#27865 closed defect (fixed)
Refactor GraphicsArray, fixing various issues
Reported by:  egourgoulhon  Owned by:  

Priority:  major  Milestone:  sage8.9 
Component:  graphics  Keywords:  graphics_array, matplotlib 
Cc:  kcrisman, chapoton, dkrenn, jdemeyer, embray  Merged in:  
Authors:  Eric Gourgoulhon  Reviewers:  Frédéric Chapoton 
Report Upstream:  N/A  Work issues:  
Branch:  36c0f17 (Commits, GitHub, GitLab)  Commit:  36c0f178353017ac12573ff038c40ed55a24ba2d 
Dependencies:  Stopgaps: 
Description (last modified by )
This ticket makes GraphicsArray
derive from a new class, MultiGraphics
, which is more generic (arbitrary positions of graphics objects on a canvas) and paves the way towards graphics insets in #27866.
GraphicsArray
is now endowed with a matplotlib()
function (inheritated from MultiGraphics
). This fixes the issues reported in #10466, #10657, #11160 and #12591 (see :comment:3 and comment:5 below for a summary).
Moreover, this simplifies sphinx_plot()
(defined in src/doc/common/conf.py
), avoiding code duplication.
Beside introducing matplotlib()
at the graphics array level, two bugs had to be corrected in Graphics.matplotlib()
:
_set_scale
was called on the whole figure, while it should be called on the current subplottick_params
was called onfigure.get_axes()[0]
, i.e. the first subplot of the figure, while it should be called on the current subplot.
The documentation of Graphics.matplotlib()
is also improved in this ticket.
Another bug has been corrected in Graphics.save()
: contrary to what was claimed in the documentation g.save("filename")
with "filename"
having no extension did not save in a sobj
file but yielded to an error.
Another modification is the introduction of the helper function _parse_figsize()
in src/sage/plot/graphics.py
to avoid code duplication: it is used in Graphics.matplotlib()
, MultiGraphics.matplotlib()
and sphinx_plot()
.
Since the file src/sage/plot/graphics.py
was already quite long (3736 lines!), the class GraphicsArray
was moved to the new file src/sage/plot/multigraphics.py
, which contains the definition of the base class MultiGraphics
. This makes things more consistent:
src/sage/plot/graphics.py
: onlyGraphics
objectssrc/sage/plot/multigraphics.py
: onlyMultiGraphics
objects
Besides the bugs reported in the tickets #10466, #10657, #11160 and #12591, this ticket fixes two other bugs:
 if any plot in the array had a log scale, the latter was erroneously applied to the first plot of the array
 the computation of
nrows
andncols
in the functiongraphics_array()
(defined insrc/sage/plot/plot.py
) yielded unnecessary large numbers in certain cases. For instance we have in Sage 8.7:sage: graphics_array([plot(sin)]*4, ncols=4) Graphics Array of size 2 x 4
with the second raw that is entirely blank. With the code in this ticket the output isGraphics Array of size 1 x 4
This fix explains the change of doctest outputs insrc/sage/categories/finite_posets.py
andsrc/sage/repl/rich_output/pretty_print.py
A preview (including the functionalities introduced in #27866) is available here.
Attachments (2)
Change History (24)
comment:1 Changed 4 years ago by
Authors:  → Eric Gourgoulhon 

Branch:  → public/graphics/multi_graphics 
Commit:  → 3a5ef55af4d104c840107f46abbcba90fa401a18 
comment:2 Changed 4 years ago by
Description:  modified (diff) 

Changed 4 years ago by
Attachment:  graphics_array_bug.png added 

Changed 4 years ago by
Attachment:  graphics_array_ok.png added 

comment:3 Changed 4 years ago by
Here is an example summarizing some the GraphicsArray
issues. In Sage 8.7, the following code:
sage: g1 = plot(sin(x^2), (x, 0, 6), ....: axes_labels=[r'$\theta$', r'$\sin(\theta^2)$'], fontsize=14) sage: g2 = circle((0,0), 1, fill=True, color='red', alpha=0.4, axes=False) \ ....: + text("This is a disk", (0.9, 1.1), color='red', alpha=0.4, ....: fontsize=12) sage: g3 = plot(x^3, (x, 1, 100), axes_labels=[r'$x$', r'$y$'], ....: legend_label=r'$y = x^3$', scale='semilogy', frame=True, ....: gridlines='minor') \ ....: + text("This is a semilogy plot", (80, 1e5), color='red', alpha=0.4, ....: fontsize=12) sage: graphics_array([g1, g2, g3])
results in this figure:
We see that
 the
semilogy
scale asked forg3
is actually applied tog1
 the fontsize asked for
g1
is not taken into account (this is #10657)  the option
axes=False
asked forg2
is not taken into account (#10466 and #10657)  the legend of
g3
is doubled (#12591)  the color of the text in
g3
is not the same as ing2
, while they both defined ascolor='red', alpha=0.4
(#12591)
With the code introduced in this ticket, the output becomes
We see that all the above issues are gone.
comment:4 Changed 4 years ago by
Cc:  kcrisman chapoton dkrenn jdemeyer added 

