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math domain error using symlog norm #7595
Description
I stumbled across this regression trying to use the matplotlib 2.0 release candidate with yt.
In yt we have a plotting class called SlicePlot that will switch to a symlog colorbar if a user tries to plot a field that we want to be log-scaled because it has a lot of dynamic range but that also has negative values. A very simple yt script (that works fine under matplotlib 1.5.3 but dies with a traceback under 2.0.0rc1) that triggers this looks like:
import yt
ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
p = yt.SlicePlot(ds, 2, 'x-velocity')
p.save()To make this easier for people who aren't familiar with yt internals to digest, I've come up with the following test script that only uses matplotlib but triggers what I think is the same error:
import matplotlib
import numpy as np
from matplotlib import pyplot as plt
image = np.array(
[[-1, -1, -1],
[0, 0, 0],
[1, 1, 1]]
)
fig, ax = plt.subplots()
cax = fig.add_axes([0.85, 0.1, 0.1, 0.8])
norm = matplotlib.colors.SymLogNorm(0.1, vmin=-1, vmax=1)
image = ax.imshow(image, norm=norm, vmin=-1, vmax=1)
fig.colorbar(image, cax, format=matplotlib.ticker.LogFormatterMathtext())
plt.savefig('img.png')It produces the following traceback:
Traceback (most recent call last):
File "test2.py", line 20, in <module>
fig.colorbar(image, cax, format=matplotlib.ticker.LogFormatterMathtext())
File "/usr/local/lib/python3.5/site-packages/matplotlib/figure.py", line 1601, in colorbar
cb = cbar.colorbar_factory(cax, mappable, **kw)
File "/usr/local/lib/python3.5/site-packages/matplotlib/colorbar.py", line 1347, in colorbar_factory
cb = Colorbar(cax, mappable, **kwargs)
File "/usr/local/lib/python3.5/site-packages/matplotlib/colorbar.py", line 926, in __init__
ColorbarBase.__init__(self, ax, **kw)
File "/usr/local/lib/python3.5/site-packages/matplotlib/colorbar.py", line 326, in __init__
self.draw_all()
File "/usr/local/lib/python3.5/site-packages/matplotlib/colorbar.py", line 351, in draw_all
self._config_axes(X, Y)
File "/usr/local/lib/python3.5/site-packages/matplotlib/colorbar.py", line 447, in _config_axes
self.update_ticks()
File "/usr/local/lib/python3.5/site-packages/matplotlib/colorbar.py", line 376, in update_ticks
ticks, ticklabels, offset_string = self._ticker()
File "/usr/local/lib/python3.5/site-packages/matplotlib/colorbar.py", line 615, in _ticker
formatter.set_locs(b)
File "/usr/local/lib/python3.5/site-packages/matplotlib/ticker.py", line 920, in set_locs
vmin = math.log(vmin) / math.log(b)
ValueError: math domain errorUnder matplotlib 1.5.3 the same script produces the following image:
Activity
efiring commentedon Dec 9, 2016
Thanks for the clear example. It looks like this is part of what I am trying to sort our right now, so this additional case is very helpful.
efiring commentedon Dec 9, 2016
If you omit the 'format' kwarg, the colorbar tick formatting works as expected.
ngoldbaum commentedon Dec 9, 2016
Hmm, I don't actually know why that was ever necessary. Looks like it was added to yt in 2014 when we added support for symlog scaling:
https://bitbucket.org/yt_analysis/yt/commits/06c5cb9b11174a8d24c6e9f30181c0f03a0da3d9
I think the ticks are still correct under both 1.5.3 and 2.0.0rc1 when I remove the
formatterkwarg, would your suggestion just be to remove it?efiring commentedon Dec 9, 2016
I added explicit SymlogNorm support, causing use of the LogFormatterSciNotation, in 2.0. In 1.5.3 it doesn't treat the SymlogNorm specially, so the labels are formatted as ordinary scalars and the ticks are linearly placed. So the format kwarg as you have it helps with 1.5.3. The problem is that with changes in 2.0, the formatter needs an additional kwarg, 'linthresh' (which did not exist in 1.5.3). I think I see how to make it work without that kwarg in a case like this, but without the improvements you get with 2.0 when you don't use the kwarg.
BUG: fix minpos handling and other log ticker problems
BUG: fix minpos handling and other log ticker problems
BUG: fix minpos handling and other log ticker problems