Add example of creating tools using HoloViz Panel and HoloViews #6033

MarcSkovMadsen · 2021-11-13T07:56:27Z

Description

Adds an example of creating tools using HoloViz Panel and Holoviews requested in #6023

sobel-algo-with-save-speedup.mp4

Todo

Add Panel and HoloViews to dependencies
Fix pep8 issues
Find a way to build and test docs when on Windows
Test that example works

For reviewers

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.

pep8speaks · 2021-11-13T07:56:30Z

Hello @MarcSkovMadsen! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file doc/examples/applications/plot_tool_using_holoviz.py:

Line 15:80: E501 line too long (113 > 79 characters)
Line 22:70: W291 trailing whitespace
Line 30:80: E501 line too long (120 > 79 characters)

Comment last updated at 2022-02-19 15:27:12 UTC

MarcSkovMadsen · 2021-11-13T08:04:35Z

I'm not able to install latex on my constrained, windows laptop and thus cannot build the docs and test them.

I've tried using binder without being able to get a development environment up and running.

If somebody knows a working, easy way to get a dev/ test environment up and running please let me know. Thanks.

mkcor · 2021-11-16T12:09:04Z

Dear @MarcSkovMadsen,

Thank you for this great contribution. I have fetched your branch locally and was able to build the docs successfully! 🎉

Your addition renders like this:

In fact, with Sphinx-Gallery, the syntax to use in your Python files is reStructuredText (not Markdown). For example, for external links:

scikit-image/doc/examples/applications/plot_3d_image_processing.py

Line 228 in fa43626

# `Gamma correction <https://en.wikipedia.org/wiki/Gamma_correction>`_

Do you mind updating your contribution accordingly? Then I'm happy to review it thoroughly!

MarcSkovMadsen · 2021-11-16T13:26:37Z

Thanks @mkcor. Will do 👍

MarcSkovMadsen · 2021-12-19T06:55:05Z

I cannot include an .mp4 in the document. But I can include a .gif. For now I upload here to get a url to include.

MarcSkovMadsen · 2021-12-19T07:06:04Z

Thanks @mkcor

Thanks for your patience. I got distracted. It's updated now. Have a nice Christmas.

mkcor

Thank you, @MarcSkovMadsen!

Please improve the writeup along the lines of this quick review. The text can be very concise but it should flow well. Feel free to draw inspiration from well-written gallery examples, such as "Estimate anisotropy in a 3D microscopy image."

doc/examples/applications/plot_tool_using_holoviz.py

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

MarcSkovMadsen · 2021-12-20T17:50:42Z

Thanks @mkcor . I've tried to apply the inspiration from plot_3d_structure_tensor.py. I hope you can provide me some more guidance. Thanks.

mkcor · 2022-01-02T09:33:09Z

PS: @MarcSkovMadsen did you know you could apply suggested changes as a batch? https://docs.github.com/en/github/collaborating-with-pull-requests/reviewing-changes-in-pull-requests/incorporating-feedback-in-your-pull-request

MarcSkovMadsen · 2022-01-02T18:21:42Z

Thx. I did not know.

requirements/docs.txt

mkcor

Please proofread your text and please wrap your lines at 79 characters. Let me know when you're done and I'll review! Thanks.

doc/examples/applications/plot_tool_using_holoviz.py

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

MarcSkovMadsen · 2022-02-19T15:29:39Z

I've relaxed the versions, fixed the spelling error, tried to identify more spelling errors, updated to respect 79 character limit.

In the two places below, I've not been able to respect the 79 character limit. I've tried to google to find out how I can break lines in figure and code block without luck. So I've kept them as they are.

Please let me know if there is more I should do @mkcor . Thanks.

mkcor · 2022-02-23T19:05:00Z

doc/examples/applications/plot_tool_using_holoviz.py

+In this tutorial, we build interactive tools and an application using
+`Panel <https://panel.holoviz.org>`_ and `HoloViews <https://holoviews.org>`_.


Suggested change

In this tutorial, we build interactive tools and an application using

`Panel <https://panel.holoviz.org>`_ and `HoloViews <https://holoviews.org>`_.

In this tutorial, we build interactive tools using

`Panel <https://panel.holoviz.org>`_ and `HoloViews <https://holoviews.org>`_,

two visualization libraries maintained by `HoloViz <https://holoviz.org/>`_.

Since 'HoloViz' appears in the title, it must appear in the body text at some point, preferably towards the beginning, so the reader knows what we are talking about...

mkcor · 2022-02-23T19:22:28Z

doc/examples/applications/plot_tool_using_holoviz.py

+
+We will build an application based on the Sobel algorithm to interactively
+find a great color map for the visualization. We will add some nice features,
+like a download button, to make sharing your findings easier.


Suggested change

We will build an application based on the Sobel algorithm to interactively

find a great color map for the visualization. We will add some nice features,

like a download button, to make sharing your findings easier.

We build a web application based on the Sobel algorithm which lets the user

find interactively a great color map for the visualization.

Then we add interaction features such as a download button.

Keep the same tense.

What is "finding a great color map [for the visualization]" supposed to mean? Even if we're not dealing with a scientific problem, the question should be somewhat interesting, so the reader can see the point of building this app... From your animation, it looks like the app is only about changing the color map interactively (not really finding... some kind of optimum, as the verb 'finding' implies). If the app is 'based on the Sobel algorithm' as you write, then what seems 'interesting' would be for the user to vary the mode and/or cval values...