Status:  new → needs_review 
comment:5 Changed 4 years ago by
Another bug fixed by this ticket regards the options passed to the method GraphicsArray.show()
. This bug shows up in the
2D plotting section of the reference manual. In the example starting with "The basic options for filling a plot", the figure resulting from
sage: p1 = plot(sin(x), pi, pi, fill='axis') sage: p2 = plot(sin(x), pi, pi, fill='min', fillalpha=1) sage: p3 = plot(sin(x), pi, pi, fill='max') sage: p4 = plot(sin(x), pi, pi, fill=(1x)/3, fillcolor='blue', fillalpha=.2) sage: graphics_array([[p1, p2], [p3, p4]]).show(frame=True, axes=False)
has obviously some axes and no frame...
Compare with the figure produced by the code in this ticket here.
comment:6 Changed 4 years ago by
Description:  modified (diff) 

comment:7 followups: 8 16 Changed 4 years ago by
THIS IS AMAZING!
I (as usual the past few years, I am sorry) will not be able to provide code review. But I think this is a great improvement. The multigraphics examples at the end of the example page are particularly impressive, and bring us a long ways toward having a "mathematical" way to interface with the stuff matplotlib provides  I could imagine it being particularly helpful with SageTeX. Thank you.
As my only suggestion, I would just urge you to be sure all previously "wrong" behavior shows up in the tests section, and that any errors be tested as well. As an example, you mention
For instance, G[0, 1] will throw an error.
so might as well put in
sage: G[0,1] IndexError ...
or whatever is appropriate. We've definitely caught subtle things over the years with those kinds of tests.
comment:8 Changed 4 years ago by
Replying to kcrisman:
As my only suggestion, I would just urge you to be sure all previously "wrong" behavior shows up in the tests section, and that any errors be tested as well. As an example, you mention
For instance, G[0, 1] will throw an error.
so might as well put in
sage: G[0,1] IndexError ...or whatever is appropriate. We've definitely caught subtle things over the years with those kinds of tests.
OK, no problem, I'll introduce these tests. And thanks for your comments.
comment:9 Changed 4 years ago by
Cc:  embray added 

comment:10 Changed 4 years ago by
During the preparation of this ticket, two questions arose:
 the method
Graphics.matplotlib()
has the optional argumentfilename=None
, which is not used in the function body; can we get rid of it?  the method
Graphics.save_image()
merely falls back toGraphics.save()
; can we remove it?
comment:12 Changed 4 years ago by
Commit:  3a5ef55af4d104c840107f46abbcba90fa401a18 → af2bf46ee0fc9cc5d24a696d55f4a1af1cc45f52 

comment:13 followup: 15 Changed 4 years ago by
Replying to chapoton:
some failing doctests, see patchbot reports
From all the errors reported bu the patchbots, it seems that only one pertains to this ticket:
File "src/sage/plot/multigraphics.py", line 427, in sage.plot.multigraphics.MultiGraphics._latex_ Failed example: A._latex_()[:40] Exception raised: ... File "/Users/jpalmier/Desktop/Sage/git/patchbot/sage/local/lib/python2.7/sitepackages/matplotlib/backends/backend_pgf.py", line 315, in __init__ "or error in preamble:\n%s" % stdout) LatexError: LaTeX returned an error, probably missing font or error in preamble: ... ! Package fontspec Error: The font "Bitstream Vera Serif" cannot be found.
This doctest is passed on my computer (Ubuntu 18.04). It fails on macOS patchbots. The reason seems to be this Matplotlib issue: https://github.com/matplotlib/matplotlib/issues/10307
Actually, this doctest was borrowed from the previous method GraphicsArray._latex_()
, since now the method _latex_()
is defined at the level of the base class MultiGraphics
. Its failure had not been revealed previously by the macOS patchbots because the doctest was marked with # not tested
. When I transferred the method _latex_()
from GraphicsArray
to MultiGraphics
, I suppressed the marker # not tested
because the doctest passed on my computer and I though there was then no reason for such a marker.
I have restored the # not tested
marker in the above commit, along with a comment about the Matplotlib issue on macOS.
The patchbots also complain about 4 pyflakes issues. However, these reports are spurious for 2 of them:

