matplotlib-users Mailing List for matplotlib

Hi-

Thanks for the help. A comment below...

> Andrew Jaffe wrote:
>> Eric (etc)-
>>
>> Sorry, no dice... in fact I was already using the CVS version so  
>> this  was the to_rgba() method that failed originally!
>>
>> Any other possibilities? Could the problem be just a coincidental   
>> error elsewhere?
>>
>> Andrew
>>
>>
>
> Andrew and Eric:  I apologize, this latest glitch was all my  
> fault.  I had made a modification to colors.py to workaround an  
> apparenty bug in numpy masked arrays, and that modification was  
> wrong.  It's now fixed in CVS, revision 1.26
>
> Index: colors.py
> ===================================================================
> RCS file: /cvsroot/matplotlib/matplotlib/lib/matplotlib/colors.py,v
> retrieving revision 1.25
> diff -r1.25 colors.py
> 659c659
> <             result = (vmax-vmin)/(val-vmin)  <-- this is wrong
> ---
> >             result = (val-vmin)/(vmax-vmin)  <-- this is right
>
> Originally (in 0.87) there was
>
> result = (1.0/(vmax-vmin))*(val-vmin)
>
> which raised an exception when val was a numpy masked array.

However, I expect the original line was like this in case vmax, vmin  
and val are all integers, in which case without 'truedivision' (or  
'from __future__ import division'), result will use integer division  
which probably isn't desired.

So this may need to be fixed to force floating-point division. Not  
sure the robust way to do this with possibly-masked arrays, etc.

Andrew

Hi guys,

Just to add to this issue, I have been profiling my own code which  
embeds matplotlib inside a Cocoa app, and uses Agg to draw to an  
NSView. (I posted a howto on this recently to the user list). I am  
drawing a grayscale image (an array with values 0-255), and then  
drawing lines over the top.

I have noticed that most of the time is spend in the ma.asarray(x)  
method (specifically the ma.__init__ method) and discounted this as  
too hard for me to figure on. But these posts point out that this is  
a slow point in the code. Now it is faster for RGB images. I'm  
wondering if there is a way to optimise this method for the (fairly  
common, I imagine) case of using imshow on grayscale, non-masked  
numpy arrays. Can this be done?

Your help is appreciated.
Josh

Eric Firing wrote:
> Jeff,
>
> I really blew it on that one--it looked so simple!  OK, I think this
> version is correct; it will land in CVS in a few minutes.
>
>      def to_rgba(self, x, alpha=1.0):
>          '''Return a normalized rgba array corresponding to x.
>          If x is already an rgb or rgba array, return it unchanged.
>          '''
>          if hasattr(x, 'shape') and len(x.shape)>2: return x
>          x = ma.asarray(x)
>          x = self.norm(x)
>          x = self.cmap(x, alpha)
>          return x
> Eric
>
> Jeff Whitaker wrote:
>
>> Eric Firing wrote:
>>
>>
>>> Ray,
>>>
>>> You tripped over a bug in cm.py: when I added masked array  
>>> support, I
>>> put the "x = ma.asarray(x)" too early in the to_rgba() method of
>>> ScalarMappable.  It is fixed now in CVS.  Thanks for finding the  
>>> problem.
>>>
>>> If you want to try the fix in your version, in place of your
>>> workaround, here is the revised method:
>>>
>>>    def to_rgba(self, x, alpha=1.0):
>>>         # assume normalized rgb, rgba
>>>         if len(x.shape)>2: return x
>>>         x = ma.asarray(x)
>>>         x = self.norm(x)
>>>         x = self.cmap(x, alpha)
>>>         return x
>>>
>>> Eric
>>>
>>>
>>
>>
>> Hi Eric:  This breaks some of the basemap demos which do this
>>
>> CS = m.contour(x,y,hgt,15,linewidths=0.5,colors='k')
>>
>> to draw solid black contour lines.  I now get
>>
>> File "/sw/lib/python2.4/site-packages/matplotlib/cm.py", line 52, in
>> to_rgba
>>    if len(x.shape)>2: return x
>> AttributeError: 'list' object has no attribute 'shape'
>>
>> It appears that colors now has to be an array?
>>
>> -Jeff
>

