Regards
Carl Kleffner
See:
ftp://tug.ctan.org/pub/tex-archive/fonts/cm/ps-type1/bakoma.zip
http://www.ctan.org/tex-archive/fonts/cm/ps-type1/bakoma/LICENCE
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Hi,
I have a problem using subplot:
if I do:
subplot(2,1,1)
plot([0,1],[0,1])
subplot(2,1,2)
plot([0,1],[0,0.8])
then the first plot is ok, but the second one never shows up (everything 
keeps being posted in the first subplot).
It only works if I am removing the commas :
subplot(211)
plot([0,1],[0,1])
subplot(212)
plot([0,1],[0,0.8])
but of course then I cannot use more than 10 Numplots.... and many of my 
scripts fail...
Any hint of what may go wrong there?
Thanks!!
Eric
-- 
===============================================================
Observatoire de Lyon ems...@ob...
9 av. Charles-Andre tel: +33 4 78 86 83 84
69561 Saint-Genis Laval Cedex fax: +33 4 78 86 83 86
France http://www-obs.univ-lyon1.fr/eric.emsellem
===============================================================

Hi list,
I need to realize with matplotlib OO same figure as in the tutorial: 
Working with multiple figure and axe.
The problem is the two subplot are overlaping on the middle of the figure.
There is no margin between the first subplot and the second.
And the vertical axe of the second subplot is overlaping the vertical 
axe of the first subplot.
How can i solve out this problem?
Thanks a lot,
Philippe Collet
Here is my sample code.
#!/usr/bin/env python
"""
A pure OO (look Ma, no pylab!) example using the agg backend
"""
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure
 
fig = Figure()
canvas = FigureCanvas(fig)
ax = fig.add_subplot(111)
ax.plot([1,2,3])
ax.set_title("hi mom")
ax.grid(True)
ax.set_xlabel("time")
ax.set_ylabel("volts")
bx = fig.add_subplot(211)
ax.plot([3,4,5])
canvas.print_figure("test2")

On 12 Jul 2005, at 19:27, John Hunter wrote:
>>>>>> "Brice" == Brice Thurin <B.P...@ci...> writes:
>
> Brice> Dear All, I am new to matplotlib and I was wondering if
> Brice> there is any functions like imcrop in matlab which allow to
> Brice> interactively select the zone of the image.
>
> I do not currently have matlab installed on my system. Could you
> describe what imcrop does. Not knowing, I'll venture and answer
When the function is called, it displays the original image. Then, the 
user can select a box with a mouse. As a result the function return the 
top left corner coordinate of the box and the size of the box.
>
> 1) you can use the zoom-to-rectangle feature on the toolbar to zoom
> to the rectangle of interest. Equivalently, you can set the axis
> xlim and ylim to view only part of the rectangle
Once I have zoomed to the area of interest, how do I recover the 
information of my box ( dimensions, coordinates). Is there a way to get 
these information and then use them to slice the array to extract the 
region of interest.
>
> 2) you can extract the region of interest from you numerix array
> using array slicing before passing it to matplotlib for plotting.
>
> JDH
>
>
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Brice

Mark Bakker wrote:
> In several of the matplotlib examples, I encounter statements using
> the built-in Python zip function. The really cool use is shown below.
> 
>>>>a = [(0,0),(1,2),(4,3)]
>>>>zip(*a)
> 
> [(0, 1, 4), (0, 2, 3)]
> 
> Now this use of '*a' as argument does not seem to be documented anywhere.
> How does it work? Why do you need the * ? Probably really simple, I
> just don't understand.
http://docs.python.org/tut/node6.html#SECTION006740000000000000000
-- 
Robert Kern
rk...@uc...
"In the fields of hell where the grass grows high
 Are the graves of dreams allowed to die."
 -- Richard Harter

In several of the matplotlib examples, I encounter statements using
the built-in Python zip function. The really cool use is shown below.
>>> a =3D [(0,0),(1,2),(4,3)]
>>> zip(*a)
[(0, 1, 4), (0, 2, 3)]
Now this use of '*a' as argument does not seem to be documented anywhere.
How does it work? Why do you need the * ? Probably really simple, I
just don't understand.
Thanks for any help,
Mark

