matplotlib-users Mailing List for matplotlib

All: I am trying to build matplotlib 0.98.3 on a Red Hat Enterprise 5 
linux box. I have Tkinter support compiled into my 
/usr/local/bin/python installation (at least "import Tkinter" raises no 
exceptions). However, when I try to build matplotlib using 
"/usr/local/bin/python setup.py build", I get the output below. Any 
hints? Is this my fault, or a bug in setup.py?
Thanks,
Mike
============================================================================
BUILDING MATPLOTLIB
 matplotlib: 0.98.3
 python: 2.5.2 (r252:60911, Sep 15 2008, 16:18:30) [GCC
 4.1.2 20071124 (Red Hat 4.1.2-42)]
 platform: linux2
REQUIRED DEPENDENCIES
 numpy: 1.1.0
 freetype2: found, but unknown version (no pkg-config)
 * WARNING: Could not find 'freetype2' headers in any
 * of '/usr/local/include', '/usr/include', '.',
 * '/usr/local/include/freetype2',
 * '/usr/include/freetype2', './freetype2'.
OPTIONAL BACKEND DEPENDENCIES
 libpng: 1.2.10
Traceback (most recent call last):
 File "setup.py", line 125, in <module>
 if check_for_tk() or (options['build_tkagg'] is True):
 File "/home/mhearne/build/matplotlib-0.98.3/setupext.py", line 841, in 
check_for_tk
 explanation = add_tk_flags(module)
 File "/home/mhearne/build/matplotlib-0.98.3/setupext.py", line 1101, 
in add_tk_flags
 module.libraries.extend(['tk' + tk_ver, 'tcl' + tk_ver])
UnboundLocalError: local variable 'tk_ver' referenced before assignment
-- 
------------------------------------------------------
Michael Hearne
mh...@us...
(303) 273-8620
USGS National Earthquake Information Center
1711 Illinois St. Golden CO 80401
Senior Software Engineer
Synergetics, Inc.
------------------------------------------------------

The SciPy conference proceedings are finally available online:
http://conference.scipy.org/proceedings/SciPy2008 .
I hope you enjoy them. I find it great to have this set of excellent
articles talking about works done with, or for, Python in science. For
me, it is a reference to remember what was said at the conference. I hope
it can also be interesting for people who were not present at the
conference.
I apologize for being so slow at publishing them. In addition to the
round trip between authors and editors taking a while, I have been
travelling back home and spent way too much time last week finishing off
administrative duties in the US.
Gaël

On 9/22/2008 7:59 AM Jeff Whitaker apparently wrote:
> we can't do much if you 
> don't provide a self-contained script, that I can run, which reproduces 
> the problem.
Ideally, a *short* self-contained script.
Or as Simon Tatham puts it, "show me":
http://www.chiark.greenend.org.uk/~sgtatham/bugs.html
Alan Isaac

On Monday 22 September 2008 07:55:57 am John Hunter wrote:
> On Mon, Sep 22, 2008 at 5:19 AM, dmitrey <dmi...@uk...> wrote:
> > John Hunter wrote:
> >> On Sun, Sep 21, 2008 at 3:28 PM, dmitrey <dmi...@sc...>
> >> Could you be more precise about what you mean when you say it doesn't
> >> work? It works for me, in that the figure window that was created is
> >> raised, plotted into, and then destroyed. Please tell us what you
> >> expect to happen and what actually happens, as well as what backend
> >> and matplotlib version you are using/. Best is to put your code into
> >> a script and run it with --verbose-helpful and post the output here
> >> along with the other requested info.
> >
> > Thanks for the feedback, I found that the code works OK from terminal, it
> > just fails to close from Eric IDE (the figure continue to exist). Here's
> > --verbose-helpful output (while running from the IDE)
>
> [Please "reply to all" to respond on list so others can contribute to
> an participate in the discussion.]
>
> One problem is you have set your backend in your matplotlibrc ile to
> GTKAgg (this is the default) and Eric is a Qt editor. For starters,
> you will want to set the backend the qt4agg -- see
> http://matplotlib.sourceforge.net/doc/html/faq/installing_faq.html#backends
>
> Getting interactive python shells embedded in user interfaces to work
> with matplotlib is tricky because of GUI threading issues. ipython
> has tackled this for most major GUIs, and I think they have support
> for qt. Fernando and crew will be able to advise further.
Ipython does support the qt backends. I also use eric4, which works just fine 
with the qt4 backend.
Darren

