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On vendredi 3 octobre 2008, Alan wrote:

> We are developing an application (CING: cing.googlecodes.com) and we

  You mean http://cing.googlecode.com  (no "s")

[...]
> I don't have much idea at moment how to debug it better, but it seems
> that I cannot generate the PDFs because mtplib functions don't guess a
> finite number of pages.

[...]
> "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", line
> 124, in pdfRepr
>     raise ValueError, "Can only output finite numbers in PDF"
> ValueError: Can only output finite numbers in PDF

  Is this not a problem with non-finite *values* in your data ? Do you have 
NaN of Inf numbers oin your data ?

-- 
Vincent Favre-Nicolin                   http://vincefn.net
Université Joseph Fourier       http://www.ujf-grenoble.fr
CEA/ Institut Nanosciences & Cryogénie  http://inac.cea.fr
ObjCryst & Fox             http://objcryst.sourceforge.net

Are you perhaps trying to plot data containing NaN or Inf?  If so, this 
is a known bug in 0.98.3 that has seen been corrected on SVN trunk.

A workaround is to pass masked arrays (where the NaNs and Infs are 
masked out) to matplotlib instead.

But this bug should be gone in the next release of matplotlib.  If 
you're comfortable building from SVN, you could even try that now.

Cheers,
Mike

Alan wrote:
> Dear all,
>
> I don't know much how to express this issue I am having but I will try.
>
> We are developing an application (CING: cing.googlecodes.com) and we
> have some routines to test the sanity of our code.
>
> I am developing in python, on a mac book pro with Mac OSX tiger and FINK.
>
> So when we were using matplotlib 0.90.1 and numpy 1.0.4 the routine
> below was running fine.
>
> Then I updated all from Fink, having now mtplib 0.98.3 and numpy 1.1.1
> and problems started to appear.
>
> I could solve all (e.g. replace verify_intervals()) but one, as shown below.
>
> I don't have much idea at moment how to debug it better, but it seems
> that I cannot generate the PDFs because mtplib functions don't guess a
> finite number of pages.
>
> I hope someone can give any idea.
>
> Many thanks in advance.
>
> Alan
>
> ======================================================================
> ERROR: testMoleculePlot (cing.Libs.test.test_NTMoleculePlot.AllChecks)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Users/alan/workspace/cingWork/python/cing/Libs/test/test_NTMoleculePlot.py",
> line 178, in testMoleculePlot
>     createPngCopyToo=True  )
>   File "/Users/alan/workspace/cingWork/python/cing/Libs/NTmoleculePlot.py",
> line 176, in renderMoleculePlotSet
>     if ps.hardcopy(fileNameList[r-1]):
>   File "/Users/alan/workspace/cingWork/python/cing/Libs/NTplot.py",
> line 1201, in hardcopy
>     savefig(fileName)
>   File "/sw/lib/python2.5/site-packages/matplotlib/pyplot.py", line
> 342, in savefig
>     return fig.savefig(*args, **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line
> 964, in savefig
>     self.canvas.print_figure(*args, **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
> line 1310, in print_figure
>     **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
> line 1204, in print_pdf
>     return pdf.print_pdf(*args, **kwargs)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 1864, in print_pdf
>     self.figure.draw(renderer)
>   File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line 759, in draw
>     for a in self.axes: a.draw(renderer)
>   File "/sw/lib/python2.5/site-packages/matplotlib/axes.py", line 1523, in draw
>     a.draw(renderer)
>   File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line 437, in draw
>     markerFunc(renderer, gc, tpath, affine.frozen())
>   File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line
> 885, in _draw_plus
>     path, path_trans)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 1253, in draw_markers
>     marker, Op.use_xobject)
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 451, in output
>     self.write(fill(map(pdfRepr, data)))
>   File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
> line 124, in pdfRepr
>     raise ValueError, "Can only output finite numbers in PDF"
> ValueError: Can only output finite numbers in PDF
>
> ----------------------------------------------------------------------
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Dear all,

I don't know much how to express this issue I am having but I will try.

We are developing an application (CING: cing.googlecodes.com) and we
have some routines to test the sanity of our code.

I am developing in python, on a mac book pro with Mac OSX tiger and FINK.

So when we were using matplotlib 0.90.1 and numpy 1.0.4 the routine
below was running fine.

Then I updated all from Fink, having now mtplib 0.98.3 and numpy 1.1.1
and problems started to appear.

I could solve all (e.g. replace verify_intervals()) but one, as shown below.

I don't have much idea at moment how to debug it better, but it seems
that I cannot generate the PDFs because mtplib functions don't guess a
finite number of pages.

I hope someone can give any idea.

Many thanks in advance.

Alan

======================================================================
ERROR: testMoleculePlot (cing.Libs.test.test_NTMoleculePlot.AllChecks)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/alan/workspace/cingWork/python/cing/Libs/test/test_NTMoleculePlot.py",
line 178, in testMoleculePlot
    createPngCopyToo=True  )
  File "/Users/alan/workspace/cingWork/python/cing/Libs/NTmoleculePlot.py",
line 176, in renderMoleculePlotSet
    if ps.hardcopy(fileNameList[r-1]):
  File "/Users/alan/workspace/cingWork/python/cing/Libs/NTplot.py",
line 1201, in hardcopy
    savefig(fileName)
  File "/sw/lib/python2.5/site-packages/matplotlib/pyplot.py", line
342, in savefig
    return fig.savefig(*args, **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line
964, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 1310, in print_figure
    **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 1204, in print_pdf
    return pdf.print_pdf(*args, **kwargs)
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 1864, in print_pdf
    self.figure.draw(renderer)
  File "/sw/lib/python2.5/site-packages/matplotlib/figure.py", line 759, in draw
    for a in self.axes: a.draw(renderer)
  File "/sw/lib/python2.5/site-packages/matplotlib/axes.py", line 1523, in draw
    a.draw(renderer)
  File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line 437, in draw
    markerFunc(renderer, gc, tpath, affine.frozen())
  File "/sw/lib/python2.5/site-packages/matplotlib/lines.py", line
885, in _draw_plus
    path, path_trans)
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 1253, in draw_markers
    marker, Op.use_xobject)
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 451, in output
    self.write(fill(map(pdfRepr, data)))
  File "/sw/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py",
line 124, in pdfRepr
    raise ValueError, "Can only output finite numbers in PDF"
ValueError: Can only output finite numbers in PDF

----------------------------------------------------------------------
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

I am under the impression that the way to go is now the mlab interface 
to mayavi2. Here is a nice talk by Gael : 
http://gael-varoquaux.info/physics/slides_Scipy2007.pdf
Johann

Eric Firing wrote:
> Lisa Tauxe wrote:
>   
>> Are there any plans for incorporating this (what used to be mplot3d)  
>> into the new matplotlib version?
>>     
>
> Not that I know of.  It was not being maintained even before the move to 
> 0.98.x.
>
> Eric
>
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