Andrew Jaffe wrote:

> Eric (etc)-
>
> Sorry, no dice... in fact I was already using the CVS version so this  
> was the to_rgba() method that failed originally!
>
> Any other possibilities? Could the problem be just a coincidental  
> error elsewhere?
>
> Andrew
>
>

Andrew and Eric:  I apologize, this latest glitch was all my fault.  I 
had made a modification to colors.py to workaround an apparenty bug in 
numpy masked arrays, and that modification was wrong.  It's now fixed in 
CVS, revision 1.26

Index: colors.py
===================================================================
RCS file: /cvsroot/matplotlib/matplotlib/lib/matplotlib/colors.py,v
retrieving revision 1.25
diff -r1.25 colors.py
659c659
<             result = (vmax-vmin)/(val-vmin)  <-- this is wrong
---
 >             result = (val-vmin)/(vmax-vmin)  <-- this is right

Originally (in 0.87) there was

result = (1.0/(vmax-vmin))*(val-vmin)

which raised an exception when val was a numpy masked array.

Sorry for the screwup.

-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-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Eric (etc)-

Sorry, no dice... in fact I was already using the CVS version so this  
was the to_rgba() method that failed originally!

Any other possibilities? Could the problem be just a coincidental  
error elsewhere?

Andrew


On 23 Feb 2006, at 17:31, Eric Firing wrote:

> Andrew,
>
> Unfortunately, the 0.87 release was packed up immediately after I  
> made the first of two changes to cm.py, so it contains the bug  
> referred to below.  Most likely that is what is wrecking your  
> imshow plots.  Please try substituting the revised function in  
> cm.py, and let us know if that solves the problem.
>
>     def to_rgba(self, x, alpha=1.0):
>         '''Return a normalized rgba array corresponding to x.
>         If x is already an rgb or rgba array, return it unchanged.
>         '''
>         if hasattr(x, 'shape') and len(x.shape)>2: return x
>         x = ma.asarray(x)
>         x = self.norm(x)
>         x = self.cmap(x, alpha)
>         return x
>
> Eric
>
> Andrew Jaffe wrote:
>> Jeff Whitaker wrote:
>>> Eric Firing wrote:
>>>
>>>> Jeff,
>>>> I really blew it on that one--it looked so simple!  OK, I think  
>>>> this version is correct; it will land in CVS in a few minutes.
>>>>
>>>>     def to_rgba(self, x, alpha=1.0):
>>  >>    [[[ code removed ]]]
>>  >>
>>> Eric:  Thanks for the quick fix - that seems to have done the job.
>>> -Jeff
>> I don't know if it's related, but as of the latest version, all of  
>> my imshow() commands show a single color, no structure at all.

______________________________________________________________________
Andrew Jaffe                                    a....@im...
Astrophysics Group                                    +44 207 594-7526
Blackett Laboratory, Room 1013                    FAX             7541
Imperial College, Prince Consort Road
London SW7 2AZ ENGLAND              http://astro.imperial.ac.uk/~jaffe

Could that be because interactive mode was set in your previous install ?
(in .matplotlibrc file)
if I try:

#!/usr/bin/python
import matplotlib
import pylab
matplotlib.interactive(True)
pylab.figure()
pylab.close()

Then it works...
Hope this  could help you...

