Colorbar with imshow(logNorm) shows unexpected minor ticks #8307

billtau · 2017-03-16T13:04:16Z

Bug report

Bug summary

When using colorbar with imshow(image, norm=LogNorm()), the produced colorbar automatically adds minorticks, and cannot be turned off with cbar.ax.minorticks_off(). Also the font of the tick label is not the same as the font set in matplotlibrc.

Code for reproduction

# This is modified from an example in matplotlib gallery.

import matplotlib.pyplot as plt
import numpy as np
from numpy import ma
from matplotlib import colors, ticker, cm
from matplotlib.mlab import bivariate_normal

N = 100
x = np.linspace(-3.0, 3.0, N)
y = np.linspace(-2.0, 2.0, N)

X, Y = np.meshgrid(x, y)

z = (bivariate_normal(X, Y, 0.1, 0.2, 1.0, 1.0)
     + 0.1 * bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0))

z = ma.masked_where(z <= 0, z)

fig, ax = plt.subplots()

from matplotlib.colors import LogNorm

cs = ax.imshow(z,norm=LogNorm())

cbar = fig.colorbar(cs)

cbar.ax.minorticks_off()

plt.show()

Actual outcome

Expected outcome

I would expect the colorbar to not have minorticks and to use the same font as other tick labels (I set font to be Arial in matplotlibrc).

Matplotlib version

Matplotlib version, Python version and Platform (Windows, OSX, Linux ...)

2.0.0_1, OSX

How did you install Matplotlib and Python (pip, anaconda, from source ...)
Macports

Edit by @afvincent: removed the unnecessary instructions coming from the bug report template.

QuLogic · 2017-03-17T00:05:41Z

It appears you also have some custom rcParam settings; the ticks should not be pointing inward. In any case, I can still reproduce myself.

These minor ticks are not supposed to be shown with so many major decades visible, right @efiring? @NelleV?

The font weirdness is probably #8017.

billtau · 2017-03-17T00:12:23Z

Oh, yes, I changed rcParam so that so ticks point inward. Sorry I didn't mention that. First time to report something here.

NelleV · 2017-03-17T00:41:28Z

Indeed, I would not have expected minor ticks to appear.

afvincent · 2017-10-23T23:21:17Z

FWIW this issue still present on Matplotlib 2.1.

If that was not obvious, please note that the problem does not come from ax.minorticks_off as the subticks are actually major ticks in the case of LogLocator. I did not find where is located the problem in LogLocator for the moment, but in the meantime a possible workaround is:

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.mlab import bivariate_normal
from matplotlib.ticker import LogLocator
from matplotlib.colors import LogNorm

N = 100
x = np.linspace(-3.0, 3.0, N)
y = np.linspace(-2.0, 2.0, N)
X, Y = np.meshgrid(x, y)

z = (bivariate_normal(X, Y, 0.1, 0.2, 1.0, 1.0)
     + 0.1 * bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0))
z = np.ma.masked_where(z <= 0, z)

fig, ax = plt.subplots()
cs = ax.imshow(z, norm=LogNorm())
cbar = fig.colorbar(cs)
# print(cbar.ax.yaxis.get_major_locator())  # => <matplotlib.ticker.FixedLocator object at 0x7f0691e57748> : beware, not a LogLocator instance!
cbar.ax.yaxis.set_major_locator(LogLocator())  # <- Why? See above.
cbar.set_ticks(cbar.ax.yaxis.get_major_locator().tick_values(z.min(), z.max()))
fig.show()

afvincent · 2017-10-24T01:57:43Z

Well, the handling of the tick locator seems a bit convoluted with colorbars, at least for my current understanding ^^... Nevertheless, here is a workaround that is bit simpler than my previous one (it was not obvious to me that one could simply pass a Locator instance to cbar.set_ticks...):

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.mlab import bivariate_normal
from matplotlib.ticker import LogLocator
from matplotlib.colors import LogNorm

