Thanks for the report.  I have created a pull request with a solution 
for this bug here:

https://github.com/matplotlib/matplotlib/pull/403

If you are able to build from git, test these changes and give me 
feedback in your specific environment, that would be great.

Cheers,
Mike

On 07/14/2011 04:59 PM, Christopher Brown wrote:
> Hi,
>
> The following code displays a figure with both a red and a blue arrow
> (generated by annotate). But the pdf that is saved only shows the red
> one. It seems that the line ax1.set_xscale('log') is causing the
> trouble, because if it is commented out, the blue arrow reappears in the
> pdf. Any hints?
>
> import numpy as np
> from matplotlib import pyplot as pp
>
> fig = pp.figure()
> ax2 = fig.add_subplot(111)
> ax1 = ax2.twinx()
> ax1.set_xlim(xmin=100,xmax=10000)
> ax1.set_ylim(ymin=-60, ymax=5)
> ax1.set_xscale('log')
> ax2.set_xlim(xmin=100,xmax=10000)
> ax2.set_ylim(ymin=-5,ymax=35)
> ax2.set_xscale('log')
>
> ax1.annotate("", (10000,-30), (2000,-30),
>                arrowprops=dict(arrowstyle="-|>",fc="b", ec="b"))
> ax2.annotate("", (100, 5), (2000, 5),
>                arrowprops=dict(arrowstyle="-|>",fc="r", ec="r"))
> pp.savefig('test_arrow.pdf')
> pp.show()
>


-- 
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA


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