I think everyone knows what a download button is for... To make the comment relevant, it should specify what exactly is being downloaded upon clicking the download button in question: a CSV of the full dataset? a CSV of the subset currently displayed? a PNG of the static picture? I think it would be more fitting to specify this when we are at that point in the tutorial.

mkcor · 2022-02-23T19:23:08Z

doc/examples/applications/plot_tool_using_holoviz.py

+   Screencast showcasing the example application.
+
+
+You can develop using notebooks or .py files. You can use it with a very


What does 'it' refer to?

mkcor · 2022-02-23T19:33:16Z

doc/examples/applications/plot_tool_using_holoviz.py

+
+These techniques can make your analyses more interactive and, hence, powerful.


Suggested change

These techniques can make your analyses more interactive and, hence, powerful.

Interactive applications provide flexible ways to visualize and explore data,

making data analysis more powerful and, at the same time, accessible to

non-technical audiences.

You might as well stick with a very generic sentence.

mkcor · 2022-02-23T19:37:25Z

In the two places below, I've not been able to respect the 79 character limit. I've tried to google to find out how I can break lines in figure and code block without luck. So I've kept them as they are.

Sure, that's fine.

mkcor · 2022-02-23T20:04:14Z

doc/examples/applications/plot_tool_using_holoviz.py

+    width=width,
+    cmap="binary_r",
+    title="Before",
+    active_tools=["box_zoom"],


@MarcSkovMadsen could we do without option 'active_tools' so that we could use a backend other than 'bokeh' and, hence/perhaps, have the figure display in the static HTML page?

add first version of holoviz example

6f75946

Marc Skov Madsen added 2 commits November 13, 2021 09:02

fix pep8 issues

b3a9ad6

add dependencies

607d29c

Marc Skov Madsen added 2 commits December 19, 2021 07:57

convert markdown to restructuredText

95499ae

added links to more inspiration

06b6ab3

fix misspelling

9a1c502

mkcor reviewed Dec 20, 2021

View reviewed changes

MarcSkovMadsen and others added 8 commits December 20, 2021 18:17

Update doc/examples/applications/plot_tool_using_holoviz.py

6b389e7

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

Update doc/examples/applications/plot_tool_using_holoviz.py

b72f2d4

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

Update doc/examples/applications/plot_tool_using_holoviz.py

b4c24dd

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

Update doc/examples/applications/plot_tool_using_holoviz.py

56904e8

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

Update doc/examples/applications/plot_tool_using_holoviz.py

634f7f2

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

Update doc/examples/applications/plot_tool_using_holoviz.py

8ca7efa

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

get inspiration from plot_3d_structure_tensor

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add suggestions from review

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mkcor reviewed Jan 13, 2022

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MarcSkovMadsen and others added 3 commits February 19, 2022 16:07

fix spelling error

ce5f107

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

relax requirements

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respect 79 character limit

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grlee77 mentioned this pull request Feb 20, 2022

2021's calendar of community management #5169

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mkcor mentioned this pull request Feb 28, 2022

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Add example of creating tools using HoloViz Panel and HoloViews #6033

Add example of creating tools using HoloViz Panel and HoloViews #6033

MarcSkovMadsen commented Nov 13, 2021 •

edited by mkcor

pep8speaks commented Nov 13, 2021 •

edited

MarcSkovMadsen commented Nov 13, 2021 •

edited

mkcor commented Nov 16, 2021

MarcSkovMadsen commented Nov 16, 2021

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edited

mkcor Feb 23, 2022

mkcor Feb 23, 2022

mkcor Feb 23, 2022

mkcor Feb 23, 2022

mkcor commented Feb 23, 2022

mkcor Feb 23, 2022

		In this tutorial, we build interactive tools and an application using
		`Panel <https://panel.holoviz.org>`_ and `HoloViews <https://holoviews.org>`_.

-In this tutorial, we build interactive tools and an application using
-`Panel <https://panel.holoviz.org>`_ and `HoloViews <https://holoviews.org>`_.
+In this tutorial, we build interactive tools using
+`Panel <https://panel.holoviz.org>`_ and `HoloViews <https://holoviews.org>`_,
+two visualization libraries maintained by `HoloViz <https://holoviz.org/>`_.

		Screencast showcasing the example application.


		You can develop using notebooks or .py files. You can use it with a very


		These techniques can make your analyses more interactive and, hence, powerful.

-These techniques can make your analyses more interactive and, hence, powerful.
+Interactive applications provide flexible ways to visualize and explore data,
+making data analysis more powerful and, at the same time, accessible to
+non-technical audiences.

Add example of creating tools using HoloViz Panel and HoloViews #6033

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Add example of creating tools using HoloViz Panel and HoloViews #6033

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MarcSkovMadsen commented Nov 13, 2021 • edited by mkcor

Description

Todo

For reviewers

pep8speaks commented Nov 13, 2021 • edited

Comment last updated at 2022-02-19 15:27:12 UTC

MarcSkovMadsen commented Nov 13, 2021 • edited

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MarcSkovMadsen commented Nov 13, 2021 •

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