Description

ddale

opened on Jun 20, 2011

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Original report at SourceForge, opened Wed Sep 1 13:52:54 2010

When using log scale, if the error is larger than flux, the error bar does not plot at all:

import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt

fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ax.errorbar([1.],[1.],yerr=[2.])
ax.set_yscale('log')
fig.savefig('test.png')

However, I think it would make more correct to plot the line for the errorbar, and to make it go down to -infinity.

Activity

1. M-funk commented on Mar 19, 2012

   

   M-funk

   on Mar 19, 2012

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   The error bar does plot, but for some reason, it doesn't show the vertical connecting bar. You'll see if you do this:

   fig = plt.figure()
   ax = fig.add_subplot(111)
   ax.errorbar([1.,2.,3.],[1.,1.,1.],yerr = [0.1,3.,0.4])
   ax.set_yscale('log')
   fig.savefig('test.png')

   something like this outputs:
   http://i.imgur.com/LOIi7.png

   I think the problem lies in the fact that numpy computes log(1), in any base, equal to 0
2. pelson commented on Aug 19, 2012

   

   pelson

   on Aug 19, 2012

   Member

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   Confirming. Pretty sure this is related to the fact that you are trying to plot an error bar down to log(0). This works if your not trying log(0). For instance:

   ax.errorbar([10, 11, 12], [8, 9, 10], yerr=[0.5, 0.7, 0.9])
   

   Looks fine. @M-funk: can you confirm what you are expecting to see? I can't see that there is an action on this issue (perhaps a warning might be suitable when you are at log(0))?
3. neggert commented on Mar 18, 2013

   

   neggert

   on Mar 18, 2013

   Contributor

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   This can be worked around by doing

   ax.set_yscale('log', nonposy="clip")
   

   Maybe this should be the default for set_yscale? This seems to cause quite a few problems.
4. kreczko commented on May 13, 2013

   

   kreczko

   on May 13, 2013

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   @neggert : Nice workaround.
   Wish I had seen it before I wasted 1 hour to try and fix it ;)

   From a beginners standpoint I would definitely vote for making it the default (unless there are obvious reasons not to do so).
5. mdboom commented on May 13, 2013

   

   mdboom

   on May 13, 2013

   Member

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   👍 on making the default clip, with the appropriate API change warning.
6. dmcdougall

   closed this as completedin #2147on Aug 18, 2013
7. SebastianoF commented on Jan 24, 2019

   

   SebastianoF

   on Jan 24, 2019

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   Uhm... No, the errorbar should not be asymmetric when passing in log scale.
   Please consider
   http://faculty.washington.edu/stuve/uwess/log_error.pdf
   If I understood correctly the documentation, I would consider nonposx="mask" as the best option of the default behavour.

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