Combine Axes.{lines,images,collections,patches,text,tables} into single list #18216

QuLogic · 2020-08-11T04:00:19Z

PR Summary

This mostly fixes #17247; combining artists into a single list has several benefits to draw ordering. You can see some of the effects in the changed test images. For simplification, the default labels for artists will now be numbered by overall children count, instead of a type-specific count.

There are a few remaining lists, but they require additional work first, or can be ignored:

Axes.artists; this would fix inconsistencies in bxp, but breaks Colorbar as it relies on Axes.artists drawing last to produce its outline.
Axes.collections; changes streamplot slightly, and errorbar is now correctly drawn as a group. See commit message for exact details.
Axes.containers; appears to not be used in the draw tree, ~~or anything at all, really?~~ Maybe for legends only.
Axes.images
Axes.lines
Axes.patches
Axes.tables
Axes.texts

PR Checklist

Has Pytest style unit tests
Code is Flake 8 compliant
[n/a] New features are documented, with examples if plot related
Documentation is sphinx and numpydoc compliant
[n/a] Added an entry to doc/users/next_whats_new/ if major new feature (follow instructions in README.rst there)
Documented in doc/api/next_api_changes/* if API changed in a backward-incompatible way

dopplershift · 2020-08-11T05:21:54Z

😱

For future reviewers, that line count is only because of changes to a couple of SVG files.

tacaswell · 2020-08-12T19:46:23Z

I am 100% sure that this will break people who are relying on ax.lines.clear() to remove all of the lines. I suspect that if we are going to go this route we are going to have to return a list sub-class that warns a lot if you mutate it, but forwards those changes through as the opening pass. We can then see much much push back we get to either move to read-only / remove it.

I'm also a bit worried about relying on type checking to re-construct the old lists, but the docs strings do name the types so I think my worries would be placated by adding a warning to those methods if the artist is of a type that would not then show up in the list.

jklymak · 2020-08-13T15:00:32Z

I am 100% sure that this will break people who are relying on ax.lines.clear()

So, should these lists ever have been made public in the first place? ax.lines.clear() is not going to delete the lines, it will just mean they are never drawn. Not quite sure how we move them to being private or immutable without causing a lot of breakage.

QuLogic · 2020-08-14T05:52:20Z

ax.lines.clear() is not going to delete the lines,

It is pretty close though, since Line2D._remove_method would be ax.lines.remove, and the remaining stuff in Artist.remove is mostly about staleness:

matplotlib/lib/matplotlib/artist.py

Lines 163 to 180 in d9fd7f9

    
           if self._remove_method is not None: 
        
               self._remove_method(self) 
        
               # clear stale callback 
        
               self.stale_callback = None 
        
               _ax_flag = False 
        
               if hasattr(self, 'axes') and self.axes: 
        
                   # remove from the mouse hit list 
        
                   self.axes._mouseover_set.discard(self) 
        
                   # mark the axes as stale 
        
                   self.axes.stale = True 
        
                   # decouple the artist from the axes 
        
                   self.axes = None 
        
                   _ax_flag = True 
        
               if self.figure: 
        
                   self.figure = None 
        
                   if not _ax_flag: 
        
                       self.figure = True

QuLogic · 2020-08-25T03:47:33Z

Now that #18320 is in, I can push the last step of merging Axes.artists. I'll work on the fancy list thing now.

QuLogic · 2020-08-25T05:13:15Z

Sigh, tests are fine, but doc examples trigger both self.blah.remove and self.blah.append.

QuLogic · 2020-08-27T02:52:25Z

I believe this is now fully working; several tests required small tweaks since things are now drawn more correctly. See the individual commit messages for further details.

dopplershift

This looks pretty good to me. In addition to the question below: I think I actually like the old boxplot behavior of drawing the box edges over the whiskers slightly better. No way to easily preserve?

lib/matplotlib/axes/_base.py

QuLogic · 2020-08-28T06:49:55Z

I think I actually like the old boxplot behavior of drawing the box edges over the whiskers slightly better. No way to easily preserve?

