Re: [Matplotlib-users] Bug in pylab?

[Darren D. <dar...@co...>]

Hi Lorenzo,

On Tuesday 15 January 2008 4:14:24 pm Lorenzo Isella wrote:
> Dear All,
> I am sending this email out of frustration, but I hope that someone will
> be able to tell me what is going on.
> I am using pylab on a Debian testing box.
> I have the feeling that there is some problem with pylab when I
> alternate, as I am doing now, many linear and log-log plots. Very often,
> pylab complains about the fact that I cannot take the log of a negative
> number even if all the quantities are positive or even if I have
> replaced the loglog with a linear plot...
> An example (sorry but there are long arrays involved and I cannot
> reproduce all my code here):
>
>
> #! /usr/bin/env python
>
> import scipy as s
> import numpy as n
> import pylab as p
> #from rpy import r
> #import distance_calc as d_calc
>
> # now I try performing a least-square fitting
> import scipy.optimize as sopt
>
>
> #do my stuff here
>
> print "my_n_clus_fit is, ", my_n_clus_fit
> print "my_r_sq_fit",my_r_sq_fit
> print "n_clu_rep2 is, ", n_clu_rep2
> print "R_sq is", R_sq
>
> p.plot(n_clu_rep2,R_sq,"bo",my_n_clus_fit,my_r_sq_fit, "ro")
> p.xlabel('particles in cluster')
> p.ylabel('R square')
> #p.legend(('beta=1e-2,100 part','beta=1e-1, 100 part', 'beta=1e-1, 200
> part'))
> p.title('Cluster-size vs average radius of gyration')
> p.grid(True)
> p.savefig("R_gyr_vs_N_fit.pdf")
> p.hold(False)
>
> and the relevant part of the output is:

[...]
> Traceback (most recent call last):
>   File "./r_gyr.py", line 322, in ?
>     p.plot(n_clu_rep2,R_sq,"bo",my_n_clus_fit,my_r_sq_fit, "ro")
>   File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line
> 2028, in plot
>     ret =  gca().plot(*args, **kwargs)
>   File "/usr/lib/python2.4/site-packages/matplotlib/axes.py", line 2540,
> in plot
>     self.autoscale_view(scalex=scalex, scaley=scaley)
>   File "/usr/lib/python2.4/site-packages/matplotlib/axes.py", line 1207,
> in autoscale_view
>     self.set_xlim(XL)
>   File "/usr/lib/python2.4/site-packages/matplotlib/axes.py", line 1493,
> in set_xlim
>     raise ValueError('Cannot set nonpositive limits with log transform')
> ValueError: Cannot set nonpositive limits with log transform


I think this is a bug. It sounds like the same issue I reported a while back: 
http://www.nabble.com/Cannot-set-nonpositive-limits-with-log-transform-to12154187.html

I havent had a chance to look into a solution. I filed a bug report at 
sourceforge (1872462). I'm worried the fix will be disruptive, but several 
people have run into this. I'm sorry you got bit as well.

Darren