De Pauw Antoine wrote:
> Jeff,
>
> I included here a figure where you'll see the border problem for imshow in
> my case
>
> http://img217.imageshack.us/img217/5240/testfigzp3.png
>
> The border wraps at -180 and 180 to form the white line
>
> PS: it is atmospheric ice and not SO2, I just omitted to change the title ^^
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
> 
Antoine: I hate to keep repeating myself - but we can't do much if you 
don't provide a self-contained script, that I can run, which reproduces 
the problem. My guess is that the line along the dateline, and the 
point at the South Pole are missing values (which griddata set to 
missing because they are outside the extent of the data) - but that's 
just a guess until I can reproduce it.
-Jeff
>
> -----Original Message-----
> From: Antoine De Pauw [mailto:and...@ul...] 
> Sent: jeudi 18 septembre 2008 17:23
> To: Jeff Whitaker; and...@ul...
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: re:Re: [Matplotlib-users] Information request
>
> Jeff,
>
> No the example doesn't show that line
>
> If I reduce the amount of data, the border will be on every side of the plot
>
> I'll show you an orthographic plot with no maskinf tomorrow and you will see
> the problem easily, it wraps in a white line along the 0° meridian and a
> white circle in the pole
>
> I think it's the imshow layer that is not totally transparent on the map
> background.. I tried every trick I could for example to put some zero-valued
> points on each corner to make imshow interpolate correctly the sides, but
> that doesn't make any difference
>
> 
>> De Pauw Antoine wrote:
>> 
>>> Jeff,
>>>
>>> Yes they disappear, and they fluctuate with the interpolation method used
>>>
>>> For example, nearest interpolation don't show the line
>>>
>>> Also, if I reduce the grid resolution, the line is thicker, and if I use
>>> 
> a
> 
>>> masked array to get rid of undesired values, the border shows really
>>> strongly
>>>
>>> Here's an example everyone will see:
>>>
>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>
>>> (everything except the clouds is noise)
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>> 
>>> 
>> Antoine: Sorry to seem dense, but I don't see anything wrong with that 
>> plot. I see a white border along the north and south pole, but I 
>> intrepret that to be missing values. However, my eyes are notoriously 
>> bad. I'd like to be to run a script that generates the artifacts 
>> myself, so I can zoom in and see the problem myself. Does the 
>> griddata_demo.py script show the same problem for you?
>>
>> -Jeff
>> 
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:js...@fa...] 
>>> Sent: mercredi 17 septembre 2008 19:05
>>> To: John Hunter
>>> Cc: De Pauw Antoine; Matplotlib Users
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> John Hunter wrote:
>>> 
>>> 
>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jd...@gm...> wrote:
>>>>
>>>> 
>>>> 
>>>> 
>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>> axes border. The black horizontal line is the top axes border, the
>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>> grid line. I don't know if this offers a clue, but if you look at a
>>>>> zoom in the upper right corner, the grey line seems to break up and
>>>>> curve down and to the right (corner.png)
>>>>> 
>>>>> 
>>>>> 
>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>> screenshot). The correct screenshot is attached
>>>> 
>>>>
>>>>
>>>> 
>>>> 
>>> John: OK, now I finally see it. Antoine: Do these artifacts 
>>> disappear if you comment out the imshow call?
>>>
>>> -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
>>
>>
>>
>> 
>
>
> 
-- 
Jeffrey S. Whitaker Phone : (303)497-6313
NOAA/OAR/CDC R/PSD1 FAX : (303)497-6449
325 Broadway Boulder, CO, USA 80305-3328