Much like the tests, we 'just' have to add the box edges to the plot later to do that. But note that this will mean that when using patch_artist=False (the default), the result will change (so there would be test result changes either way).

lib/matplotlib/axes/_base.py

jklymak · 2020-08-28T16:17:05Z

lib/matplotlib/axes/_base.py

-            # these attributes don't even exist yet, in which case
+            # ``hasattr(ax, "_children")`` is necessary because this can be
+            # called very early in the axes init process (e.g., for twin axes)
+            # when these attributes don't even exist yet, in which case
            # `get_children` would raise an AttributeError.
            if self._xmargin and scalex and self._autoscaleXon:
                x_stickies = np.sort(np.concatenate([


I find this 5 lines of code completely incomprehensible. having two for statements and an if statement in a list comprehension is too cute in my opinion.

tacaswell · 2020-09-23T19:13:52Z

We should note that doing ax.lines = [...] currently works (and I can imaging an defend-able use case for flipping between two sets of lines), however I do not think that this is worth the machinery to make work. I'm inclined to document this as something that is broken (and then re-address shimming it if it causes significant user pain).

lib/matplotlib/axes/_base.py

lib/matplotlib/axes/_axes.py

timhoffm · 2020-10-10T10:25:03Z

lib/mpl_toolkits/mplot3d/axes3d.py

+            _tight = self._tight
+            if not _tight:
+                # if image data only just use the datalim
+                for artist in self._children:
+                    if isinstance(artist, mimage.AxesImage):
+                        _tight = True
+                    elif isinstance(artist, (mlines.Line2D, mpatches.Patch)):
+                        _tight = False
+                        break


Suggested change

_tight = self._tight

if not _tight:

# if image data only just use the datalim

for artist in self._children:

if isinstance(artist, mimage.AxesImage):

_tight = True

elif isinstance(artist, (mlines.Line2D, mpatches.Patch)):

_tight = False

break

has_image = any(isinstance(c, mimage.AxesImage)

for c in self._children)

has_line_or_patch = any(isinstance(c, (mlines.Line2D, mpatches.Patch))

for c in self._children)

_tight = self._tight or (has_image and not has_line_or_patch)

Trying to avoid iterating self._children twice here.

Why? Optimization? - I don't think that's relevant, 'cause we usually don't have thousands of Artists. And if so, iterating twice through them is probably the least of our problems. Moreover, if performance is a real concern, have you profiled this? List comprehensions are better optimized in Python than equivalent for loops, so I wouldn't even know which solution is faster.

Given the early exit condition of any the performance should be something measured/profiled. In the absence of that, we should go with clarity. It's not clear to me which of those that is.

If I've done this correctly, I'm pretty certain that the single loop is faster than the comprehensions, whether the first condition exits early, the second does, or neither:

