matplotlib-users Mailing List for matplotlib (Page 5)

Hello,

I am using matplotlib in combination with QT4 as part of an audio
application I am building. Part of this involves plotting an
oscilloscope-style display (time vs intensity) for sets of raw audio data,
which I have through necessity converted to arrays of floating point data.

The problem I have is that Pylab/QT slow down an unacceptable amount once
the amount of audio is more than a few seconds long. This is not too
surprising - typically a minute of stereo audio data will have 44100 * 60 *
2 = 5292000 points. I need to deal with, at minimum, 15 minute clips
efficiently

I have tried downsampling the audio dramatically and although this helps a
little, it is not enough for really large data sets. Downsampling also
reduces the accuracy of any editing of the audio, so it's not the ideal
solution.

I've read about 'data clipping' functionality in matplotlib, but can't seem
to get it working - has it been removed?

If so, does anybody have any ideas as to the sort of approach I could take
to solve this?

Thanks
Rob

Jeff,

I still don't know how to either remove this artifact or fill my arrays with
values to remove empty regions, and I'll make a last attempt to resolve it

I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56

The actual code snippet is here:
http://snipplr.com/view/8307/map-plotting-python-code-temporary/

I hope you'll be able to reproduce it, I set the cmap to winter for you to
see the gap... setting it to hot will make the grayish border visible in
high resolution by zooming it... I think the border (not the empty zone)
could be an artifact with the hot colormap


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

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

> 
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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.

Laurent Dufrechou wrote:
> Hello all,
> 
> I’m playing with FFT currently.
> 
> Here is the display under scilab (from wich I’m proting the code to 
> matplotlib)
> 
>  
> 
> And the display under matplotlib :
> 
>  
> 
> Display under matplotlib is done via: plot(freq, 
> abs(FreqI[0:len(FreqI)/2+1]), 'b', linewidth=.25)
> 
> To match let say “granularity” of scilab I had to add linewidth=.25.
> 
> What is the best linewidth value there, I mean to use 1 pixel for each 
> frequency?
> 
> .25  is not so bad but still blurry.
> 
> .1 gives excellent result but seems like if I have applied an alpha value:
> 
>  
> 
> Is it possible to get .1 result but with more stronger colors (without 
> alpha effect?)?

I suspect that what you are calling the alpha effect (or the blurry 
effect with 0.25) is really antialiasing, which scilab likely does not 
have.  You can turn it off by adding the aa=False kwarg setting to your 
plot command.

Eric


> 
>  
> 
> Cheers,
> 
> Laurent
> 
>  
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
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On Sun, Sep 21, 2008 at 3:28 PM, dmitrey <dmi...@sc...> wrote:
> Hi all,
> how to close (complitly destroy) pylab figure?
>
> The feature is highly required for my module "openopt".
>
> I expected something like this will work but it doesn't

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.

JDH

Hi all,
how to close (complitly destroy) pylab figure?

The feature is highly required for my module "openopt".

I expected something like this will work but it doesn't

from pylab import *
ion()
plot([1, 2, 3, 4], [1, 2, 3, 4])
draw()
# optional: ioff(); doesn't help as well
close('all')

Thank you in advance,
Dmitrey.

Had the same problem, solved with the setup.py attached ;)
Just modify it to fit your needs, should be a good start.
Works under vista + matplotlib 0.98.3
Cheers
Laurent

> -----Message d'origine-----
> De : Ron Adelman [mailto:Ron...@st...]
> Envoyé : samedi 20 septembre 2008 23:17
> À : mat...@li...
> Objet : [Matplotlib-users] py2exe with pylab
> 
> I followed the thread in Sept 2007 that covers the same problem I am
> having, but it seems to just end without a solution.
> 
> I have attached the setup file I am using.  When my application is
> packaged, installed and I try to get my graph I get the following
> message.  The graph works fine while I am working from just the python
> script in idle.
> 
> Traceback (most recent call last):
>   File "WxPyETn.py", line 4070, in GetRevGraph
>   File "matplotlib\__init__.pyc", line 677, in <module>
>   File "matplotlib\__init__.pyc", line 598, in rc_params
>   File "matplotlib\__init__.pyc", line 552, in matplotlib_fname
>   File "matplotlib\__init__.pyc", line 242, in wrapper
>   File "matplotlib\__init__.pyc", line 482, in _get_data_path_cached
>   File "matplotlib\__init__.pyc", line 478, in _get_data_path
> RuntimeError: Could not find the matplotlib data files
> 
> I really try to avoid posting and believe me, I have spent hours trying
> to figure a solution, but I am just plain ignorant with this and I
> feel there is a common solution out there someplace.
> 
> 
> Ron Adelman, CGFM
> Fiscal Consultant
> Dept. of Education (SouthWest District)
> 314 E. Main
> Jackson, TN   38301
> Phone: 731-927-8787
> State Cell:  615-306-4062
> Cell:  731-697-0967
> Fax: 731-422-1406

I followed the thread in Sept 2007 that covers the same problem I am having, but it seems to just end without a solution.

