Re: [scikit-image] Releasing 0.14

[Egor Panfilov]

Probably, the most convenient option is to use this temporary PR -
https://github.com/scikit-image/scikit-image/pull/3102 , and write the
comments as reviews.
I'll later make the proposed changes directly in the v0.14.x branch.

Regards,
Egor

чт, 24 мая 2018 г. в 22:30, Stefan van der Walt <stef...@berkeley.edu>:

> On Wed, 23 May 2018 18:08:10 +0300, Egor Panfilov wrote:
> > I've started to prepare for the release, and have already created the
> > release branch. If some of you would like to review the release notes,
> > please, take a look at
> >
> https://github.com/scikit-image/scikit-image/blob/v0.14.x/doc/release/release_0.14.rst
>
> Where should comments on this document be made?  Is there a PR or an
> easy way to annotate the document on GitHub?
>
> Stéfan
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Re: [scikit-image] Python 3 transition

[Egor Panfilov]

Hi all,

>I recall this too. =)
I'm still in charge! ;)

Actually, mid-January | early February sounds OK now. We need some time to
awaken the reviewers, and catch up with the scheduled issues/PRs. And then,
fortunately or not, everyone is having Christmas and Happy New Year :).
This is the best we can do for now, but (sorry in advance) during the next
year I'll be pushing more to have the releases more frequently
(1/6-9month). :)

Regards,
Egor

2017-11-15 9:55 GMT+03:00 Stefan van der Walt :

> On Tue, Nov 14, 2017, at 22:41, Juan Nunez-Iglesias wrote:
>
>  I think we can hold off a bit on 0.14: our last release was in
> September, and there are a few PRs in the pipeline near completion.
> How about we split off the 0.14.x branch beginning of February?
>
>
> Feb! That seems excessive? I don’t think our bug fix backport releases
> really count as releases.
>
>
> How about this, then: Egor, give us a date that you'd like to release
> (taking into consideration that you'd then need to do the work ;), leaving
> at least one month before that to finish pending PRs.
>
> Stéfan
>
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Re: [scikit-image] Interested in Contributing to scikit-image

[Egor Panfilov]

Hello Kumar,

Thanks for your interest in `scikit-image`!

Firstly, we've a very informative guide on contribution proccess in
http://scikit-image.org/docs/dev/contribute.html .

Secondly, we've a wide variety of open issues, feature requests, and
enhancement proposals. You can look through them at
https://github.com/scikit-image/scikit-image/issues, and select one in
accordance with your expertise in Python and image processing.
For the beggining, I'd recommend to start with GitHub issues marked with
`difficulty: novice` or `type: documentation` tag. This should help you to
get better acquainted with the contribution proccess, as well as with
`scikit-image` codebase.

Good luck! :)

Regards,
Egor Panfilov

2017-11-12 2:05 GMT+03:00 Kumar Ashutosh <kumar.ashutosh...@gmail.com>:

> Hello,
>
> I found this project quite interesting. I am interested in contributing to
> the repository. Can anyone of you guide me on how can I start contribution
> and what part of the project is being majorly worked upon?
> I am currently contributing to scikit-learn, with approximately 9 bugs
> solved and a few being reviewed.
>
> Thanks,
>
> Kumar Ashutosh
> Undergraduate
> IIT Bombay
> India
> ᐧ
>
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Re: [scikit-image] 回复： Python 3 transition

[Egor Panfilov]

Hi all,

I'd also support this decision.
For information, here is an another link to a related discussion -
https://groups.google.com/forum/#!msg/scikit-image/7aH6hshJJg0/ykjxdZ8uMQAJ
.

Juan,
I don't think we're there yet for 1.0, though :). From my standpoint,
several important aspects (metaparams handling, API, xy->rc, etc) have to
be addressed first (see `discussion` tag on GitHub).

Stefan,
Has the schedule been changed? I remember we were planning to release 0.14
in November 2017 (see
https://mail.python.org/pipermail/scikit-image/2017-September/005352.html).