import timeit class AxesImage: pass class Line2D: pass class Patch: pass class Other: pass def loop(_tight, children): if not _tight: # if image data only just use the datalim for artist in children: if isinstance(artist, AxesImage): _tight = True elif isinstance(artist, (Line2D, Patch)): _tight = False break return _tight def comprehension(_tight, children): has_image = any(isinstance(c, AxesImage) for c in children) has_line_or_patch = any(isinstance(c, (Line2D, Patch)) for c in children) tight = _tight or (has_image and not has_line_or_patch) return tight setup = 'from __main__ import AxesImage, Line2D, Patch, Other, children' for N in [10, 100, 1000]: print('N =', N) children = [Other()] * N print('No early exit') print('loop', timeit.timeit('loop(False, children)', setup=f'{setup}, loop', number=1000000)) print('comprehension', timeit.timeit('comprehension(False, children)', setup=f'{setup}, comprehension', number=1000000)) children = [Other()] * N children[1] = AxesImage() print('First loop early exit') print('loop', timeit.timeit('loop(False, children)', setup=f'{setup}, loop', number=1000000)) print('comprehension', timeit.timeit('comprehension(False, children)', setup=f'{setup}, comprehension', number=1000000)) children = [Other()] * N children[-2] = AxesImage() print('First loop late exit') print('loop', timeit.timeit('loop(False, children)', setup=f'{setup}, loop', number=1000000)) print('comprehension', timeit.timeit('comprehension(False, children)', setup=f'{setup}, comprehension', number=1000000)) children = [Other()] * N children[1] = Line2D() print('Second loop early exit') print('loop', timeit.timeit('loop(False, children)', setup=f'{setup}, loop', number=1000000)) print('comprehension', timeit.timeit('comprehension(False, children)', setup=f'{setup}, comprehension', number=1000000)) children = [Other()] * N children[-2] = Line2D() print('Second loop late exit') print('loop', timeit.timeit('loop(False, children)', setup=f'{setup}, loop', number=1000000)) print('comprehension', timeit.timeit('comprehension(False, children)', setup=f'{setup}, comprehension', number=1000000)) print() print()

I don't expect people to have 1000 artists, but the order of 10-100 might be possible in 3D. Not having benchmarked the rest of the 3D code though, I don't know if this difference is particularly significant.

lib/matplotlib/axes/_base.py

doc/api/next_api_changes/behavior/18216-ES.rst

doc/api/next_api_changes/deprecations/18216-ES.rst

lib/matplotlib/tests/test_axes.py

lib/mpl_toolkits/mplot3d/axes3d.py

timhoffm · 2021-04-01T21:23:37Z

lib/matplotlib/axes/_base.py

+
+    @property
+    def collections(self):
+        return self.ArtistList(self, 'collections', 'add_collection',


Wouldn't it be simpler to warn here and return a plain list compared to defining the ArtistList class?

That's how it used to be before #18216 (comment)

Fair enough.

The lines can still be accessed via a read-only property.

The patches can still be accessed via a read-only property, but now are combined with lines for sorting and overall drawing purposes.

The texts can still be accessed via a read-only property, but now are combined with lines and patches for sorting and drawing purposes.

The tables can still be accessed via a read-only property, but now are combined with lines, patches and texts for sorting and drawing purposes.

The images can still be accessed via a read-only property, but now are combined with lines, patches, tables and texts for sorting and drawing purposes.

The collections can still be accessed via a read-only property, but now are combined with images, lines, patches, tables and texts for sorting and drawing purposes. There was a quite a bit more fallout from this one: * `streamplot` had to add the arrows after the line collection, so they would remain on top. Because `FancyArrowPatch` is created in display coordinates, this meant that their limits changed slightly, as adding the line collection would have re-adjusted the `Axes.transData`. * The `test_pre_transform_plotting` image needed to be regenerated because of the above limit change. I took this opportunity to clean up some of the previous keep-image-the-same hacks. * The `test_arrow_contains_point` test image now has 'contained' scatter points correctly over the arrows. * Tests in `test_patches.py` needed to be re-ordered slightly as they were checking alpha between collections and non-collection artists. * The `test_fancy` legend images needed to be regenerated because errorbars are correctly drawn as a group now.

Note, that the legend `test_fancy` test needed an ordering change because legends handles are no longer grouped by type.

The artists can still be accessed via a read-only property, but now are combined with collections, images, lines, patches, tables and texts for sorting and drawing purposes. Additionally, anything added using `Axes.add_artist` will now appear in the correct type sublist, and may not appear in `Axes.artists` if it matches any of the other lists. There are two test image changes, both of which have to do with `bxp` and its `patch_artist=True` option. This uses a `Patch` with `Axes.add_artist` instead of `Axes.plot` and so used to appear in different order. This change now makes `patch_artist=True` and `path_artist=False` order the same way, since there's no special grouping.

lib/matplotlib/tests/test_transforms.py

tacaswell · 2021-04-02T23:22:05Z

anyone can merge on CI green.