src/doc/common/conf.py:4: 'sage.misc.sagedoc.extlinks' imported but unused
=> if one suppresses this import, then the documentation fails to build (stating that:trac:
is unknown) 
src/sage/plot/plot.py:585: 'sage.plot.line.line2d' imported but unused
=> this line is preceded by the following comment:# import of line2d below is only for redirection of imports
so I guess one should keep it.
The other 2 pyflakes errors are
src/sage/repl/rich_output/pretty_print.py:34: 'types' imported but unused src/sage/repl/rich_output/pretty_print.py:35: 'collections' imported but unused
These imports have not been introduced by the currrent ticket and I am not sure whether one could removed them without any subtle side effect...
Besides, the above commit implements the G[0, 1]
error example suggested by KarlDieter in comment:7.
comment:14 Changed 4 years ago by
Commit:  af2bf46ee0fc9cc5d24a696d55f4a1af1cc45f52 → 36c0f178353017ac12573ff038c40ed55a24ba2d 

Branch pushed to git repo; I updated commit sha1. New commits:
36c0f17  Error message valid for py3 only in a multigraphics doctest

comment:15 Changed 4 years ago by
Replying to egourgoulhon:
Besides, the above commit implements the
G[0, 1]
error example suggested by KarlDieter in comment:7.
I've prepared the G[0, 1]
example with py3 Sage and it turns out that the error message is different in py2. This triggered a new doctest error for the py2 patchbot. The above commit (comment:14) fixes this.
comment:16 followup: 18 Changed 4 years ago by
Replying to kcrisman:
As my only suggestion, I would just urge you to be sure all previously "wrong" behavior shows up in the tests section
Actually, the previous wrong behaviors were "silent" errors, which showed up only in the figures, as illustrated in comment:3. Their fixes therefore cannot be checked in doctests. I've however chosen the doctests in the EXAMPLES section of sage.plot.plot.graphics_array
and sage.plot.multigraphics.GraphicsArray
to include most of (if not all) the issues exhibited in comment:3 and comment:5. But at the end, the fix can only be judged by a human eye.
comment:17 Changed 4 years ago by
It seems there is no longer any failing doctest reported by the patchbots (except for spurious ones, i.e. failures that appear on the ticket 0 as well: https://patchbot.sagemath.org/ticket/0/)...
comment:18 Changed 4 years ago by
As my only suggestion, I would just urge you to be sure all previously "wrong" behavior shows up in the tests section
Actually, the previous wrong behaviors were "silent" errors, which showed up only in the figures, as illustrated in comment:3. Their fixes therefore cannot be checked in doctests. I've however chosen the doctests in the EXAMPLES section of
sage.plot.plot.graphics_array
andsage.plot.multigraphics.GraphicsArray
to include most of (if not all) the issues exhibited in comment:3 and comment:5. But at the end, the fix can only be judged by a human eye.
Oh, that was all I meant. Yes, at one point we considered trying to automate doctesting the images themselves (!) but especially now that a lot of images are created for the documentation, regressions should be easier to identify, and we would like to have those available. Thanks!
comment:19 followup: 20 Changed 4 years ago by
Reviewers:  → Frédéric Chapoton 

Status:  needs_review → positive_review 
I am giving a positive review. This is a very nice progress, that fixes a whole lot of longstanding bugs. Fixed tickets will have to be closed later, with appropriate doctests if necessary.
comment:20 Changed 4 years ago by
Replying to chapoton:
I am giving a positive review. This is a very nice progress, that fixes a whole lot of longstanding bugs. Fixed tickets will have to be closed later, with appropriate doctests if necessary.
Thanks for the review!
comment:21 Changed 4 years ago by
Branch:  public/graphics/multi_graphics → 36c0f178353017ac12573ff038c40ed55a24ba2d 

Resolution:  → fixed 
Status:  positive_review → closed 
comment:22 Changed 4 years ago by
Milestone:  sage8.8 → sage8.9 

Not in Sage 8.8. Let's please to try keep tickets' milestones related to the release in which we actually intend to include them, and in particular the release in which they were actually included, especially when closing tickets.
Last 10 new commits:
Add helper function _parse_figsize in module graphics and use it in matplotlib() methods of classes Graphics and MultiGraphics
Add documentation in module multigraphics
Improve documentation of GraphicsArray
More documentation in classes MultiGraphics and GraphicsArray
Completed documentation of MultiGraphics and GraphicsArray
Small cleaning in MultiGraphics
Fix some doctests after the improved computation of nrows and ncols in graphics_array
Some cleaning in MultiGraphics.matplotlib
Minor cleaning in GraphicsArray
Change index range in GraphicsArray._add_subplot()