Regards,
Egor Panfilov

2017-11-12 2:55 GMT+03:00 Juan Nunez-Iglesias <jni.s...@gmail.com>:

> I agree. I would suggest backporting bugfixes to 0.14 for 2 years, or not
> naming it LTS because 1y is not “long term” by most definitions.
>
> imho we should aim for 1.0 for this time next year and maybe *that* can
> depend on Python >= 3.6. =)
>
> Juan.
>
> On 11 Nov 2017, 6:52 PM +1100, imag...@sina.com, wrote:
>
> Just my own opinion. we can give up python2.x  -- YXDragon
> - 原始邮件 -
> 发件人：Stefan van der Walt <stef...@berkeley.edu>
> 收件人：scikit-image@python.org
> 主题：[scikit-image] Python 3 transition
> 日期：2017年11月11日 14点34分
>
> Hi, everyone
> I'd like to make a 4th attempt to determine our transition pathway to
> Python 3. The last thread is here:
> https://mail.python.org/pipermail/scikit-image/2017-July/005304.html
> I would like to propose that the next version, 0.14 (scheduled for March
> of next year), becomes the last targeted for Python 2. It will also be
> an LTS (Long Time Support), which means we will backport serious fixes
> for a period of one year. 0.15 will then target Python >= 3.5 only
> (sorry, no f-strings yet!).
> Let me know your thoughts.
> Stéfan
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Re: [scikit-image] Community guidelines

[Egor Panfilov]

Looks good to me as well.

Regards,
Egor Panfilov

2017-10-26 17:54 GMT+03:00 Chris Colbert <sccolb...@gmail.com>:

> That's one of the best codes of conduct I've seen. +1 from me.
>
> On Thu, Oct 26, 2017 at 4:58 AM, Steven Silvester <
> steven.silves...@gmail.com> wrote:
>
>> I agree with Juan.  Also, I had not heard of neurotype, great vocabulary
>> word for the day.
>>
>>
>> Regards,
>>
>> Steve
>>
>>
>> On Oct 25, 2017, at 11:21 PM, Stefan van der Walt <stef...@berkeley.edu>
>> wrote:
>>
>> Thanks for letting me know, Juan.
>>
>> I'd also like to hear from the rest of the community---what are your
>> thoughts?
>>
>> Stéfan
>>
>> On Wed, Oct 25, 2017, at 01:58, Juan Nunez-Iglesias wrote:
>>
>> +1 from me. I specifically like having external people to report
>> incidents to.
>>
>> Juan.
>>
>> On 25 Oct 2017, 5:33 AM +1100, Stefan van der Walt <stef...@berkeley.edu>,
>> wrote:
>>
>> Hi, everyone
>>
>> SciPy just merged their Code of Conduct documents after a long
>> discussion [0]:
>>
>> https://github.com/scipy/scipy/blob/master/doc/source/dev/
>> conduct/code_of_conduct.rst
>> https://github.com/scipy/scipy/blob/master/doc/source/dev/
>> conduct/report_handling_manual.rst
>>
>> I have been hesitant to include anything similar for scikit-image before
>> (other than http://scikit-image.org/community_guidelines.html ), because
>> I did not feel comfortable with the aloof policing tone typically
>> employed in similar documents elsewhere.
>>
>> But, I think the SciPy documents make an important statement about our
>> vision for an inclusive community, and does so in a friendly but serious
>> way.
>>
>> How would you feel about adopting these documents for scikit-image?
>>
>> Best regards
>> Stéfan
>>
>> [0]: https://github.com/scipy/scipy/pull/7963
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[scikit-image] Release date for 0.14

[Egor Panfilov]

Dear all,

I propose to set a release date for scikit-image 0.14 on the mid of October
(15th should do). Also, I'd volunteer to be a release manager for the
release.
Please, let me know if you agree. If so, I kindly ask you to take a deep
breath and try to review some of the scheduled PRs in the coming month.

Thanks in advance, and have a nice we!

Regards,
Egor Panfilov
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Re: [scikit-image] ValueError: too many values to unpack for measure.marching_cubes

[Egor Panfilov]

Hi,

Functions in Python return objects packed in a tuple. When you write
`verts, faces = marching_cubes(...)`, Python computes
`marching_cubes(...)`, takes the output, and tries to unpack it (i.e. to
assign to the names on the left-hand side of `=`) to 2 objects. The error
tells you that the number of objects in a returned tuple is too high (>2).

Here is an example to better understand the issue:

In [1]: a, b = (1, 2)
In [2]: a, b, c = (1, 2)
---
ValueErrorTraceback (most recent call last)
 in ()
> 1 a, b, c = (1, 2)

ValueError: not enough values to unpack (expected 3, got 2)

In [3]: a, b = (1, 2, 3)
---
ValueErrorTraceback (most recent call last)
 in ()
> 1 a, b = (1, 2, 3)

ValueError: too many values to unpack (expected 2)


In skimage 0.13, as far as I remember, `marching_cubes` is actually an
alias to `marching_cubes_lewiner` (
http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.marching_cubes_lewiner)
which returns 4 objects, not 2. In skimage 0.14dev we've already removed
this alias.
You should either use `marching_cubes_classic` (not recommended), or update
your code to use `marching_cubes_lewiner` and unpack the output to 4
variables.