With matplotlib#18216, the order that artists are added to an Axes is their canonical order. The dialog should not be sorting them in some other manner. Additionally, this fixes a bug in that `apply_callback` indexes back to the original list, which means that changes will be made to the *wrong* artist if sorting actually occurred. It also makes the legend almost entirely wrong as well. See https://discourse.matplotlib.org/t/bug-on-re-generate-automatic-legend-of-matplotlib-figure-property/22511

@jklymak

_axstack whitespace _parent._axstack move clear functions into figurebase clear subfigures first Clear child subfigures tests move property back to init changelog reduce changelog TEST: partial subfig clearing Clear all children subfigs in parent Clear toolbars only in Figure Restore whitespace on :684 flake8 old comment TITLE UNDERLINE Expire mathttext-related deprecations Fixed review comments and a few more removals Use PNG image as the icon for Tk plot windows Fix loading user-defined icons for Tk toolbar Co-Authored-By: Elliott Sales de Andrade <quantum.analyst@gmail.com> Prevent tooltips from overlapping buttons in NavigationToolbar2Tk Update doc/api/next_api_changes/behavior/22135-JSS3.rst Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com> Fix loading user-defined icons for Qt plot window Update both zoom/pan states on wx when triggering from keyboard. 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Clean up 3d plot box_aspect zooming linting Cleanup Make zoom and dist private attrs Deprecate Axes3D.dist Deprecate Axes3D.dist DOC: Fix upstream URL for merge in CircleCI DOC: Add hatch API to reference DOC: Document default cap styles - remove '(default)' from cap style demo as this is only true for Line2D and the default rcParameters - document default cap styles for Line2D and Patch in their cap style setters - document default cap style for GraphicsContextBase in the same way as it's already done for joinstyle Factor out underline-thickness lookups in mathtext. Just adding a small helper function. Fix merge Update _formlayout.py Bump minimum NumPy to 1.19 Fix name typo in API changes DOC: git:// is deprecated. See https://github.blog/2021-09-01-improving-git-protocol-security-github/ Today is a brownout day. I removed the sentence that git:// is RO and https:// is RW as you soon won't be able to use git:// Personally I use https:// as RO and ssh:// as RW, but I understand it might not be convenient on windows. Stop sorting artists in Figure Options dialog With matplotlib#18216, the order that artists are added to an Axes is their canonical order. The dialog should not be sorting them in some other manner. Additionally, this fixes a bug in that `apply_callback` indexes back to the original list, which means that changes will be made to the *wrong* artist if sorting actually occurred. It also makes the legend almost entirely wrong as well. See https://discourse.matplotlib.org/t/bug-on-re-generate-automatic-legend-of-matplotlib-figure-property/22511 Document ArtistList DOC: Document default join style in the same way as the default cap styles. Jointly track x and y in PolygonSelector. It's easier to track them in a single list. 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This prints out human-readable error messages for failures. As an example, `FT2Font("setup.py")` now raises ``` RuntimeError: In FT2Font: Can not load face (unknown file format; error code 0x2) ``` Ensure that all toolbar (old/new) subclasses can be init'ed consistently i.e. with the same signature: with `canvas` as sole arg for the old-style toolbars, with `toolmanager` as sole arg for the new ones. Subclasses that explicitly support setting a parent widget keep that support (except for gtk, which stashed that in the `.win` attribute but never used it), but that argument is always optional now; the default is the canvas' parent. The goal is to later replace all _get_toolbar implementations by a simple call (always with the same signature (dependent on the value of rcParams["toolbar"])) to the correct class in the FigureManagerBase constructor. DOC: More capitalization of Axes In line with matplotlib#18726. Triggered by matplotlib#22242. Started deprecating afm, fontconfig_pattern, and type1font Recreated deprecated files and changed references DOC: add dropdown DOC: add