I have attached the setup file I am using.  When my application is packaged, installed and I try to get my graph I get the following message.  The graph works fine while I am working from just the python script in idle.

Traceback (most recent call last):
  File "WxPyETn.py", line 4070, in GetRevGraph
  File "matplotlib\__init__.pyc", line 677, in <module>
  File "matplotlib\__init__.pyc", line 598, in rc_params
  File "matplotlib\__init__.pyc", line 552, in matplotlib_fname
  File "matplotlib\__init__.pyc", line 242, in wrapper
  File "matplotlib\__init__.pyc", line 482, in _get_data_path_cached
  File "matplotlib\__init__.pyc", line 478, in _get_data_path
RuntimeError: Could not find the matplotlib data files

I really try to avoid posting and believe me, I have spent hours trying to figure a solution, but I am just plain ignorant with this and I  feel there is a common solution out there someplace.


Ron Adelman, CGFM   
Fiscal Consultant
Dept. of Education (SouthWest District)
314 E. Main
Jackson, TN   38301
Phone: 731-927-8787
State Cell:  615-306-4062
Cell:  731-697-0967
Fax: 731-422-1406

That does the trick!  Thanks Eric.

==========

The 2nd Law of Thermodynamics... If you think things are a mess now, JUST
WAIT!


On Sat, Sep 20, 2008 at 12:47 PM, Eric Firing <ef...@ha...> wrote:

> charles reid wrote:
>
>> Hi there -
>>
>> I'm wondering if there is a way to do this, since I haven't found anything
>> online or in the mailing list archives that covers it.  I'd like to draw a
>> line from inside the plot area to outside the plot area (see attached image
>> - the blue line is what I plot, but I'd like to know how to create something
>> like the red line, which goes beyond the axes of the plot).  I'm guessing I
>> would create an additional layer in the same figure, but make a layer
>> without axes.  However, I'm not exactly sure what I should do - add an
>> additional canvas?  a new renderer?  If you can point me to the right
>> documentation or give me some idea of how I should be doing this, I would
>> really appreciate it.
>>
>
> You can turn off the clipping to the axes box on a per-artist basis.
> Something like this:
>
> import matplotlib.pyplot as plt
> import numpy as np
> x = np.arange(10)
> y = np.ones_like(x)
> ll = plt.plot(x,y) # returns a sequence of line objects
> ll[0].set_clip_on(False)
> plt.axis([0,3,0,3])
> plt.show()
>
> Eric
>
>
>
>>
>> Charles
>>
>> ==========
>>
>> The 2nd Law of Thermodynamics... If you think things are a mess now, JUST
>> WAIT!
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> -------------------------------------------------------------------------
>> 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
>>
>
>

charles reid wrote:
> Hi there -
> 
> I'm wondering if there is a way to do this, since I haven't found 
> anything online or in the mailing list archives that covers it.  I'd 
> like to draw a line from inside the plot area to outside the plot area 
> (see attached image - the blue line is what I plot, but I'd like to know 
> how to create something like the red line, which goes beyond the axes of 
> the plot).  I'm guessing I would create an additional layer in the same 
> figure, but make a layer without axes.  However, I'm not exactly sure 
> what I should do - add an additional canvas?  a new renderer?  If you 
> can point me to the right documentation or give me some idea of how I 
> should be doing this, I would really appreciate it.

You can turn off the clipping to the axes box on a per-artist basis. 
Something like this:

import matplotlib.pyplot as plt
import numpy as np
x = np.arange(10)
y = np.ones_like(x)
ll = plt.plot(x,y) # returns a sequence of line objects
ll[0].set_clip_on(False)
plt.axis([0,3,0,3])
plt.show()

Eric


> 
> 
> Charles
> 
> ==========
> 
> The 2nd Law of Thermodynamics... If you think things are a mess now, 
> JUST WAIT!
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
> 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

Excellent!
That's was EXACTLY what I needed!
Thanks a lot Friedrich!