David

2006/2/23, Emmanuel Pecontal <pec...@ob...>:
>
> Hello,
>
> If I run the following script on my system (SuSE 10.0, matplotlib-0.87 bu=
t
> same behaviour with 0.86):
>
> #!/usr/bin/python
>
> import matplotlib
> import pylab
>
> pylab.figure()
> pylab.close ()
>
> It crashes with the following error message:
>
> Traceback (most recent call last):
>   File "./tmp.py", line 8, in ?
>     pylab.close()
>   File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 768,
> in
> close
>     else: _pylab_helpers.Gcf.destroy(figManager.num)
>   File "/usr/lib/python2.4/site-packages/matplotlib/_pylab_helpers.py",
> line
> 28, in destroy
>     figManager.destroy()
>   File
> "/usr/lib/python2.4/site-packages/matplotlib/backends/backend_gtk.py",
> line 456, in destroy
>     gtk.main_quit()
> RuntimeError: called outside of a mainloop
>
> Does someone has an idea of the problem?
> I didn't have this kind of problem with my SuSE 9.3 and matplotlib-0.85
>
> --
> Emmanuel P=E9contal
>
> CRAL - Observatoire de Lyon
> 9, Av. Charles Andre
> F-69561 Saint Genis Laval Cedex
>
> tel (33) (0)4.78.86.83.76 - fax (33) (0)4.78.86.83.86
>
> email : pec...@ob...
>

Hello,

If I run the following script on my system (SuSE 10.0, matplotlib-0.87 but=
=20
same behaviour with 0.86):

#!/usr/bin/python

import matplotlib
import pylab

pylab.figure()
pylab.close()

It crashes with the following error message:

Traceback (most recent call last):
  File "./tmp.py", line 8, in ?
    pylab.close()
  File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 768, in=
=20
close
    else: _pylab_helpers.Gcf.destroy(figManager.num)
  File "/usr/lib/python2.4/site-packages/matplotlib/_pylab_helpers.py", lin=
e=20
28, in destroy
    figManager.destroy()
  File "/usr/lib/python2.4/site-packages/matplotlib/backends/backend_gtk.py=
",=20
line 456, in destroy
    gtk.main_quit()
RuntimeError: called outside of a mainloop

Does someone has an idea of the problem?
I didn't have this kind of problem with my SuSE 9.3 and matplotlib-0.85

=2D-=20
Emmanuel P=E9contal

CRAL - Observatoire de Lyon
9, Av. Charles Andre
=46-69561 Saint Genis Laval Cedex

tel (33) (0)4.78.86.83.76 - fax (33) (0)4.78.86.83.86

email : pec...@ob...
~

Andrew,

Unfortunately, the 0.87 release was packed up immediately after I made 
the first of two changes to cm.py, so it contains the bug referred to 
below.  Most likely that is what is wrecking your imshow plots.  Please 
try substituting the revised function in cm.py, and let us know if that 
solves the problem.

     def to_rgba(self, x, alpha=1.0):
         '''Return a normalized rgba array corresponding to x.
         If x is already an rgb or rgba array, return it unchanged.
         '''
         if hasattr(x, 'shape') and len(x.shape)>2: return x
         x = ma.asarray(x)
         x = self.norm(x)
         x = self.cmap(x, alpha)
         return x

Eric

Andrew Jaffe wrote:
> Jeff Whitaker wrote:
> 
>> Eric Firing wrote:
>>
>>> Jeff,
>>> I really blew it on that one--it looked so simple!  OK, I think this 
>>> version is correct; it will land in CVS in a few minutes.
>>>
>>>     def to_rgba(self, x, alpha=1.0):
> 
>  >>    [[[ code removed ]]]
>  >>
> 
>> Eric:  Thanks for the quick fix - that seems to have done the job.
>> -Jeff
> 
> 
> I don't know if it's related, but as of the latest version, all of my 
> imshow() commands show a single color, no structure at all.

Hi

Some time ago I installed (Debian sarge) the mpl 0.82 .debs
(by placing deb http://anakonda.altervista.org/debian packages/ in my 
/etc/apt/sources.list) .

Now I wanted to make a "clean" install of mpl 0.87. So what I did was

	dpkg -l matplot
	dpkg -P <all mpl packages>

	updatedb
	locate matplotlib

and then removing everything found related to mpl (form various other 
from-source-installs).

After that I installed 0.87 as usual (python setup.py build/install).