dropdown Fix topbar DOC: Add all the releases Just last point releases before 3.0 DOC: update release_guide DOC: rename versions [skip azp] [skip appveyor] [skip actions] BLD: pin sphinx data theme [skip actions] [skip appveyor] [skip azp] Add some tests for minspan{x,y} in RectangleSelector Skip tests on the -doc branches DOC: fix version switcher json [skip actions] [skip appveyor] [skip azp] DOC: fix version switcher [skip actions] [skip appveyor] [skip azp] FIX Fix Qt enum access. This was missed in the global fixing of enums for PyQt6 (now using _enum everywhere). To trigger, try to interactively save a figure but input an invalid format, e.g. "foo.bar". MNT: deprecate filled parameter to colorbar The *filled* kwarg doesn't directly do anything and filling is completely controlled by the mappable. OTOH, maybe we want to reinstate the ability of *filled* to fill contours? Deprecate colorbar.draw_all. Merge main and "other" params docs in colorbar.make_axes. `colorbar.make_axes` (and `make_axes_gridspec`) are low-level enough that it's not worth the complexity in docstring interpolation to split out "main" parameters and "other" parameters, when the docstring of the more commonly used `plt.colorbar` smashes them together. (Also, `pad` is not really much more low-level than `shrink` or `aspect`...) Numpydocify _colormap_kw_doc and use it in Colorbar too. 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I had something like `for i in range(n): plot(..., f"oC{i}")` which works for n up to 10, but for greater values one gets "oC10" which is not supported (which is reasonable, as some single-digit strings are actually *marker* abbreviations); mentioning the full format string in the error message ("Unrecognized character 0 in format string 'oC10'") makes it clearer. FIX: bury import of matplotlib.font_manager We need to ensure that the sub-module matplotlib.font_manager is imported when it is used in SclarFormater, however if we import it at the top level we will get circular imports. closes matplotlib#22305 In mpl_toolkits, use the same floating point slop as for standard ticks. Standard ticks use _interval_contains_close (in Axis._update_ticks); do the same in mpl_toolkits and deprecate the custom slops delta1, delta2 (if such knobs are really needed, we should try to have the same API in the main library anyways). FIX: use window_extent instead Add set_cursor method to FigureCanvasTk Don't warn on grid removal deprecation is grid is hidden Fixes matplotlib#21723. See matplotlib#21723 (comment) for a full desciption of motivation and edge cases. Modify example for x-axis tick labels at the top Primarily describe how to do this for a single Axes (using `tick_params`). Only mention the `rcParams` in a note. Globally changing `rcParams` is usually not a good idea and should not be demonstrated. The whole topic of `rcParams` (global, context, matplotlibrc) is too long to be discussed here and not the focus of the example. Remove Axes sublist modification from docs Make bar of pie example more explicit ... by saving and using the results from Axes method calls. Also, replace the colour palette in the bar chart. Respect `position` argument in Tk toolmanager Set focus properly to ensure mouse events get delivered to Tk canvas Rework/fix Text layout cache. 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The motivation is also to in the future let the renderer have better control on cache invalidation (with a yet-to-be-added renderer method), e.g. multiple instances of the same renderer cache could share the same layout info. Rename outdated seaborn styles. They are kept available under a versioned name for backcompat. dangling clf Silently discard blits if bbox is outside canvas Custom cap widths in box and whisker plots in bxp() and boxplot() Add pre-commit config and dev instructions Update pre-commit hooks rst format Disable autofixes on PRs Unless manually triggered. 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QuLogic added the Maintenance label Aug 11, 2020

QuLogic added this to the v3.4.0 milestone Aug 11, 2020

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QuLogic marked this pull request as ready for review August 27, 2020 02:36

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dopplershift mentioned this pull request Sep 30, 2020