Regards,
Egor

2017-08-07 17:16 GMT+03:00 wine lover :

> Hello,
>
> I have been trying to follow the tutorial here https://www.kaggle.com/
> gzuidhof/full-preprocessing-tutorial
>
> However, verts, faces, , = measure.marching_cubes(p, threshold) in the
> function of plot_3d gives the following error message
>
>  File "guidozuidhof_fullprocessing.py", line 90, in plot_3d
> verts, faces = measure.marching_cubes(p, threshold)
> ValueError: too many values to unpack
>
>
> What does that mean, and how to solve it, thanks a lot!
>
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Re: [scikit-image] Refactoring ndimage

[Egor Panfilov]

Hi Jaime,

Very nice to hear that there is a major improvement to `scipy` on its way
:).

Regarding your questions:
- Typically, our `master` branch is pretty stable, and we're fixing the
arising bugs as fast as possible, so you might rely on our CI to be green.
>From my point of view, `skimage` could be a good place to host more or less
domain-specific tests, although I'm not really sure what does specificity
mean in case of `ndimage`: convolutions, rescaling, interpolation, basic
filtering are pretty generic;
- Please, also notice that we've recently switched from `nose` to `pytest`
(thanks to Nelle ;)), and any new tests should not have `nose` dependency;
- Not sure that I'll find enough time to contribute to the code by myself,
but it won't harm if you could provide to the public some directions on
where to start with `scipy.ndimage` C-code.

Keep up the great work, and best of luck! :)

Regards,
Egor Panfilov

2017-06-26 12:30 GMT+03:00 Jaime Fernández del Río <jaime.f...@gmail.com>:

> Hi all,
>
> I have started working on an ambitious refactor of scipy.ndimage. Some
> more context on what I would like to achieve can be found here
> <https://mail.python.org/pipermail/scipy-dev/2017-June/021986.html>.
>
> scikit-image is probably the biggest "customer" of ndimage, so even though
> the API and performance are not expected to change, you may want to have a
> say.
>
> Assuming there is no major concern with the overall plan, I would also
> like to poke this community for help with:
>
>- figuring out a sensible test strategy: Ralf Gommers points out that
>we should probably use scikit-image's test suite regularly to complement
>the relatively few tests currently in ndimage: is the development version
>of scikit-image stable enough for this purpose or do you suggest using a
>specific stable release? Any other ideas?
>- PR reviewing. The idea is to make this refactor as incremental as
>possible. That means many smaller interdependent PRs. Even if you don't
>have commit rights to the scipy repository you are probably better versed
>than most of us in image processing algorithms, so if anyone can keep an
>eye on ndimage PRs
>
> <https://github.com/scipy/scipy/pulls?q=is%3Apr+is%3Aopen+label%3Ascipy.ndimage>
>and provide occasional reviews it would be greatly appreciated.
>- expert consulting: some of the code in ndimage is pretty hard to
>understand, e.g. I struggle with spline interpolation. If anyone with the
>proper academic knowledge is willing to answer stupid questions, please let
>me know.
>- the refactoring itself: if anyone would like to be a part of this,
>it would be my pleasure! A basic command of the C language is needed, but
>I'm more than willing to mentor beginners.
>
> Thanks!
>
> Jaime
>
> --
> (\__/)
> ( O.o)
> ( > <) Este es Conejo. Copia a Conejo en tu firma y ayúdale en sus planes
> de dominación mundial.
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Re: [scikit-image] Website updates

[Egor Panfilov]

Hi Stefan,

I like the new layout. Especially, the gallery looks much better now.

Some remarks:
1. As Francois mentioned, 0.13 is missing from the version selector on the
left;
2. Should we consider moving the `Search documentation` textbox to the
header for all the pages, not just the main one?
3. As long as we have a complicated navigation (
https://github.com/scikit-image/scikit-image-web/issues/40), I'd suggest to
push the changes also for the pages with documentation version 0.13. This
way we'll have a single design for both stable and dev versions, and will
avoid users confusion.

Regards,
Egor

2017-04-22 8:25 GMT+03:00 François Boulogne :

> Hi Stefan,
>
> I like the box on the left. To me, the version number looks more visible.
>
> I noticed that the doc for 0.13 is missing. What happened to that one? :)
>
> Best,
>
> --
> François Boulogne.
> http://www.sciunto.org
> GPG: 32D5F22F
>
>
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[scikit-image] Important change in testing environment

[Egor Panfilov]

Dear contributors,

We'd like to notify your that we have just finished a transition of our
testing environment from `nose` to `pytest` (see
https://github.com/scikit-image/scikit-image/pull/2468 for the details).

