Fwd: PyData Community Cookbook - August Update

[Stefan van der Walt]

Hi everyone

Is anyone interested in writing a scikit-image chapter for the following book?

Stéfan

----- Original message -----

From: Andy Ray Terrel <an...@numfocus.org>

Subject: PyData Community Cookbook - August Update

Date: Sat, 20 Aug 2016 07:14:58 -0500

Hello everyone,

You are receiving this email because you were either invited and committed to join our project. Please feel free to forward this message to a more appropriate list or person. For questions please email pydata-...@numfocus.org.

Katy Huff and myself are starting a project to build a cookbook of advanced material for the PyData community. The cookbook will be published by Addison-Wesley. We have invited a number of contributors to see if such a project would have some interest and received overwhelmingly positive feedback. 

The book will cover several major topics, organized as such, with some sample packages:

- IDE: IPython/Jupyter

- Data Structures / Numerics: NumPy, Pandas, Xray, PyTables

- Viz: Matplotlib, Bokeh, Seaborn, yt

- Algorithms / Science: SciPy, Scikit-learn, Scikit-image, statsmodels, sympy, gensim

- Performance / Scale: Cython, Numexpr, Numba, Dask, pyspark

We expect each submission to be about 15 - 20 pages describing an example of the power of each library. While we have reached out to the projects about putting each submission together we are happy to accept chapters for libraries we did not initially identify.

To facilitate the book we have put together a repository for collecting and reviewing submissions at https://github.com/pydata/pydata-cookbook . We are asking for submissions in rst but would appreciate any other files, such as jupyter notebooks or code, for a digital appendix as well.

If you read this far and are interested in contributing.  The proposed schedule is the following:

Sept 1: Submit a pull request with a title, abstract and author list for the submission.

Nov 15: Submit a completed chapter.

Dec 31: Reviews for chapters finished.

Jan 31: All chapter revisions due.

Thanks for you time!

--

Andy R. Terrel, PhD

President, NumFOCUS

an...@numfocus.org

[Emmanuelle Gouillart]

Hi Stéfan,

is it something that we could re-use for the documentation of
scikit-image, in the user guide for example?

Best
Emma

[Alexandre Fioravante de Siqueira]

Hi all,

I'd be glad to contribute, if you're still searching. I could use some previous written material I have here.

If it is ok, please tell me what I need to do.

Kind regards,

Alex 

[Stefan van der Walt]

On Mon, Aug 29, 2016, at 13:44, Emmanuelle Gouillart wrote:
> is it something that we could re-use for the documentation of
> scikit-image, in the user guide for example?

Good question! Let's ask Andy (on CC).

Stéfan

[Emmanuelle Gouillart]

Probably we would not include the chapter as published on the website,
the idea would be more to take some of the materials for the user guide.

[Egor Panfilov]

Sounds interesting, and I'd be glad to contribute. Although, it is not clear what kind of content do authors expect. I believe that the vast majority of `skimage` functionality is already well-described in the documentation and conference notebooks.

If someone of `skimage` original authors could prepare a draft of the planned chapter (i.e. table of contents), I think it would be quite easy to make it happen soon and in the best possible way.

Regards,

Egor

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[Alexandre Fioravante de Siqueira]

Dear all,

have you figured it out? The deadline is tomorrow, and I would really like to participate.

Thanks!

Alex

Em quarta-feira, 31 de agosto de 2016 15:37:06 UTC+2, Egor Panfilov escreveu:

Sounds interesting, and I'd be glad to contribute. Although, it is not clear what kind of content do authors expect. I believe that the vast majority of `skimage` functionality is already well-described in the documentation and conference notebooks.

If someone of `skimage` original authors could prepare a draft of the planned chapter (i.e. table of contents), I think it would be quite easy to make it happen soon and in the best possible way.

Regards,

Egor

[Stefan van der Walt]

Hi Alex

On Wed, Aug 31, 2016, at 10:41, Alexandre Fioravante de Siqueira wrote:
> have you figured it out? The deadline is tomorrow, and I would really
> like to participate.