Upgrading from 2.1.1 to 3.3.2 Causes plot3 lines to be behind plot_surface objects #18612

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tacaswell mentioned this pull request Oct 2, 2020

Errorbar lines are not present in the Qt NavToolBar --> curves tab #18631

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QuLogic force-pushed the combine-Axes-children branch from 8308603 to b2e3f7e Compare October 10, 2020 04:15

timhoffm reviewed Oct 10, 2020

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anntzer mentioned this pull request Oct 14, 2020

Use ax.add_image rather than ax.images.append in NonUniformImage example #18729

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7 tasks

QuLogic force-pushed the combine-Axes-children branch from b2e3f7e to 27c7d53 Compare October 17, 2020 03:28

QuLogic force-pushed the combine-Axes-children branch from 27c7d53 to 9da646a Compare December 19, 2020 06:05

timhoffm reviewed Apr 1, 2021

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QuLogic added 12 commits April 1, 2021 19:12

Move Axes.lines into a hidden children attribute.

af6fce7

The lines can still be accessed via a read-only property.

Move Axes.patches into hidden children attribute.

20198b8

The patches can still be accessed via a read-only property, but now are combined with lines for sorting and overall drawing purposes.

Move Axes.texts into hidden children attribute.

174a5c9

The texts can still be accessed via a read-only property, but now are combined with lines and patches for sorting and drawing purposes.

Move Axes.tables into hidden children attribute.

71f5775

The tables can still be accessed via a read-only property, but now are combined with lines, patches and texts for sorting and drawing purposes.

Move Axes.images into hidden children attribute.

278de8f

The images can still be accessed via a read-only property, but now are combined with lines, patches, tables and texts for sorting and drawing purposes.

Remove redundant iteration through Axes._children.

94da8c9

Note, that the legend `test_fancy` test needed an ordering change because legends handles are no longer grouped by type.

Add warn-on-modification wrappers around Axes.* lists.

0135146

Deprecate passing incorrect types to Axes.add_*.

4aa99c3

Document API changes for Axes sublists.

669cb82

Add __iter__ implementation to ArtistList.

8737ac3

QuLogic force-pushed the combine-Axes-children branch from 1edcfe8 to 8737ac3 Compare April 1, 2021 23:23

timhoffm approved these changes Apr 2, 2021

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tacaswell reviewed Apr 2, 2021

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lib/matplotlib/tests/test_transforms.py Show resolved Hide resolved

tacaswell approved these changes Apr 2, 2021

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tacaswell merged commit 4085fc7 into matplotlib:master Apr 2, 2021

tacaswell mentioned this pull request Apr 3, 2021

zorder is not respected by all parts of errorbar #1622

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QuLogic deleted the combine-Axes-children branch April 5, 2021 21:13

QuLogic mentioned this pull request Apr 5, 2021

Fix errobar order #17231

Closed

6 tasks

tacaswell mentioned this pull request Apr 6, 2021

errorbar doesn't follow plot order #17139

Closed

This was referenced Apr 7, 2021

Include length in ArtistList repr. #19889

Merged

Should ArtistList implement __add__? #19890

Closed

QuLogic mentioned this pull request Sep 2, 2021

Test failures with Matplotlib 3.5.0b1 jswhit/pygrib#188

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QuLogic mentioned this pull request Jan 12, 2022

Stop sorting artists in Figure Options dialog #22208

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1 task

ksunden mentioned this pull request Feb 14, 2023

Matplotlib 3.7.0 breaks circleci and refguide checks in Numpy 1.24.x numpy/numpy#23209

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Combine Axes.{lines,images,collections,patches,text,tables} into single list #18216

Combine Axes.{lines,images,collections,patches,text,tables} into single list #18216

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tacaswell commented Apr 2, 2021

Combine Axes.{lines,images,collections,patches,text,tables} into single list #18216

Combine Axes.{lines,images,collections,patches,text,tables} into single list #18216

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