Jeff,
The code snippet has been provided, if you run it with the csv reading code
instead of my binary file reading code you'll see it works
I have added some points at each corner of the map (-180:90 180:90 -180:-90
180:-90) with zero values and the white gap persists
If you cannot help me, that's not a problem, I just cannot give you a better
explanation...
Empty data is something normal in my files, sometimes the satellite has gaps
on its measurements and empty zones on the map are normal
The only problem is that it surrounds all the plot with a grayish border or
shadow when I plot it (a mickey-shaped data plot with white zeroed values
would give a mickey-shaped grey border), and all I want to know is if it is
normal that imshow has such a border, and if it is possible that it comes
from the library
I'll keep searching till I have a solution
Is there another plotting method than imshow which also has interpolation?
Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB
-----Original Message-----
From: Jeff Whitaker [mailto:js...@fa...] 
Sent: lundi 22 septembre 2008 13:59
To: De Pauw Antoine
Cc: 'John Hunter'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request
De Pauw Antoine wrote:
> Jeff,
>
> I included here a figure where you'll see the border problem for imshow in
> my case
>
> http://img217.imageshack.us/img217/5240/testfigzp3.png
>
> The border wraps at -180 and 180 to form the white line
>
> PS: it is atmospheric ice and not SO2, I just omitted to change the title
^^
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
> 
Antoine: I hate to keep repeating myself - but we can't do much if you 
don't provide a self-contained script, that I can run, which reproduces 
the problem. My guess is that the line along the dateline, and the 
point at the South Pole are missing values (which griddata set to 
missing because they are outside the extent of the data) - but that's 
just a guess until I can reproduce it.
-Jeff
>
> -----Original Message-----
> From: Antoine De Pauw [mailto:and...@ul...] 
> Sent: jeudi 18 septembre 2008 17:23
> To: Jeff Whitaker; and...@ul...
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: re:Re: [Matplotlib-users] Information request
>
> Jeff,
>
> No the example doesn't show that line
>
> If I reduce the amount of data, the border will be on every side of the
plot
>
> I'll show you an orthographic plot with no maskinf tomorrow and you will
see
> the problem easily, it wraps in a white line along the 0° meridian and a
> white circle in the pole
>
> I think it's the imshow layer that is not totally transparent on the map
> background.. I tried every trick I could for example to put some
zero-valued
> points on each corner to make imshow interpolate correctly the sides, but
> that doesn't make any difference
>
> 
>> De Pauw Antoine wrote:
>> 
>>> Jeff,
>>>
>>> Yes they disappear, and they fluctuate with the interpolation method
used
>>>
>>> For example, nearest interpolation don't show the line
>>>
>>> Also, if I reduce the grid resolution, the line is thicker, and if I use
>>> 
> a
> 
>>> masked array to get rid of undesired values, the border shows really
>>> strongly
>>>
>>> Here's an example everyone will see:
>>>
>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>
>>> (everything except the clouds is noise)
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>> 
>>> 
>> Antoine: Sorry to seem dense, but I don't see anything wrong with that 
>> plot. I see a white border along the north and south pole, but I 
>> intrepret that to be missing values. However, my eyes are notoriously 
>> bad. I'd like to be to run a script that generates the artifacts 
>> myself, so I can zoom in and see the problem myself. Does the 
>> griddata_demo.py script show the same problem for you?
>>
>> -Jeff
>> 
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:js...@fa...] 
>>> Sent: mercredi 17 septembre 2008 19:05
>>> To: John Hunter
>>> Cc: De Pauw Antoine; Matplotlib Users
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> John Hunter wrote:
>>> 
>>> 
>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jd...@gm...>
wrote:
>>>>
>>>> 
>>>> 
>>>> 
>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>> axes border. The black horizontal line is the top axes border, the
>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>> grid line. I don't know if this offers a clue, but if you look at a
>>>>> zoom in the upper right corner, the grey line seems to break up and
>>>>> curve down and to the right (corner.png)
>>>>> 
>>>>> 
>>>>> 
>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>> screenshot). The correct screenshot is attached
>>>> 
>>>>
>>>>
>>>> 
>>>> 
>>> John: OK, now I finally see it. Antoine: Do these artifacts 
>>> disappear if you comment out the imshow call?
>>>
>>> -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
>>
>>
>>
>> 
>
>
> 
-- 
Jeffrey S. Whitaker Phone : (303)497-6313
NOAA/OAR/CDC R/PSD1 FAX : (303)497-6449
325 Broadway Boulder, CO, USA 80305-3328

On Mon, Sep 22, 2008 at 5:19 AM, dmitrey <dmi...@uk...> wrote:
> John Hunter wrote:
>>
>> On Sun, Sep 21, 2008 at 3:28 PM, dmitrey <dmi...@sc...>
>> Could you be more precise about what you mean when you say it doesn't
>> work? It works for me, in that the figure window that was created is
>> raised, plotted into, and then destroyed. Please tell us what you
>> expect to happen and what actually happens, as well as what backend
>> and matplotlib version you are using/. Best is to put your code into
>> a script and run it with --verbose-helpful and post the output here
>> along with the other requested info.
>>
>
> Thanks for the feedback, I found that the code works OK from terminal, it
> just fails to close from Eric IDE (the figure continue to exist). Here's
> --verbose-helpful output (while running from the IDE)
[Please "reply to all" to respond on list so others can contribute to
an participate in the discussion.]
One problem is you have set your backend in your matplotlibrc ile to
GTKAgg (this is the default) and Eric is a Qt editor. For starters,
you will want to set the backend the qt4agg -- see
http://matplotlib.sourceforge.net/doc/html/faq/installing_faq.html#backends
Getting interactive python shells embedded in user interfaces to work
with matplotlib is tricky because of GUI threading issues. ipython
has tackled this for most major GUIs, and I think they have support
for qt. Fernando and crew will be able to advise further.
JDH

