Show our data in the gallery #3388

sciunto · 2018-09-03T08:33:27Z

Description

To pursue on the idea in #3384 I thought that it would be useful to show the data we are shipping with scikit-image. We could separate images for general purposes, scientific images and other specific images (like stereo).

Checklist

[It's fine to submit PRs which are a work in progress! But before they are merged, all PRs should provide:]

Clean style in the spirit of PEP8
Docstrings for all functions
Gallery example in ./doc/examples (new features only)
Benchmark in ./benchmarks, if your changes aren't covered by an
existing benchmark
Unit tests

[For detailed information on these and other aspects see scikit-image contribution guidelines]

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(Don't remove the checklist below.)

Check that the PR title is short, concise, and will make sense 1 year
later.
Check that new functions are imported in corresponding __init__.py.
Check that new features, API changes, and deprecations are mentioned in
doc/release/release_dev.rst.
Consider backporting the PR with @meeseeksdev backport to v0.14.x

pep8speaks · 2018-09-03T08:33:30Z

Hello @sciunto! Thanks for updating the PR.

There are no PEP8 issues in the file doc/examples/data/plot_general.py !
There are no PEP8 issues in the file doc/examples/data/plot_scientific.py !
In the file doc/examples/data/plot_specific.py, following are the PEP8 issues :

Line 43:27: E226 missing whitespace around arithmetic operator

Comment last updated on October 02, 2018 at 10:02 Hours UTC

codecov-io · 2018-09-03T11:07:03Z

Codecov Report

Merging #3388 into master will increase coverage by <.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #3388      +/-   ##
==========================================
+ Coverage   86.81%   86.81%   +<.01%     
==========================================
  Files         339      341       +2     
  Lines       27385    27412      +27     
==========================================
+ Hits        23773    23798      +25     
- Misses       3612     3614       +2

Impacted Files	Coverage Δ
skimage/__init__.py	`67.85% <0%> (-3.12%)`	⬇️
skimage/feature/setup.py	`17.24% <0%> (-1.28%)`	⬇️
skimage/draw/_random_shapes.py	`96.84% <0%> (-1.06%)`	⬇️
skimage/filters/tests/test_gaussian.py	`100% <0%> (ø)`	⬆️
skimage/restoration/tests/test_denoise.py	`99.47% <0%> (ø)`	⬆️
skimage/future/__init__.py	`100% <0%> (ø)`	⬆️
skimage/feature/__init__.py	`100% <0%> (ø)`	⬆️
skimage/util/tests/test_dtype.py	`100% <0%> (ø)`	⬆️
skimage/util/dtype.py	`90.74% <0%> (ø)`	⬆️
skimage/feature/tests/test_cascade.py	`100% <0%> (ø)`
... and 4 more

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emmanuelle

I like the idea of displaying pictures of available images in the gallery. My only concern is that the thumbnails will be unreadable with a large number of subplots, maybe organize the images with several rows for the general-purpose images? I had a quick look at the gallery, 6 subplots is still OK, 9 is very crowded.

emmanuelle · 2018-09-05T19:43:48Z

doc/examples/data/plot_general.py

+#'lfw_subset',
+
+fig, axes = plt.subplots(len(images), 1, figsize=(8, 4 * len(images)),
+                         sharex=False, sharey=False)


isn't sharex/y False by default?

Yes, I can get ride of it.

emmanuelle · 2018-09-05T19:46:56Z

doc/examples/data/plot_general.py

+for i, image in enumerate(images):
+    caller = getattr(data, image)
+    ax[i].imshow(caller())
+    ax[i].set_title(image)


``ax[i].axis('off')```to gain some space in a crowded figure?

I preferred to keep it as it gives an idea of the image size.

emmanuelle · 2018-09-05T19:52:23Z

doc/examples/data/plot_general.py

@@ -0,0 +1,42 @@
+"""
+======================
+General purpose images


General-purpose

sciunto · 2018-09-06T06:26:43Z

You are absolutely right for the thumbnail. It's an issue. The idea I got in the mean time to solve this is to take one image as an example for the thumbnail, and then display them all. I'm afraid that, even if we succeed in generating a correct rendering, the future additions will destroy it anyway.

emmanuelle · 2018-09-07T06:01:42Z

@sciunto you can do that by displaying a first image in the example, and then the whole subplots. I don't remember if sphinx-gallery takes the first or the last figure for the thumbnail, and whether it can be configured. The doc of sphinx-gallery is quite thorough, but its organization is sometimes a bit weird.

sciunto · 2018-09-12T07:40:40Z

It's now ready for reviews.

sciunto · 2018-09-17T14:26:40Z

@scikit-image/core Anyone for reviewing this please?

soupault · 2018-09-30T12:25:03Z

The added gallery examples don't seem to show up under "Examples using ..." sections of skimage.data (i.e. http://scikit-image.org/docs/dev/api/skimage.data.html#examples-using-skimage-data-astronaut). Any ideas on this?