Would you please submit an initial pull request on the team's behalf?
You can add me, Egor, Emmanuelle, and anyone else who expresses interest
here as co-authors.

Emmanuelle, I will double check that the chapter is fully open when it
is done so that we can remix parts for the user guide.

Thanks
Stéfan

[Alexandre Fioravante de Siqueira]

Hi all,

Stéfan, thanks for that. I'm working on it.
I need your e-mails and institutions for the commit:

"""

:author: Stéfan van der Walt

:email: 

:institution: 

:corresponding:

:author: Emmanuelle Gouillart

:email: 

:institution: 

:institution: 

:equal-contributor:

:author: Egor Panfilov

:email: 

:institution: 

:equal-contributor:

:author: Alexandre de Siqueira

:email: 

:institution: University of Campinas

:institution: TU Bergakademie Freiberg

:equal-contributor: 

"""

We need an abstract too:

"""

scikit-image is an image processing toolbox for SciPy which provides easy access for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. It is available free of charge and restriction, and the code is written by an active community of volunteers.

(...)

"""

As you may see I need some ideas for that :) Since this is a cookbook, I think it would be aimed to "recipes" using different functions/objects from the library. Maybe we could specify some examples on the abstract. Do you have any ideas?

I'll wait until 10hPM (Berlin time; 8hPM UTC) to submit that, so we can discuss some ideas if you have time.

Thanks! I'm here if you need.

Kind regards,

Alex

[Emmanuelle Gouillart]

Hi Alexandre,

thanks for taking care of this.

My details
e-mail: emmanuelle...@nsup.org
institution: Joint Unit CNRS/Saint-Gobain Surface of Glass and
Interfaces, Aubervilliers, France

For the abstract I think you can also re-use materials from the
scikit-image paper, the abstract is

********
scikit-image is an image processing library that implements algorithms
and utilities for use in research, education and industry applications.
It is released under the liberal Modified BSD open source license,
provides a well-documented API in the Python programming language, and is
developed by an active, international team of collaborators. In this
paper we highlight the advantages of open source to achieve the goals of
the scikit-image library, and we showcase several real-world image
processing applications that use scikit-image. More information can be
found on the project homepage, http://scikit-image.org.
********

Don't worry too much about the abstract now, we'll have time to change
it. I'm not sure we have to give examples in the abstract, which should
be general enough.

But it's a good time to start thinking about the content. Even if it's
advertised as a "cookbook", I think that a length of 15-20 pages is
enough to present both "recipes" and also some big picture stuff (why and
when use scikit-image or other image processing libraries? what are the
typical coding patterns? etc.). As for the recipes, if we can re-use some
of our gallery examples it will save us some precious time. How about we
select one example if each of the chapters of the gallery and we take
advantage of the cookbook to improve it?

Best,
Emma

[Alexandre Fioravante de Siqueira]

Hi all,

we're in! I think... I sent the pull request:

http://github.com/pydata/pydata-cookbook/pull/6

 * Egor: sorry man, I didn't find any info about you. However, I added your name. I'll wait for the other information, ok?

 * Stéfan: I got your info on BIDS site. Please check if there's something I need to change.

 * Emma: thank you very much for sending your data, I had only your previous e-mail. I used the abstract you sent, thanks for helping with that.

I think you're right about the "cookbook" think, we have space for doing an overview of scikit-image and presenting some nice stuff :)

"""

How about we select one example if each of the chapters of the gallery and we take advantage of the cookbook to improve it?

"""

That would be great!

Now I'm waiting for the action.

Kind regards y'all, have a nice night.

Alex

[Stefan van der Walt]

On Thu, Sep 1, 2016, at 13:14, Alexandre Fioravante de Siqueira wrote:

"""

How about we select one example if each of the chapters of the gallery and we take advantage of the cookbook to improve it?

