ENH: adjustable colorbar ticks by jklymak · Pull Request #9903 · matplotlib/matplotlib

jklymak · 2017-12-01T19:09:34Z

PR Summary

This PR changes colorbar to draw from self.vmin to self.vmax instead of from 0 to 1 so that AutoTickLocator can work. Only modifies ticks if no boundaries are specified (i.e. contours).

See #9246

example:

import matplotlib.pyplot as plt
import matplotlib.colors as mcolors
import numpy as np

X = np.random.randn(32, 32)


fig, ax = plt.subplots(2, 2, figsize=(5, 5), tight_layout=True)
for nn, shrink in enumerate([1., 0.4]):
    for mm, log in enumerate([False, True]):
        if log:
            norm = mcolors.LogNorm()
            Y = 10**X
        else:
            norm = None
            Y = X
        pc = ax[nn, mm].pcolormesh(Y, norm=norm)
        ax[nn, mm].set_xticks([])
        ax[nn, mm].set_yticks([])
        fig.colorbar(pc, ax=ax[nn,mm], shrink=shrink, extend='both')

plt.show()
fig.savefig('ExampleCBOld.png')

before:

after:

PR Checklist

Test/get to work LogNorm
Has Pytest style unit tests
Code is PEP 8 compliant
Added an entry to doc/users/next_whats_new/ if major new feature (follow instructions in README.rst there)
Documented in doc/api/api_changes.rst if API changed in a backward-incompatible way

jklymak · 2017-12-01T20:24:22Z

OK, this failed enough tests that there are a bunch more edge cases I need to consider. Good thing there are tests. I'll probably re-do this from scratch and try to make it less invasive. I do think this is reasonable for 2.2, though, because I'll keep plugging away at it.

jklymak · 2017-12-02T16:30:05Z

This is redone, and much simpler now. 4 image files had to be changed...

jklymak · 2017-12-19T21:07:10Z

Ping @efiring LogNorm() now works. I'm too lazy to do SymLogNorm() (well actually I disapprove of that normalization as a valid thing to do to data), but someone could easily figure it out.

The diff looks worse than it is because I moved a bit of code around.

jklymak · 2017-12-19T21:15:17Z

lib/matplotlib/colorbar.py


        self._set_label()

+    def _get_ticker_locator_formatter(self):


Much of this was jut factored out of _ticker() But note the new locators for LogNorm and the fallback...

dstansby

Some questions/comments, looks like this is good overall though

dstansby · 2017-12-24T11:54:26Z

lib/matplotlib/colorbar.py

+        This locator is just a `.MaxNLocator` except the min and max are
+        clipped by the norm's min and max (i.e. vmin/vmax from the
+        image/pcolor/contour object).  This is necessary so ticks don't
+        extrude into the "extend regions".


Shouldn't the docstring line up with the left of the quote marks?

dstansby · 2017-12-24T11:55:12Z

lib/matplotlib/colorbar.py

+        extrude into the "extend regions".
+    """
+
+    def __init__(self, colorbar, *args, **kwargs):


Why are there args and kwargs here if they're not used? Can this also get a docstring (just for the colorbar parameter is probably fine)

dstansby · 2017-12-24T11:56:11Z

lib/matplotlib/colorbar.py

+    extrude into the "extend regions".
+
+    """
+    def __init__(self, colorbar, *args, **kwargs):


Same as above comment on __init__

dstansby · 2017-12-24T11:56:57Z

lib/matplotlib/colorbar.py

        self._config_axes(X, Y)
        if self.filled:
            self._add_solids(X, Y, C)
+        # self._set_view_limits()


Is this old debug code that needs to be removed?

dstansby · 2017-12-24T11:58:18Z

lib/matplotlib/colorbar.py

+            if (isinstance(self.norm, colors.LogNorm)
+                    and self._use_adjustable()):
+                ax.set_xscale('log')
+                ax.set_yscale('log')


and only the yscale be log here?

