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Well I had originally tried adding to logs just as you had suggested, so that seems to be a logical solution that doesn’t require a new keyword.
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<div class="">Douglas Rudd</div>
<div class="">Scientific Computing Consultant<br class="">
Research Computing Center<br class="">
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<div class=""><a href="mailto:drudd@uchicago.edu" class="">drudd@uchicago.edu</a></div>
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<div class="">On Oct 31, 2014, at 4:29 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" class="">nathan12343@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">I see how this works now: ProfilePlot by default will take the logging behavior from the take_log attribute of the FieldInfo instance associated with the field.
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<div class="">This is definitely a bug: ProfilePlot should at least be smart enough to see that all of the data values are zero or negative and automatically switch the logging behavior so you can at least create a plot without erroring out inside matplotlib.</div>
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<div class="">A quick fix would be to manually change take_log for the field you're plotting, or to create an alias derived field that has a custom take_log choice. </div>
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<div class="">I could also see an argument for adding a keyword argument to control the plot field logging in the ProfilePlot constructor - although we usually have a pretty high bar for solving problems by adding new keyword arguments.</div>
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<div class="gmail_quote">On Fri, Oct 31, 2014 at 2:23 PM, Douglas Harvey Rudd <span dir="ltr" class="">
<<a href="mailto:drudd@uchicago.edu" target="_blank" class="">drudd@uchicago.edu</a>></span> wrote:<br class="">
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<div style="word-wrap:break-word" class="">For profiles where at least one data point is positive I can alter the log-edness once I have the ProfilePlot object using set_log.
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<div class="">Douglas Rudd</div>
<div class="">Scientific Computing Consultant<br class="">
Research Computing Center<br class="">
</div>
<div class=""><a href="mailto:drudd@uchicago.edu" target="_blank" class="">drudd@uchicago.edu</a></div>
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<div class="">On Oct 31, 2014, at 4:18 PM, Douglas Harvey Rudd <<a href="mailto:drudd@uchicago.edu" target="_blank" class="">drudd@uchicago.edu</a>> wrote:</div>
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<div style="word-wrap:break-word" class="">I believe it only works for axis fields. From the docstrings:
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<div class="">logs : dict of boolean values</div>
<div class=""> Whether or not to log the bin_fields for the profiles.</div>
<div class=""> The keys correspond to the field names. Defaults to the take_log</div>
<div class=""> attribute of the field.</div>
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<div class="">and adding velocity_magnitude to logs generates the same error as before.</div>
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<div class="">Douglas Rudd</div>
<div class="">Scientific Computing Consultant<br class="">
Research Computing Center<br class="">
</div>
<div class=""><a href="mailto:drudd@uchicago.edu" target="_blank" class="">drudd@uchicago.edu</a></div>
</div>
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<div class="">On Oct 31, 2014, at 4:10 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">What happens if you use the 'logs' keyword for create_profile to control the logging for temperature, velocity_magnitude, and dx?</div>
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<div class="gmail_quote">On Fri, Oct 31, 2014 at 2:08 PM, Douglas Harvey Rudd <span dir="ltr" class="">
<<a href="mailto:drudd@uchicago.edu" target="_blank" class="">drudd@uchicago.edu</a>></span> wrote:<br class="">
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Hi all,<br class="">
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Is there a way to specify the log/non-log scaling of a y-axis variable in create_profile or ProfilePlot.from_profiles? I have some profiles that start flat at an initial time and so the velocity_magnitude is everywhere 0. create_profile succeeds, but ProfilePlot.from_profiles
generates a Matplotlib error before I have the ability to specify a scaling:<br class="">
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sph = ds.sphere(ds.domain_center, ds.domain_width[0]/2)<br class="">
profile = yt.create_profile(sph, "radius",<br class="">
["density", "temperature", "velocity_magnitude", "dx"],<br class="">
extrema={'radius':(ds.domain_width[0]/ds.num_grid,ds.domain_width[0]/2.)},<br class="">
n_bins=int(ds.domain_width[0]*2.**(ds.max_level-1)),<br class="">
logs={'radius':False},<br class="">
units={'radius':'pc'})<br class="">
plot = yt.ProfilePlot.from_profiles(profile)<br class="">
<br class="">
Relevant part of the dump:<br class="">
/software/python-2.7-2014q3-el6-x86_64/lib/python2.7/site-packages/matplotlib-1.4.0-py2.7-linux-x86_64.egg/matplotlib/ticker.pyc in view_limits(self, vmin, vmax)<br class="">
1523 if minpos <= 0 or not np.isfinite(minpos):<br class="">
1524 raise ValueError(<br class="">
-> 1525 "Data has no positive values, and therefore can not be "<br class="">
1526 "log-scaled.")<br class="">
1527<br class="">
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<br class="">
Douglas Rudd<br class="">
Scientific Computing Consultant<br class="">
Research Computing Center<br class="">
<a href="mailto:drudd@uchicago.edu" target="_blank" class="">drudd@uchicago.edu</a><br class="">
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