Now testing my fresh install

	ipython -pylab
	plot([1,2,3])
	xlabel("lala")

I found the xlabel not centered but on the leftmost side of the axis (I 
reported this earlier for 0.86.2 ...)

I remembered that I haven't had this problem if I did *not* uninstall 
the 0.82 .debs before installing a newer version. So I removed 0.87, 
re-installed my 0.82 .debs and *after* that installed 0.87 and there was 
the xlabel, sitting centered where it should be.

Did anyone have similar issues or has an idea as to what might cause 
this?? Is 0.82 writing some (config) files that 0.87 should not read but 
does? Thanks for any hint.

cheers,
steve

-- 
Random number generation is the art of producing pure gibberish as 
quickly as possible.

>>>>> "Keith" ==   <kei...@bt...> writes:

    Keith> None of the links at
    Keith> http://matplotlib.sourceforge.net/tutorial.html work.
    Keith> E.g. See the plot
    Keith> <http://matplotlib.sourceforge.net/pylab.html#-plot>
    Keith> documentation

Oops, OK, fixed.  

Thanks,
JDH

>>>>> "George" == George Nurser <ag...@no...> writes:

    George> The problem had arisen because I had installed matplotlib
    George> to a nonstandard directory with python setup.py install
    George> --home=$PREFIX From the documentation
    George> [http://matplotlib.sourceforge.net/ installing.html] I had
    George> got the impression that MATPLOTLIBDATA also needed to be
    George> set= to the directory on which I wanted to install
    George> matplotlib ... of course this is *not* the data directory.

Oh yeah, I think the docs are out of date since the data dirs were
recently moved into the matplotlib/mpl-data dir and so you no longer
need to set MATPLOTLIBDATA when installing to non-standard locations,
but if you do set it, it will be respected, for better or worse as you
found out.

An update of the web site docs is sorely needed.  Moving it OT the top
of the TODO list....

    George> Thanks for your help, & for a really professional piece of
    George> software.

You're welcome -- thanks for the kind words.

JDH

None of the links at http://matplotlib.sourceforge.net/tutorial.html =
work.

E.g. See the plot <http://matplotlib.sourceforge.net/pylab.html#-plot> =
documentation=20

*click*

An error has been encountered in accessing this page.=20

1. Server: matplotlib.sourceforge.net
2. URL path: /pylab.html
3. Error notes: File does not exist: =
/home/groups/m/ma/matplotlib/htdocs/pylab.html
4. Error type: 404
5. Request method: GET
6. Request query string:=20
7. Time: 2006-02-23 05:31:23 PST (1140701483)

Reporting this problem: The problem you have encountered is with a =
project web site hosted by SourceForge.net. This issue should be =
reported to the SourceForge.net-hosted project (not to SourceForge.net). =


If this is a severe or recurring/persistent problem, please do one of =
the following, and provide the error text (numbered 1 through 7, above): =


1.	Contact the project via their designated support resources =
<http://sourceforge.net/support/prweb-lookup.php?host=3Dmatplotlib.source=
forge.net&support=3D1>.=20
2.	Contact the project administrators of this project via email (see the =
upper right-hand corner of the Project Summary page =
<http://sourceforge.net/support/prweb-lookup.php?host=3Dmatplotlib.source=
forge.net> for their usernames) at use...@us...

If you are a member of the project that maintains this web content, =
please refer to the Site Documentation regarding the project web service =
<https://sourceforge.net/docs/E07/> for further assistance.=20

After upgrading from MPL 0.82 to 0.87 and tried again, the message
from MPL was that I needed tex version 0.31415 or later. I have
0.3141592 and the reason why MPL didn`t find it is described in bugs
on Sourceforge with the title
"Bug with text.usetex =3D true on WinXP with MiKTeX". So I just edited
__init__.py and latex now seems to work with MPL.