Jeff,
I included here a figure where you'll see the border problem for imshow in
my case
http://img217.imageshack.us/img217/5240/testfigzp3.png
The border wraps at -180 and 180 to form the white line
PS: it is atmospheric ice and not SO2, I just omitted to change the title ^^
Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB
-----Original Message-----
From: Antoine De Pauw [mailto:and...@ul...] 
Sent: jeudi 18 septembre 2008 17:23
To: Jeff Whitaker; and...@ul...
Cc: 'John Hunter'; 'Matplotlib Users'
Subject: re:Re: [Matplotlib-users] Information request
Jeff,
No the example doesn't show that line
If I reduce the amount of data, the border will be on every side of the plot
I'll show you an orthographic plot with no maskinf tomorrow and you will see
the problem easily, it wraps in a white line along the 0° meridian and a
white circle in the pole
I think it's the imshow layer that is not totally transparent on the map
background.. I tried every trick I could for example to put some zero-valued
points on each corner to make imshow interpolate correctly the sides, but
that doesn't make any difference
>De Pauw Antoine wrote:
>> Jeff,
>>
>> Yes they disappear, and they fluctuate with the interpolation method used
>>
>> For example, nearest interpolation don't show the line
>>
>> Also, if I reduce the grid resolution, the line is thicker, and if I use
a
>> masked array to get rid of undesired values, the border shows really
>> strongly
>>
>> Here's an example everyone will see:
>>
>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>
>> (everything except the clouds is noise)
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>> 
>
>Antoine: Sorry to seem dense, but I don't see anything wrong with that 
>plot. I see a white border along the north and south pole, but I 
>intrepret that to be missing values. However, my eyes are notoriously 
>bad. I'd like to be to run a script that generates the artifacts 
>myself, so I can zoom in and see the problem myself. Does the 
>griddata_demo.py script show the same problem for you?
>
>-Jeff
>>
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:js...@fa...] 
>> Sent: mercredi 17 septembre 2008 19:05
>> To: John Hunter
>> Cc: De Pauw Antoine; Matplotlib Users
>> Subject: Re: [Matplotlib-users] Information request
>>
>> John Hunter wrote:
>> 
>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jd...@gm...> wrote:
>>>
>>> 
>>> 
>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>> axes border. The black horizontal line is the top axes border, the
>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>> grid line. I don't know if this offers a clue, but if you look at a
>>>> zoom in the upper right corner, the grey line seems to break up and
>>>> curve down and to the right (corner.png)
>>>> 
>>>> 
>>> Sorry, screwed up corner.png (I attached the original and not the
>>> screenshot). The correct screenshot is attached
>>> 
>>>
>>>
>>> 
>>
>> John: OK, now I finally see it. Antoine: Do these artifacts 
>> disappear if you comment out the imshow call?
>>
>> -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
>
>
>

G Jones wrote:
> Hello,
> Is it possible to label the axes of an imshow plot with something other 
> than pixel number? I want to use imshow for speed, but also would like 
> to be able to put arbitrary X and Y axes vectors on, as in pcolor(x,y,z)
> Thanks,
> Glenn
Using the extent kwarg, you can apply any linear scale to the imshow 
axes. An alternative is to use the Axes.pcolorfast method, which uses 
the imshow code (but without interpolation) if the grid is regular, and 
slower codes, but still much faster than pcolor, if the grid is 
irregular, or not rectangular.
Eric
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hello,
Is it possible to label the axes of an imshow plot with something other than
pixel number? I want to use imshow for speed, but also would like to be able
to put arbitrary X and Y axes vectors on, as in pcolor(x,y,z)
Thanks,
Glenn

Hello,
I am a beginner in matplotlib. I am trying to get pretty svg output, but it 
does not work the way I want it to :)
The bitmap image in svg file does not match the axes box. For example please 
see the code below or image_demo.py from matplotlib sources.
The bitmap overlaps axes box about 2-3 pixels (see right upper corner of the 
produced image). It looks like pdf output has the similar feature. 
I use matplotlib 0.98.3. 
Can you confirm this problem?
---------------------
#!/usr/bin/env python
from pylab import *
a=ones((256, 256))
a[100, 100]=122
a[100, 100]=44
a[0, :]=22
a[255, :]=22
a[:, 0]=22
a[:, 255]=22
figure(1)
imshow(a, interpolation='nearest')
savefig("image.svg")
Best regards,
Dmitri.