Hi
Just to be clear at this point. I get this mixing issue both on Linux 
(GTKAgg, mpl 0.81) and Win (TkAgg, mpl 0.82) in the .eps outputs as well 
as in the interactive plots.
cheers,
steve
Steve Schmerler wrote:
> Hi
> 
> Hmmm now that you mention antialiasing ... I turned it off in my 
> .matplotlibrc but my plots (GTKAgg on Linux) are still antialiased. I 
> had the same problem on Win (TkAgg) but didn't bother too much. I 
> remember that there was a discussion before about this. I'm using mpl 
> 0.81. Would upgrading fix this issue?
> 
> cheers,
> steve
> 
> Robert Kern wrote:
> 
>> Steve Schmerler wrote:
>>
>>> Hi
>>>
>>> Well this is kinda strange. I checked with gsview (on Win) and ggv and
>>> gv on Linux. The 'mixed' points (4 and 5) _are_ purple/dark red while
>>> the others are blue and (light)red.
>>
>>
>>
>> I blame antialiasing. Using Preview.app on OS X, when zoomed out, yes, 
>> I can see that the middle points appear to be somewhat darker than the 
>> "pure" red ones. Zooming in, however, I see little difference except 
>> for a bit of fuzz. Using "DigitalColor Meter.app", I can verify that 
>> the color of the middle crosses is indeed pure red with some purplish 
>> fuzz at the edges. When zoomed out enough, all of the pixels are 
>> antialiased fuzz and so it mixes both the top color and the bottom.
>>
>> IOW, it's an issue with how the display program handles antialiasing 
>> of overlaid colors, not the output generated by matplotlib.
>>
> 
> 
> -------------------------------------------------------
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> 
> 
-- 
Women are like cell phones. They like to be held and talked to, but push 
the wrong button, and you'll be disconnected.

Hi
Hmmm now that you mention antialiasing ... I turned it off in my 
.matplotlibrc but my plots (GTKAgg on Linux) are still antialiased. I 
had the same problem on Win (TkAgg) but didn't bother too much. I 
remember that there was a discussion before about this. I'm using mpl 
0.81. Would upgrading fix this issue?
cheers,
steve
Robert Kern wrote:
> Steve Schmerler wrote:
> 
>> Hi
>>
>> Well this is kinda strange. I checked with gsview (on Win) and ggv and
>> gv on Linux. The 'mixed' points (4 and 5) _are_ purple/dark red while
>> the others are blue and (light)red.
> 
> 
> I blame antialiasing. Using Preview.app on OS X, when zoomed out, yes, I 
> can see that the middle points appear to be somewhat darker than the 
> "pure" red ones. Zooming in, however, I see little difference except for 
> a bit of fuzz. Using "DigitalColor Meter.app", I can verify that the 
> color of the middle crosses is indeed pure red with some purplish fuzz 
> at the edges. When zoomed out enough, all of the pixels are antialiased 
> fuzz and so it mixes both the top color and the bottom.
> 
> IOW, it's an issue with how the display program handles antialiasing of 
> overlaid colors, not the output generated by matplotlib.
> 

Steve Schmerler wrote:
> Hi
> 
> Well this is kinda strange. I checked with gsview (on Win) and ggv and
> gv on Linux. The 'mixed' points (4 and 5) _are_ purple/dark red while
> the others are blue and (light)red.
I blame antialiasing. Using Preview.app on OS X, when zoomed out, yes, I 
can see that the middle points appear to be somewhat darker than the 
"pure" red ones. Zooming in, however, I see little difference except for 
a bit of fuzz. Using "DigitalColor Meter.app", I can verify that the 
color of the middle crosses is indeed pure red with some purplish fuzz 
at the edges. When zoomed out enough, all of the pixels are antialiased 
fuzz and so it mixes both the top color and the bottom.
IOW, it's an issue with how the display program handles antialiasing of 
overlaid colors, not the output generated by matplotlib.
-- 
Robert Kern
rk...@uc...
"In the fields of hell where the grass grows high
 Are the graves of dreams allowed to die."
 -- Richard Harter

Hi
Well this is kinda strange. I checked with gsview (on Win) and ggv and
gv on Linux. The 'mixed' points (4 and 5) _are_ purple/dark red while
the others are blue and (light)red.
cheers,
steve
N. Volbers wrote:
> Steve Schmerler schrieb:
> 
>> Hi
>>
>> Here the test. As you can see the points 1,2,3 are red, 4 and 5 are 
>> purple and 6 and 7 are red.
>>
>>
> 
> Hello Steve,
> 
> I used ghostview (gv) on Linux to display the .eps and it looks 
> perfectly fine -- only blue and red crosses. Might this be a display 
> problem of your eps viewer?
> 
> Best regards,
> 
> Niklas.
> 
> 

Steve Schmerler schrieb:
> Hi
>
> Here the test. As you can see the points 1,2,3 are red, 4 and 5 are 
> purple and 6 and 7 are red.
>
>
Hello Steve,
I used ghostview (gv) on Linux to display the .eps and it looks 
perfectly fine -- only blue and red crosses. Might this be a display 
problem of your eps viewer?
Best regards,
Niklas.