Also, I'd make the font in the image titles a bit larger.

Otherwise, LGTM!

sciunto · 2018-10-02T10:05:01Z

@soupault I increased the font size. Regarding the fact it doesn't show up in section, I guess it's because we use getattr, and not a direct call. A parser cannot get the call here... but i don't think it's significant miss.

soupault · 2018-10-02T17:12:05Z

doc/examples/data/plot_specific.py

+
+from skimage import data
+
+matplotlib.rcParams['font.size'] = 18


I've just noticed that you don't set titles in this example. The font config doesn't really make sense then.

Other examples look great!

It's just to keep the tics homogeneous...

soupault · 2018-10-02T17:13:08Z

I guess it's because we use getattr, and not a direct call

@sciunto Ah, you are right. That's, most likely, the case.

soupault · 2018-10-03T09:28:36Z

Why don't we add the titles here also then? :)

…

On Wed, 3 Oct 2018 at 12.08, François Boulogne ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In doc/examples/data/plot_specific.py <#3388 (comment)> : > @@ -0,0 +1,46 @@ +""" +=============== +Specific images +=============== + +""" +import numpy as np +import matplotlib.pyplot as plt +import matplotlib + +from skimage import data + +matplotlib.rcParams['font.size'] = 18 It just to keep the tics homogeneous... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3388 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABQTBaYYt5OMSEMf2f0tRdN6XzznbGCbks5uhH54gaJpZM4WXLvW> .

sciunto · 2018-10-03T09:33:22Z

Because we have a header for each image/set of images that already introduces the content... I can add it, but I did not feel it's necessary.

sciunto · 2018-10-09T07:40:03Z

@emmanuelle I'm confused. Where do I call data.__all__? I couldn't reproduce.

emmanuelle · 2018-10-09T08:36:56Z

@sciunto sorry I got mixed up (with one of my local files). Sorry about that, ignore my comment!

emmanuelle · 2018-10-09T09:15:57Z

LGTM. It could be good to order the sections of the gallery so that the section on data appears on top (as described here https://sphinx-gallery.readthedocs.io/en/stable/advanced_configuration.html?highlight=sorting#sub-gallery-order). But we can also merge this PR first and do the ordering later, depending on your time.

sciunto · 2018-10-09T11:55:04Z

Good point. I open another issue for that. I think that ordering our examples would be useful beyond this PR (eg operation on numpy arrays could come among the first ones).

emmanuelle · 2018-10-09T19:34:25Z

Merging, thanks!

Show our data to gallery

0b0d285

sciunto added 📄 type: Documentation Updates, fixes and additions to documentation 💪 Work in progress labels Sep 3, 2018

sciunto requested a review from emmanuelle September 3, 2018 08:33

fix typo

f4d59bf

soupault added this to the 0.15 milestone Sep 4, 2018

emmanuelle reviewed Sep 5, 2018

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doc/examples/data/plot_general.py Outdated

@@ -0,0 +1,42 @@

"""

======================

General purpose images

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General-purpose

sciunto added 5 commits September 10, 2018 16:15

Apply @emmas comments

d4e6824

Add page for specific purpose images

0966ed0

Integrate lwm dataset

b1554a3

set grayscale if needed, add comments

03ee21f

First image as thumbnail

4cef9af

sciunto added 🧐 Needs review and removed 💪 Work in progress labels Sep 12, 2018

soupault self-assigned this Sep 30, 2018

inscrease font size

7d48ee0

soupault reviewed Oct 2, 2018

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soupault approved these changes Oct 4, 2018

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soupault added status: mrg+1 and removed 🧐 Needs review labels Oct 4, 2018

sciunto mentioned this pull request Oct 9, 2018

order the examples in our gallery #3462

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emmanuelle merged commit 9cb7cd3 into scikit-image:master Oct 9, 2018

sciunto deleted the doc_data branch October 9, 2018 20:02

soupault mentioned this pull request Feb 23, 2019

Make it easy to browse example images #989

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Show our data in the gallery #3388

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		from skimage import data

		matplotlib.rcParams['font.size'] = 18

Show our data in the gallery #3388

Show our data in the gallery #3388

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sciunto commented Sep 3, 2018 • edited

Description

Checklist

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