On 2/22/06, Darren Dale <dd...@co...> wrote:
> On Wednesday 22 February 2006 7:32 am, Bruce wrote:
> > Hi group,
> >
> > I wanted to try to usetex for my matplotlib plots, and thought that I
> > had everything neccessary installed, but it doesn`t work. Perhaps
> > someone in the group have some idea what is wrong here? Im using
> > MikTex on xp and have the dvipng-miktex pakage installed. thx
>
> Have you read the wiki? http://www.scipy.org/Wiki/Cookbook/Matplotlib/Usi=
ngTex
>
> An intermediate dvi file is missing, probably because the latex executabl=
e is
> not on your path.
>
> Darren
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
les
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=
=3D121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

> All the lapack stuff is linked to what you are using for Numerix: 
> Numeric, numarray or NumPy, rather than directly by MPL. It looks like 
> you may have upgraded your atlas install, and not upgraded your numerix 
> package with it. Or you're installed a Numerix binary package that 
> depends on an older lapack.

I have the same problem :  with Numeric or numarray and matplotlib-0.82 
(from ubuntu) there is no problem but when I remove matplotlib-0.82 and 
install numpy-0.92-jdh and matplotlib-0.86-cvs-jdh, I have the same 
error (with numerix : numpy in my .matplotlibrc). I don't change 
anything else/

A question : why mpl is looking at  "/home/jdhunter/debs/numpy/usr/[..]" ?

Jean-Luc

On 22 Feb 2006, at 14:30, John Hunter wrote:

>>>>>> "George" == George Nurser <ag...@no...> writes:
>
>     George> I've had various versions of matplotlib from CVS installed
>     George> on an Opteron (Red Hat LInux) here for a few weeks now. I
>     George> had to modify setupext.py to look for various libraries in
>     George> ../lib64 instead of /lib but matplotlib works very nicely
>     George> most of the time, and I have started using it for real
>     George> work.
>
>     George> One cosmetic problem: the buttons at the bottom of the
>     George> plot window have their graphics messed up. They just look
>     George> like red crosses. The floating xml works, so I know what
>     George> the buttons do, and it doesn't inconvenience me --- but it
>     George> looks bad.
>
>     George> Presumably some library is either out of date, incomplete,
>     George> or not linked correctly. I am using the default TkAgg
>     George> backend. Any thoughts on what I should look for would be
>     George> appreciated.
>
> We used to see something like this on OSX with the WX backend.  What
> version of Tk are you using?  Could this be a byte order or byte size
> problem?
>
> [snipped]
> Thanks,
> JDH

John,

Sorry to have bothered you about this -- the solution should have  
been obvious to me. The problem was simply that I had specified  
MATPLOTLIBDATA to something different to the matplotlib data  
directory where the button images actually were. This data directory  
seems to be in the default location, so unsetting MATPLOTLIBDATA  
solved the problem.

The problem had arisen because I had installed matplotlib to a  
nonstandard directory with
python setup.py install --home=$PREFIX
 From the documentation [http://matplotlib.sourceforge.net/ 
installing.html] I had got the impression that MATPLOTLIBDATA also  
needed to be set= to the directory on which I wanted to install  
matplotlib ... of course this is *not* the data directory.

Thanks for your help, & for a really professional piece of software.

George.

Jeff Whitaker wrote:
> Eric Firing wrote:
>> Jeff,
>> I really blew it on that one--it looked so simple!  OK, I think this 
>> version is correct; it will land in CVS in a few minutes.
>>
>>     def to_rgba(self, x, alpha=1.0):
 >>    [[[ code removed ]]]
 >>
> Eric:  Thanks for the quick fix - that seems to have done the job.
> -Jeff

I don't know if it's related, but as of the latest version, all of my 
imshow() commands show a single color, no structure at all.