They both need to be log to make the aspect kwarg work properly (... or we could do a bunch of math and make the X values make the aspect ratio right.)

dstansby · 2017-12-24T11:58:50Z

lib/matplotlib/colorbar.py


        self._set_label()

+    def _get_ticker_locator_formatter(self):


This method could do with a quick comment underneath to explain what it does.

dstansby · 2017-12-24T11:59:46Z

lib/matplotlib/colorbar.py

-            else:
-                b = self._boundaries[self._inside]
-                locator = ticker.FixedLocator(b, nbins=10)
+        # locator, formatter = _get_ticker_locator_formatter()


This commented out line can go

jklymak · 2018-01-10T03:39:11Z

Pushed to 3.0 as this isn't urgent. But I think it'd be easy to put in 2.2 if someone wants to dive in and re-milestone...

jklymak · 2018-02-04T18:15:48Z

rebased

jklymak · 2018-02-04T18:18:17Z

@dstansby I think I addressed all your concerns.
@efiring requesting a review from you (though no rush) as this is your bailiwick...

Old review

efiring · 2018-02-05T19:43:04Z

The before-and-after comparison looks great, but tests seem to be failing now.

jklymak · 2018-02-05T19:48:04Z

Yeah, its just the streamplot image test at 0.036 tolerance. I'll try to track it down. It passes on my machine and I took the text out so it can't be freetype. Grrrr.

skotaro · 2018-02-20T11:37:42Z

I'm not sure that this is the right place to tell this, but I recently wrote a detailed instruction on colorbar in matplotlib which might contribute for improving tutorials about colorbar.
https://qiita.com/skotaro/items/01d66a8c9902a766a2c0
It's only in Japanese for the moment but I think you can get the ideas from figures and sample codes. Main topics are 1. Anatomy of a colorbar, 2. Putting a colorbar at the right place with the right size, and 3. Changing ticker into log scale nicely. It's not comprehensive but I think it still helps users puzzled by colorbar.

After writing it, fortunately or not, I found this PR which seems to change colorbar's behavior significantly (no pseudo minor ticks, no normalization of vmin/vmax to 0/1, for example). Actually these modified behaviors are parts of the main topics in my instruction. Then I'm wondering whether I should translate the introduction as it is into English and make a PR to improve docs for the current behavior of colorbar (about cbar.ticker, especially), or I should wait for this PR to be implemented in, say, next rc version and revise the instruction to catch up the new behaviors. What do you think?

jklymak · 2018-02-20T14:45:25Z

@skotaro Sounds like we had some similar difficulties with colorbars. I will push in the near future for this PR to get in, but it won’t be part of the distribution until 3.0 (July/Aug).

You may want to checkout constrained layout in 2.2Rc1 for easier colorbar placement. That doesn’t preclude a tutorial that explains how to fix things manually, but I’d suggest such a tutorial should at least reference the automated methods.

efiring · 2018-03-18T01:34:10Z

The problem with the doc build is that after the merge, the sphinx conf.py exclude_patterns list is out of sync with the location where you are putting your users/whats_new file.
It looks like this is a bug in master: there are directories users/prev_whats_new and users/next_whats_new, but exclude_patterns = ['api/api_changes/*', 'users/whats_new/*'].

jklymak · 2018-03-18T04:59:41Z

Somehow the doc build didn't like the name I had for the whats-new file. Works fine now. 🤷‍♂️

efiring · 2018-03-18T07:55:35Z

lib/matplotlib/colorbar.py

-            ax.xaxis.get_major_formatter().set_offset_string(offset_string)
+            _log.debug('Using fixed locator on colorbar')
+            ticks, ticklabels, offset_string = self._ticker(locator, formatter)
+            if self.orientation == 'vertical':


You can use the long_axis, short_axis here, too. Initialize them prior to the _use_auto_colorbar_locator check.
Instead of ax.set_yticklabels you can use the equivalent short_axis.set_ticklabels, etc.

anntzer · 2018-03-19T19:25:34Z

doc/api/api_changes/2017-12-01-JMK.rst

+
+Colorbar ticks now adjust for the size of the colorbar if the
+colorbar is made from a mappable that is not a contour or
+doesn't have  a BoundaryNorm, or boundaries are not specified.


extra space

anntzer · 2018-03-19T19:26:13Z

lib/matplotlib/colorbar.py

+
+    def __init__(self, colorbar):
+        """
+        _ColorbarAutoLocator(colorbar)


Is there a particular need to include the signature?

jklymak · 2018-03-19T19:31:18Z

lib/matplotlib/colorbar.py

+            if type(self.norm) == colors.LogNorm:
+                long_axis.set_minor_locator(_ColorbarLogLocator(self,
+                            base=10., subs='auto'))
+                long_axis.set_minor_formatter(ticker.NullFormatter())


Need to check that some ticks are labelled...