N = 100
x = np.linspace(-3.0, 3.0, N)
y = np.linspace(-2.0, 2.0, N)
X, Y = np.meshgrid(x, y)

z = (bivariate_normal(X, Y, 0.1, 0.2, 1.0, 1.0)
     + 0.1 * bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0))
z = np.ma.masked_where(z <= 0, z)

fig, ax = plt.subplots()
cs = ax.imshow(z, norm=LogNorm())
cbar = fig.colorbar(cs)
# One-line workaround (NB: this parameter can also be directly passed to *fig.colorbar*)
cbar.set_ticks(LogLocator())  # defaults are more or less what one wants (otherwise adapt the parameters)

fig.show()

afvincent · 2017-10-24T03:21:10Z

Ok, if I understood it correctly, the “culprit” may be the following line in colorbar.ColorbarBase._ticker:

                    locator = ticker.LogLocator(subs='all')

that was introduced by 1fe5820.

Pinging @efiring, who is apparently our LogLocator & Colorbar expert :). TBH I am not sure that there is much that one can do about this “surprising behavior” (i.e. cbar.ax.minorticks_off having no effect because colorbar.ColorbarBase._ticker is called anyway in colorbar.ColorbarBase.update_ticks). Except maybe adding some proper example, something like:

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import LogLocator
from matplotlib.colors import LogNorm

# Dummy data
N = 101
x = np.linspace(-3.0, 3.0, N)[np.newaxis, :]
y = np.linspace(-1.0, 1.0, N)[:, np.newaxis]
z = (x.max() - np.abs(x))*(y.max() - np.abs(y))**2 + 1e-3

fig, (ax0, ax1) = plt.subplots(ncols=2, figsize=(9.6, 4.8))

for ax, title, ticks in [
        (ax0, "Default colorbar\nwith “minor” log ticks", None),
        (ax1, "Colorbar with\nonly base log ticks", LogLocator())
        ]:
    cs = ax.imshow(z, norm=LogNorm())
    ax.set_title(title)
    cbar = fig.colorbar(cs, ax=ax, ticks=ticks)

fig.show()

jklymak · 2017-10-24T05:04:45Z

ping @efiring who said he was looking at colorbar ticks...

efiring · 2017-10-24T05:26:45Z

Yes. Short of a major overhaul of the whole tick system, what is needed is to add full support for minor ticks to the colorbar. In reality this should be needed only for a log scale, but it probably makes more sense to put in all the machinery instead of special-casing log scales. Then colorbar ticking would be more similar to normal axis ticking. It will never be identical, though, because a colorbar simply is not a normal Axis in a normal Axes.

dstansby · 2019-05-04T21:12:34Z

This is working fine in 3.1; my guess is it was fixed by recent changes to how colorbar axes are handled.

tacaswell added this to the 2.1 (next point release) milestone Mar 17, 2017

tacaswell changed the title ~~Colorbar with imshow(logNorm) produce incorrect results~~ Colorbar with imshow(logNorm) shows unexpected minor ticks Mar 17, 2017

tacaswell modified the milestones: 2.1 (next point release), 2.1.1 (next bug fix release) Sep 24, 2017

tacaswell modified the milestones: 2.1.1 (next bug fix release), 2.2 (next feature release) Oct 9, 2017

tacaswell mentioned this issue Oct 24, 2017

expand log demo to a tutorial #8863

Closed

dstansby closed this as completed May 4, 2019

dstansby modified the milestones: needs sorting, v3.0.0 May 4, 2019

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Colorbar with imshow(logNorm) shows unexpected minor ticks #8307

Colorbar with imshow(logNorm) shows unexpected minor ticks #8307

billtau commented Mar 16, 2017 •

edited by afvincent

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Colorbar with imshow(logNorm) shows unexpected minor ticks #8307

Colorbar with imshow(logNorm) shows unexpected minor ticks #8307

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