We kindly ask you to revisit your open Pull Requests on GitHub, perform a
rebase onto `master` branch of `scikit-image/scikit-image` repo (see
http://scikit-image.org/docs/dev/contribute.html#divergence-between-upstream-master-and-your-feature-branch),
and rewrite your tests using `pytest` wherever is needed.

Usage of the functions from `numpy.testing` in addition to `pytest` ones is
allowed, but, please, notice that some of them (such as `assert_raises`)
rely on `nose` under the hood, and, therefore, should not be used.

Sorry for the inconvenience.
Looking forward to seeing your contributions updated and merged.

Regards,
Egor,
scikit-image core team
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Re: [scikit-image] image type issue and failed conversion

[Egor Panfilov]

Dear Yuanyuan,

First of all, it is not a good idea to initialize the array with values
using `np.empty`. I'd recommend to use either `np.random.rand` or
`np.random.randint`.

As for main point of your question, I believe you might need
http://scikit-image.org/docs/dev/api/skimage.html#img-as-float (see also
http://scikit-image.org/docs/dev/user_guide/data_types.html ).
So, you can either create an array of floats [0:1) via  `np.random.rand`,
or create an array of uints via `np.random.randint`, and call
`img_as_float`. Then `equalize_adapthist` should work flawlessly.

Regards,
Egor

2016-12-27 1:27 GMT+03:00 wine lover :

> Dear All,
>
> I was trying to use the above code segment for performing Contrast Limited
> Adaptive Histogram Equalization (CLAHE).
> def clahe_equalized(imgs):
> imgs_equalized = np.empty(imgs.shape)
> for i in range(imgs.shape[0]):
>
>  print('imgs[i,0] ',imgs[i,0].dtype)
>  print('imgs[i,0] ',imgs[i,0].max())
>  print('imgs[i,0] ',imgs[i,0].min())
>  imgs_equalized[i,0] = exposure.equalize_adapthist(
> imgs[i,0],clip_limit=0.03)
> return imgs_equalized
>
> The dtype is float64, maximum value is 255.0 and minimum value is 0.0
>
> Running the program generates the following error message ( I only
> keep the related ones)
>
> imgs_equalized[i,0] = exposure.equalize_adapthist(
> imgs[i,0],clip_limit=0.03)
>raise ValueError("Images of type float must be between -1 and 1.")
> ValueError: Images of type float must be between -1 and 1.
>
> In accordance with the above error message and image characteristics, what
> are the best way to handle this scenario.
>
> I have been thinking of two approaches
>
>
>1. add imgs[i,0] = imgs[i,0]/255.   which scale it to 0 and 1
>2.  convert imgs[i,0] from float64 to unit8
>
> but imgs[i,0] = imgs[i,0].astype(np.unit8) gives the error message such as
>  imgs[i,0]=imgs[i,0].astype(np.unit8)
>
> AttributeError: 'module' object has no attribute 'unit8'
>
> Would you like to give any advice on this problem? Thank you very much!
>
>
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Re: [scikit-image] Release schedule

[Egor Panfilov]

Hi Stefan,

>From my perspective there are still some issues to be closed before the
release (see https://github.com/scikit-image/scikit-image/milestone/6).
This year we have been using GitHub features extensively and they should
represent our current point of view regarding the codebase status. Among
the tagged issues there are some long-lasting ones, and these could be
transfered into 0.13 roadmap. As for the others, I'd prefer to solve them
first.

Regarding release schedule: we are having a discussion in
https://github.com/scikit-image/scikit-image/issues/2357. In short, the
convenient release schedule should be tied to deprecation policy timeline,
which is to be reviewed.

Above said, I'd suggest to push the release date a bit further. At least,
the freeze initiation.

Regards,
Egor Panfilov

P.S. I'm traveling on the next week, and will not be able to contribute
significant efforts till Dec'26th. However, I'll try to track the mailing
list, and participate in the discussions (if any).

2016-12-18 1:24 GMT+03:00 Stefan van der Walt <stef...@berkeley.edu>:

> Hi, everyone
>
> It's time for a new skimage release. I have the following timeline in mind:
>
> Thursday 22 Dec, feature freeze
> -- bug fixes, documentation, clean up --
> January 5th, tag pre-release
> -- developer and early adopter testing--
> January 10th, tag release
>
> How does that sound?
>
> Also, do we have a volunteer for release manager? :)
>
> Finally, I m thinking it may be a good idea to make an automated release
> schedule for the future. E.g. release every 4 months, and work out how long
> we need to freeze each time. Opinions?
>
> Stéfan
>
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