>>>>> "James" == James Boyle <bo...@ll...> writes:

    James> Running : OS X 10.3.9 - matplotlib 0.86 (Agg backend)
    James> python 2.3 Numeric 23.7

    James> I have the following command sequence:

    James> import Numeric N = Numeric from matplotlib import pylab PL
    James> = pylab

FYI, there is a more elegant way to do this import in python
(unrelated to your original question)

  import Numeric
  N = Numeric
  from matplotlib import pylab
  PL = pylab

rather

  import Numeric as N
  import matplotlib.pylab as PL

more on the other part of your question later :-)

JDH

>>>>> "Simon" == Simon Burton <si...@ar...> writes:

    Simon> from: http://matplotlib.sourceforge.net/pylab.html

    Simon> An error has been encountered in accessing this page.

Perhaps the site that is linking to matplotlib is broken, rather than
the matplotlib site itself.  I think the page you are looking for is


http://matplotlib.sourceforge.net/matplotlib.pylab.html

JDH

from:
http://matplotlib.sourceforge.net/pylab.html

An error has been encountered in accessing this page.

1. Server: matplotlib.sourceforge.net
2. URL path: /pylab.html
3. Error notes: File does not exist: /home/groups/m/ma/matplotlib/htdocs/pylab.html
4. Error type: 404
5. Request method: GET
6. Request query string:
7. Time: 2006-02-22 20:34:27 PST (1140669267)

Reporting this problem: The problem you have encountered is with a project web site hosted by SourceForge.net. This issue should be reported to the SourceForge.net-hosted project (not to SourceForge.net).

If this is a severe or recurring/persistent problem, please do one of the following, and provide the error text (numbered 1 through 7, above):

   1. Contact the project via their designated support resources.
   2. Contact the project administrators of this project via email (see the upper right-hand corner of the Project Summary page for their usernames) at use...@us...

If you are a member of the project that maintains this web content, please refer to the Site Documentation regarding the project web service for further assistance. 


Simon.

-- 
Simon Burton, B.Sc.
Licensed PO Box 8066
ANU Canberra 2601
Australia
Ph. 61 02 6249 6940
http://arrowtheory.com 

A feature I mentioned on the list a few weeks ago is in the 0.87
release that was pushed today.  It is
"matplotlib.get_py2exe_datafiles()".  You can see it used in the
sample setup.py script below.

Begin setup.py script
---------------------------------------------------------------------------=
-----------
# For py2exe only
"""
 Run with the following command (use py2exe 0.6.2 or higher)

  python.exe -OO setup.py py2exe -b 3 -c -p numarray,pytz -e numpy
"""

import os
from distutils.core import setup
import py2exe
import glob

import matplotlib

setup( version =3D '0.9.1',
      windows =3D ['nlogui.py'],
      data_files =3D [('', ['nlo.gif', '../vtkrotate/NMA.pdb']),
                    matplotlib.get_py2exe_datafiles()],
      options=3D{"py2exe":{"optimize":2}},
)


On 2/22/06, Jeff Peery <jef...@ya...> wrote:
> Hi, I'm pretty unfamiliar with py2exe and I had been using it with
> matplotlib and it was working well. I upgraded to 0.86 and now it doesn't
> work. I know this is because the installation directory is different (no
> longer the share folder).  I thought I fixed it correctly but I get an er=
ror
> that indicates py2exe "can't find
> lib/site-packages/matplotlib/backends or it is not a
> regular file".  I am assuming that it doesn't like 'backends' because it =
is
> a folder and not a file.  I changed my setup code to this:
>
>  data_files=3D[
>              ("matplotlibdata",
>                     glob.glob(os.path.join(distutils.sysconfig.PREFIX,
> 'lib', 'site-packages','matplotlib', "*")))]
>
>  setup(
>      options =3D options,
>      # The lib directory contains everything except the executab les and =
the
> python dll.
>      windows =3D [app],
>      data_files =3D data_files,
>      # use out build_installer class as extended py2exe build command
>      cmdclass =3D {"py2exe": build_installer},
>      )
>
>  how might I change this to get it working properly? thanks!!
>
>  Jeff
>
>
>  ________________________________
> Brings words and photos together (easily) with
>  PhotoMail - it's free and works with Yahoo! Mail.
>
>