:)

2008/9/20 Friedrich Hagedorn <fri...@gm...>:
> On Sat, Sep 20, 2008 at 04:06:36PM +0200, Laurent Dufrechou wrote:
>> Hello all,
>> I'm trying to show to  a friend matplotlib features via pylab interface.
>> (thus to replace matlab/scilab)
>> I've a little problem while I'm trying to display plots into subplots here
>> under vista.
>> If I add a pylab.xlabel to the subplots they are masked by the underlying
>> subplot.
>> To workaround it I need to change the window size.
>> I used for myself add_axes([0.1,0.8,0.75,.15]) but that's not that easy.
>
> That's right (but sometimes I did the same :-)
>
>> Do I miss one important thing or must I go trought add_axes functions each
>> time I call pylab.subplot?
>
> Yes, you can adjust the space between the subplot with
>
>  subplots_adjust()
>
> Look at the docstring with
>
>  In [1]: subplots-adjust?
>
> in ipython shell. Try to see the difference between
>
>  figure()
>  subplot(211)
>  subplot(212)
>  show()
>
> and
>
>  figure()
>  subplots_adjust(hspace=0.4)  # standard: 0.2
>  subplot(211)
>  subplot(212)
>  show()
>
> By,
>
>  Friedrich
>

On Sat, Sep 20, 2008 at 04:06:36PM +0200, Laurent Dufrechou wrote:
> Hello all,
> I'm trying to show to  a friend matplotlib features via pylab interface.
> (thus to replace matlab/scilab)
> I've a little problem while I'm trying to display plots into subplots here
> under vista.
> If I add a pylab.xlabel to the subplots they are masked by the underlying
> subplot.
> To workaround it I need to change the window size.
> I used for myself add_axes([0.1,0.8,0.75,.15]) but that's not that easy.

That's right (but sometimes I did the same :-)

> Do I miss one important thing or must I go trought add_axes functions each
> time I call pylab.subplot?

Yes, you can adjust the space between the subplot with

  subplots_adjust()
  
Look at the docstring with

  In [1]: subplots-adjust?

in ipython shell. Try to see the difference between

  figure()
  subplot(211)
  subplot(212)
  show()

and

  figure()
  subplots_adjust(hspace=0.4)  # standard: 0.2
  subplot(211)
  subplot(212)
  show()

By,

  Friedrich

Hello all,
I'm trying to show to  a friend matplotlib features via pylab interface.
(thus to replace matlab/scilab)
I've a little problem while I'm trying to display plots into subplots here
under vista.
If I add a pylab.xlabel to the subplots they are masked by the underlying
subplot.
To workaround it I need to change the window size.
I used for myself add_axes([0.1,0.8,0.75,.15]) but that's not that easy.
Do I miss one important thing or must I go trought add_axes functions each
time I call pylab.subplot?

Thx for any idea!

Laurent

Try something like this:

import pylab as pl

head = ((0,    0,    10),
        (1,    0,    13),
        (2,    0,    11),
        (3,    0,    12),
        (1,    2,    11))

x, y, z = zip(*head)
xi, yi = pl.arange(0, 4, 0.1), pl.arange(0, 3, 0.1)
g = pl.griddata(x, y, z, xi, yi)
pl.scatter(x, y)
pl.contour(xi, yi, g)

Level values are automatically chosen in this example but you can
provide the number of values or a sequence of them.

Note that no extrapolation is done outside convex hull defined by input
data.

Goyo

El sáb, 20-09-2008 a las 11:13 +0200, Oz Nahum escribió:
> I'm trying again to understand how to plot scattered data from array into
>    contour graph.
>    I looked at
>    http://www.scipy.org/Cookbook/Matplotlib/Gridding_irregularly_spaced_data
>    and I understand I have to grid my data. However, in most samples the plot
>    is of a function.
>    Let's say I want to plot some geological data, suppose water table head, and
>    I have the following 3D aray
>                x     y    head
>    head =  ((0,    0,    10),
>                (1,    0,    13),
>                (2,    0,    11),
>                (3,    0,    12),
>                (1,    2,    11))
>    matplotlib has lot's of restrictions about how I can plot and interpolate
>    the data, which causes a lot of confusion in my side...
>    I'll be happy if someone could supply me a clue of how to plot contours of
>    data which comes in arrays or raster format and not an equation.
>    Thanks,
>    Oz
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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> _______________________________________________
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I'm trying again to understand how to plot scattered data from array into
   contour graph.
   I looked at
   http://www.scipy.org/Cookbook/Matplotlib/Gridding_irregularly_spaced_data
   and I understand I have to grid my data. However, in most samples the plot
   is of a function.
   Let's say I want to plot some geological data, suppose water table head, and
   I have the following 3D aray
               x     y    head
   head =  ((0,    0,    10),
               (1,    0,    13),
               (2,    0,    11),
               (3,    0,    12),
               (1,    2,    11))
   matplotlib has lot's of restrictions about how I can plot and interpolate
   the data, which causes a lot of confusion in my side...
   I'll be happy if someone could supply me a clue of how to plot contours of
   data which comes in arrays or raster format and not an equation.
   Thanks,
   Oz