Fixed. LogLocator works fine here.

afvincent · 2018-03-21T21:06:38Z

@jklymak Is there an obvious reason why the ticks of the colorbar in the bottom right panel are not symmetrical (in log space) around 1 (e.g. [1e3, 1e0, 1e-3], instead of [1e2, 1e-1]), while the old one were “quite” symmetrical?

jklymak · 2018-03-21T21:09:08Z

@afvincent because the LogLocator only returned two tick marks as being able to fit and it chose those? Its just using the default LogLocator - i.e. if you had a normal yaxis that size, those are the ticks you'd get.

anntzer · 2018-10-12T17:11:28Z

@skotaro Are you still interested in including your (extensive!) colorbar tutorial into the mpl docs? Even if it needs to be updated following this PR and/or to take constrained_layout into account, feel free to open an early issue/PR to track the work.

jklymak · 2018-10-12T17:32:20Z

@anntzer @skotaro please note the start of this at https://matplotlib.org/devdocs/gallery/subplots_axes_and_figures/colorbar_placement.html#sphx-glr-gallery-subplots-axes-and-figures-colorbar-placement-py

tacaswell added this to the v2.2 milestone Dec 1, 2017

jklymak force-pushed the enh-colorbar-ticks branch 2 times, most recently from 9d1146d to 5c48c10 Compare December 2, 2017 06:48

jklymak changed the title ~~WIP: ENH: adjustable colorbar ticks~~ ENH: adjustable colorbar ticks Dec 2, 2017

jklymak force-pushed the enh-colorbar-ticks branch from 5c48c10 to 1d4160c Compare December 2, 2017 21:58

jklymak force-pushed the enh-colorbar-ticks branch from 338c0a1 to a31cadd Compare December 19, 2017 20:55

jklymak commented Dec 19, 2017

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jklymak mentioned this pull request Dec 20, 2017

Blank colorbars for high dynamic range LogNorm imshow plots #10051

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dstansby previously requested changes Dec 24, 2017

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jklymak force-pushed the enh-colorbar-ticks branch from 452e401 to 5972691 Compare December 24, 2017 18:00

dstansby self-assigned this Dec 24, 2017

jklymak requested review from efiring and removed request for efiring January 10, 2018 03:38

jklymak modified the milestones: v2.2, v3.0 Jan 10, 2018

jklymak mentioned this pull request Feb 4, 2018

[ENH] Unit support for ScalarMappables #7383

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jklymak force-pushed the enh-colorbar-ticks branch from 5972691 to 402b4d3 Compare February 4, 2018 18:15

jklymak requested a review from efiring February 4, 2018 18:18

jklymak mentioned this pull request Feb 19, 2018

FIX: No rcparam minor ticks in colorbar #8358 #10530

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jklymak force-pushed the enh-colorbar-ticks branch 5 times, most recently from 651d609 to 2c33640 Compare March 18, 2018 04:58

efiring reviewed Mar 18, 2018

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jklymak force-pushed the enh-colorbar-ticks branch from 2c33640 to 252ef97 Compare March 18, 2018 15:23

ENH: colorbar ticks adjustable to colorbar size

52e5d81

jklymak force-pushed the enh-colorbar-ticks branch from 6bdc427 to 52e5d81 Compare March 18, 2018 16:01

efiring approved these changes Mar 18, 2018

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anntzer reviewed Mar 19, 2018

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jklymak commented Mar 19, 2018

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FIX: add loglocator for minor colorbar

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jklymak added the status: needs review label Mar 19, 2018

dopplershift approved these changes Mar 22, 2018

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dopplershift merged commit dbfc79c into matplotlib:master Mar 22, 2018

Dih5 mentioned this pull request Mar 23, 2018

Minor ticks on log-scale colorbar are not cleared #8358

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QuLogic removed the status: needs review label Mar 23, 2018

This was referenced Sep 18, 2018

Incorrect placement of Colorbar ticks using LogNorm #12155

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FIX: colorbar re-check norm before draw for autolabels #12159

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anntzer mentioned this pull request Oct 12, 2018

inconsistent colorbar tick labels for LogNorm #12488

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ImportanceOfBeingErnest mentioned this pull request Oct 17, 2018

colorbar resizes in animation #12550

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ImportanceOfBeingErnest mentioned this pull request Oct 31, 2018

using AxesImage.set_clim() shrinks the colorbar #12682

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