"""

We can also select some material from the scipy lectures we've given in the past.  E.g., I think the RANSAC lecture went down well:

https://github.com/scikit-image/skimage-tutorials/blob/master/lectures/5_ransac.ipynb

Stéfan

[Josh Warner]

I would also contribute - Joshua D. Warner, email joshua dot dale dot warner at Gmail, institution Mayo Clinic.

[Alexandre Fioravante de Siqueira]

Hi Josh,

in which city is your Mayo Clinic unity?

Thanks,

Alex

[Josh Warner]

Rochester, Minnesota.

[Alexandre Fioravante de Siqueira]

Thanks. Already pushed.

Em sábado, 3 de setembro de 2016 02:49:24 UTC+2, Josh Warner escreveu:

Rochester, Minnesota.

[Alexandre Fioravante de Siqueira]

Hi all,

like Emmanuelle said in this previous e-mail, it's time to think about the content.

Would you like to point any gallery examples for that? What do you think it's important to be in that chapter?

I was thinking on a first section about the basics: open a file, separate the color channels, present histograms, all that stuff.

Thanks. Looking forward to work with you,

Alex 

Em quinta-feira, 1 de setembro de 2016 19:00:40 UTC+2, Emmanuelle Gouillart escreveu:

... it's a good time to start thinking about the content. Even if it's

[Alexandre Fioravante de Siqueira]

Hi all,

did you lose interest on working on this project?

If you don't want to work on that anymore, please tell me. I think I can't work on that alone, and I would need to stop this project.

Thanks,

Alex

[Emmanuelle Gouillart]

Hi Alex,

don't worry, it's just that it's harder to find motivation when the
deadline is not that close ;-). But of course we should get started. How
about you propose an outline with different sections (a first one with
the basics as you suggest, then different image processing tasks, ...)
and ask for volunteers for the different sections? I could take care of
segmentation for example.

Best,
Emma

[Alexandre Fioravante de Siqueira]

Hi Emma,

thank you for your answer :) I'll do that.

Kind regards,

Alex

[Stefan van der Walt]

Hi Alex

We have lots and lots of examples from all around, if you need some of those for the chapter.  In fact, I often use your work in my slides ;)

But we can also organize a video call sometime for all interested parties if you want to brainstorm.

Stéfan

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[Alexandre Fioravante de Siqueira]

Hi Stefan,

that's a nice idea! We could join to discuss the preliminar structure of the chapter.

I am in Brazil now, so my time zone is UTC-03:00. Could we separate ~ 1 h on next week for that?

I'll check some cookbooks that I have here to search for some ideas.

Kind regards,

Alex 

[Stefan van der Walt]

On Mon, Oct 10, 2016, at 05:57, Alexandre Fioravante de Siqueira wrote:

that's a nice idea! We could join to discuss the preliminar structure of the chapter.

I am in Brazil now, so my time zone is UTC-03:00. Could we separate ~ 1 h on next week for that?

I'll check some cookbooks that I have here to search for some ideas.

Sure, why don't you post a WhenIsGood poll here, then all interested parties can fill out times.

Bests regards

Stéfan

[Alexandre Fioravante de Siqueira]

Hi all,
according to Stéfan's idea, please answer to this poll. Then, we can define the best time for our meeting.
http://whenisgood.net/4kag8mp
Thanks and have a nice one,

Alex

[Stefan van der Walt]

Hi Alex

On Wed, Oct 12, 2016, at 03:57, Alexandre Fioravante de Siqueira wrote:
> according to Stéfan's idea, please answer to this poll. Then, we can
> define the best time for our meeting.
> http://whenisgood.net/4kag8mp

These times are all in the middle of the night in California :/

Stéfan

[Alexandre Fioravante de Siqueira]

Hi Stéfan,
sorry about that :) could you make the poll according to your preferences?

[Alexandre Fioravante de Siqueira]

Dear all,

trying again. Please answer.

http://whenisgood.net/m293mts

Alex